Contacts of the helix formed by residues 87 - 116 (chain J) in PDB entry 1NF6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 87 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J MET* 5.7 2.5 - - - -
85J GLY 3.5 3.2 + - - -
86J GLN* 1.3 77.0 - - - +
88J VAL* 1.3 55.4 + - - +
89J PRO* 3.5 11.2 - - + -
90J VAL* 3.3 17.2 + - + +
91J ILE* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J LEU* 4.6 10.3 - - + -
40J MET* 3.7 35.0 - - + -
42J TYR* 5.1 7.2 - - + -
45J LEU* 5.3 1.6 - - + -
87J ALA* 1.3 68.6 - - - +
89J PRO* 1.3 77.6 - - + +
91J ILE* 3.0 16.4 + - + +
92J TYR* 3.2 28.0 - - + -
146J ILE* 3.3 34.1 - - + -
154J LEU* 5.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 89 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87J ALA* 3.6 9.2 - - + -
88J VAL* 1.3 99.6 - - + +
90J VAL* 1.3 60.3 + - + +
92J TYR* 3.3 5.1 + - + +
93J GLU* 2.8 31.4 + - - +
143J GLY* 5.8 1.4 - - - -
146J ILE* 4.5 19.3 - - + -
147J LYS* 6.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J VAL* 6.2 0.2 - - + -
86J GLN* 3.6 29.4 - - + +
87J ALA* 3.3 23.3 - - + +
89J PRO* 1.3 77.1 - - + +
91J ILE* 1.3 60.9 + - - +
93J GLU* 4.2 15.0 - - + +
94J SER* 2.8 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J GLN* 3.7 43.1 - - + +
36J SER* 4.8 7.2 - - - -
37J LEU* 4.4 18.2 - - + -
40J MET* 5.0 1.3 - - + -
49J MET* 3.8 14.4 - - + -
86J GLN* 3.5 26.9 - - + +
87J ALA 2.9 16.9 + - - +
88J VAL* 3.3 18.8 - - + +
90J VAL* 1.3 76.9 - - - +
92J TYR* 1.3 67.7 + - + +
94J SER* 3.6 0.8 + - - -
95J ASP* 2.8 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 92 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J LEU* 3.5 17.4 - - + +
45J LEU* 3.3 33.6 + - + +
49J MET* 4.1 9.9 - - + +
88J VAL* 3.2 30.0 + - + +
89J PRO* 4.0 4.5 - - + +
91J ILE* 1.3 89.6 - - + +
93J GLU* 1.3 64.8 + - - +
95J ASP* 4.3 2.2 - - - +
96J ALA* 3.3 23.2 + - - +
138J TYR* 4.5 3.7 + + - -
139J TYR* 3.9 33.6 - + - +
142J ILE* 3.6 31.9 - - + -
143J GLY* 3.8 24.6 - - - +
146J ILE* 3.6 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89J PRO 2.8 17.9 + - - +
90J VAL* 3.8 15.1 - - + +
92J TYR* 1.3 78.0 - - - +
94J SER* 1.3 67.6 + - - +
96J ALA* 3.4 2.6 + - - +
97J ASP* 3.2 35.6 + - - +
147J LYS* 5.5 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J GLN* 6.0 0.2 - - - +
86J GLN* 3.0 25.2 + - - -
90J VAL* 2.8 30.2 + - - -
91J ILE 3.6 3.8 + - - -
93J GLU* 1.3 76.5 - - - +
95J ASP* 1.3 64.2 + - - +
97J ASP* 3.5 9.1 + - - +
98J GLN* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 95 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J GLN* 4.6 3.5 - - - +
30J TYR* 3.3 18.6 - - + -
33J GLN* 2.3 39.1 + - - +
49J MET* 3.2 18.9 - - - +
91J ILE* 2.8 21.6 + - - +
92J TYR 4.3 1.6 - - - +
93J GLU 3.2 0.4 - - - -
94J SER* 1.3 80.2 + - - +
96J ALA* 1.3 56.3 + - - +
98J GLN* 3.4 6.9 + - - +
99J GLU* 3.0 34.1 + - - +
139J TYR* 3.7 26.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92J TYR 3.3 17.0 + - - +
93J GLU* 3.9 3.8 - - - +
94J SER 3.4 0.2 - - - -
95J ASP* 1.3 75.0 - - - +
97J ASP* 1.3 62.0 + - - +
99J GLU* 3.5 0.6 + - - -
100J ASP* 3.0 29.1 + - - +
136J LEU* 3.4 23.6 - - + +
139J TYR* 4.0 15.4 - - + +
140J GLU* 4.2 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J GLU* 3.2 27.3 + - - +
94J SER* 3.7 10.4 - - - +
96J ALA* 1.3 79.2 - - - +
98J GLN* 1.3 57.8 + - - +
100J ASP* 3.5 5.9 - - - +
101J ALA* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J MET* 4.4 3.6 + - - +
25J HIS* 2.9 42.4 + - - -
26J ALA* 3.7 21.8 - - - +
29J GLN* 4.2 5.9 - - - +
30J TYR* 3.7 22.4 + - - +
94J SER* 2.9 19.2 + - - +
95J ASP* 3.7 5.9 - - - +
96J ALA 3.3 0.2 - - - -
97J ASP* 1.3 75.0 - - - +
99J GLU* 1.3 57.2 + - - +
101J ALA* 3.9 5.4 - - - +
102J THR* 2.7 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J ALA* 5.0 1.7 - - - +
30J TYR* 2.4 25.1 + - - +
56J GLU* 3.2 7.7 - - - +
95J ASP 3.0 20.3 + - - +
96J ALA 4.1 1.3 - - - +
98J GLN* 1.3 78.4 - - - +
100J ASP* 1.3 58.3 + - - +
102J THR* 3.7 4.8 + - - -
103J ILE* 3.0 36.0 + - - +
132J GLU* 3.2 16.5 - - - +
135J HIS* 3.0 17.0 - - + +
136J LEU* 3.8 21.8 - - + -
139J TYR* 3.7 16.6 - - + -
200J FE 2.2 30.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96J ALA 3.0 18.0 + - - +
97J ASP* 3.5 7.6 - - - +
99J GLU* 1.3 75.7 - - - +
101J ALA* 1.3 68.9 + - - +
103J ILE* 3.3 5.2 + - - +
104J GLU* 3.0 30.1 + - - +
136J LEU* 4.2 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J MET* 4.7 3.6 - - + -
97J ASP 2.8 19.5 + - - +
98J GLN* 4.0 6.7 - - - +
100J ASP* 1.3 76.9 + - - +
102J THR* 1.3 57.4 + - - +
104J GLU* 3.3 8.7 + - - +
105J ALA* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J MET* 3.4 22.8 - - + +
23J GLU* 5.5 0.2 - - - -
98J GLN* 2.7 32.0 + - - +
99J GLU* 3.7 6.4 + - - -
100J ASP 3.1 0.2 - - - -
101J ALA* 1.3 74.2 - - - +
103J ILE* 1.3 66.4 + - - +
105J ALA* 3.1 0.9 + - - -
106J TYR* 2.8 58.2 + - + +
132J GLU* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 103 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99J GLU 3.0 22.6 + - - +
100J ASP* 3.3 4.7 + - - +
102J THR* 1.3 76.1 - - - +
104J GLU* 1.3 66.0 + - - +
106J TYR* 3.3 5.4 + - - +
107J SER* 2.9 34.4 + - - +
129J ILE* 4.0 22.3 - - + +
132J GLU* 3.6 20.9 - - + -
133J GLN* 3.6 40.2 - - + +
136J LEU* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100J ASP* 3.0 20.4 + - - +
101J ALA* 3.3 13.9 - - - +
103J ILE* 1.3 82.1 - - - +
105J ALA* 1.3 62.2 + - - +
107J SER* 3.5 10.6 + - - -
108J GLN* 3.4 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J MET* 3.8 21.8 - - + -
101J ALA 2.8 16.6 + - - +
102J THR 3.1 4.2 + - - +
104J GLU* 1.3 76.6 - - - +
106J TYR* 1.3 62.2 + - + +
108J GLN* 3.1 16.8 + - - +
109J PHE* 3.0 42.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J ALA* 3.4 24.8 + - + -
22J MET* 4.0 14.1 - - - +
23J GLU* 2.8 44.0 + - - +
63J PHE* 4.0 8.5 - + - -
102J THR* 2.8 47.0 + - + +
103J ILE* 4.0 0.4 - - - +
105J ALA* 1.3 74.5 - - + +
107J SER* 1.3 56.4 + - - +
109J PHE* 3.2 19.1 + + - +
110J LEU* 2.8 29.3 + - - +
125J PHE* 3.9 14.4 - + + -
128J ILE* 3.8 24.0 - - + -
129J ILE* 3.4 27.1 - - + +
132J GLU* 4.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 107 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J ILE* 2.9 27.7 + - - +
104J GLU* 3.6 13.4 + - - -
105J ALA 3.2 0.2 - - - -
106J TYR* 1.3 77.6 - - - +
108J GLN* 1.3 61.7 + - - +
110J LEU* 3.4 8.3 - - - +
111J LYS* 3.2 23.6 + - - +
129J ILE* 3.8 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 108 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104J GLU* 3.4 27.5 + - - +
105J ALA* 3.1 14.7 + - - +
107J SER* 1.3 76.6 - - - +
109J PHE* 1.3 73.2 + - + +
111J LYS* 3.0 30.7 + - + +
112J VAL* 3.2 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 109 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J VAL* 3.6 29.8 - - + +
18J LYS* 3.8 34.3 - - + -
19J ALA* 3.9 16.6 - - - -
22J MET* 4.2 6.1 - - - -
105J ALA* 3.0 34.8 + - + -
106J TYR* 3.6 31.6 - + - +
108J GLN* 1.3 83.5 - - + +
110J LEU* 1.3 60.8 + - - +
112J VAL* 3.2 8.5 + - + +
113J CYS* 3.1 27.5 + - - -
125J PHE* 3.6 25.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106J TYR 2.8 14.8 + - - +
107J SER* 3.4 10.1 - - - +
109J PHE* 1.3 73.2 - - - +
111J LYS* 1.3 67.1 + - - +
113J CYS* 3.1 12.2 + - - +
114J LYS* 3.1 52.4 + - + +
122J ALA* 4.2 15.7 - - + +
125J PHE* 4.4 7.4 - - + -
126J GLU* 3.7 32.3 - - + +
129J ILE* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107J SER 3.2 11.6 + - - +
108J GLN* 3.0 20.9 + - + +
110J LEU* 1.3 81.4 - - - +
112J VAL* 1.3 58.6 + - + +
114J LYS* 3.0 15.3 + - - +
115J GLU* 2.8 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J LYS* 4.3 11.9 - - + +
12J VAL* 4.7 1.8 - - + -
15J VAL* 4.2 28.9 - - + -
108J GLN* 3.2 12.5 + - + +
109J PHE* 3.4 8.7 - - + +
110J LEU 3.2 0.4 - - - -
111J LYS* 1.3 80.4 - - + +
113J CYS* 1.3 54.5 + - - +
115J GLU* 3.0 18.8 + - - +
116J GLN* 2.7 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 113 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J VAL* 4.1 18.4 - - - -
15J VAL* 4.6 2.9 - - - -
109J PHE 3.1 19.0 + - - -
110J LEU 3.1 7.4 + - - +
112J VAL* 1.3 76.9 - - - +
114J LYS* 1.3 60.5 + - - +
116J GLN 3.1 2.6 + - - -
117J GLY 3.1 4.5 + - - -
118J ASP* 2.9 42.3 + - - +
121J THR* 3.3 34.3 - - - -
122J ALA* 3.8 10.5 - - + -
125J PHE* 3.7 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110J LEU* 3.1 38.7 + - + +
111J LYS* 3.0 14.0 + - - +
113J CYS* 1.3 76.8 - - - +
115J GLU* 1.3 61.5 + - + +
117J GLY* 3.2 12.6 + - - +
118J ASP 4.9 2.5 - - - +
119J ILE* 5.4 10.1 - - + +
122J ALA* 4.5 9.2 - - + -
126J GLU* 4.9 6.5 + - - +
2004J SO4 2.7 50.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J ARG* 5.6 0.2 - - - +
111J LYS* 2.8 40.6 + - + +
112J VAL* 3.0 23.6 + - - +
114J LYS* 1.3 72.6 - - + +
116J GLN* 1.3 73.7 + - - +
117J GLY 3.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J GLY* 5.7 1.9 - - - -
7J ASP 4.3 1.2 - - - +
8J ARG* 2.6 70.7 + - + +
11J LYS* 3.8 36.3 + - + +
12J VAL* 3.6 28.3 - - + -
112J VAL* 2.7 32.9 + - + +
113J CYS 3.1 1.8 + - - +
115J GLU* 1.3 86.9 + - - +
117J GLY* 1.3 59.1 + - - +
118J ASP* 4.5 1.9 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il