Contacts of the helix formed by residues 87 - 116 (chain O) 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 O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40O MET* 6.1 0.7 - - - -
85O GLY 3.5 3.9 + - - +
86O GLN* 1.3 73.4 - - - +
88O VAL* 1.3 57.5 + - - +
89O PRO* 3.3 11.0 - - + -
90O VAL* 2.7 37.3 + - + +
91O ILE* 2.9 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O LEU* 4.4 9.0 - - + -
40O MET* 3.6 37.5 - - + -
42O TYR* 4.6 9.0 - - + -
45O LEU* 4.9 2.2 - - + -
86O GLN 4.0 0.6 + - - -
87O ALA* 1.3 70.4 - - - +
89O PRO* 1.3 73.1 - - + +
91O ILE* 3.1 17.6 + - - +
92O TYR* 3.3 26.6 - - + -
146O ILE* 3.6 26.9 - - + -
154O LEU* 4.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 89 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87O ALA* 3.5 10.8 - - + -
88O VAL* 1.3 97.1 - - + +
90O VAL* 1.3 64.7 + - + +
92O TYR* 3.6 2.9 + - + +
93O GLU* 3.2 22.9 + - - +
143O GLY* 6.1 0.2 - - - -
146O ILE* 4.5 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O GLN* 4.1 20.9 - - + +
87O ALA* 2.7 29.1 + - + +
89O PRO* 1.3 75.2 - - + +
91O ILE* 1.3 59.1 + - - +
93O GLU* 4.2 13.5 - - + +
94O SER* 2.3 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O GLN* 3.6 35.2 - - + +
36O SER* 5.2 2.2 - - - +
37O LEU* 4.2 20.2 - - + -
40O MET* 4.8 5.4 - - + -
49O MET* 3.5 30.5 - - + -
86O GLN* 3.7 26.5 - - + +
87O ALA 2.9 11.0 + - - +
88O VAL* 3.1 19.3 + - - +
90O VAL* 1.3 76.9 - - - +
92O TYR* 1.3 71.2 + - + +
94O SER* 3.1 4.4 + - - -
95O ASP* 2.8 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 92 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O LEU* 3.4 26.4 - - + +
45O LEU* 3.5 24.6 + - + +
49O MET* 4.0 8.6 - - + +
88O VAL* 3.3 32.3 + - + +
89O PRO 4.4 2.2 - - - +
90O VAL 3.3 0.2 - - - -
91O ILE* 1.3 90.4 - - + +
93O GLU* 1.3 63.5 + - - +
95O ASP* 4.0 2.5 - - - -
96O ALA* 3.3 23.9 + - - +
138O TYR* 4.3 5.0 + + - -
139O TYR* 3.7 43.7 - + - +
142O ILE* 3.6 39.7 - - + -
143O GLY* 4.0 16.7 - - - -
146O ILE* 3.9 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89O PRO 3.2 17.4 + - - +
90O VAL* 3.2 14.5 + - + +
92O TYR* 1.3 80.2 - - - +
94O SER* 1.3 63.3 + - - +
96O ALA* 3.7 3.3 + - - +
97O ASP* 3.2 32.3 + - - +
143O GLY* 5.6 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O GLN* 3.6 22.9 + - - -
90O VAL* 2.3 32.8 + - - -
91O ILE* 3.1 9.7 + - - -
93O GLU* 1.3 78.1 - - - +
95O ASP* 1.3 62.3 + - - +
96O ALA 3.2 0.2 - - - -
97O ASP* 3.2 7.8 + - - +
98O GLN* 2.8 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 95 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O GLN* 4.7 1.9 - - - +
30O TYR* 3.6 16.3 - - + -
33O GLN* 2.5 47.0 + - - +
49O MET* 3.0 18.2 - - - +
91O ILE* 2.8 22.6 + - - +
92O TYR 4.4 0.4 - - - +
94O SER* 1.3 73.6 + - - +
96O ALA* 1.3 63.7 + - - +
98O GLN* 3.4 6.5 + - - +
99O GLU* 2.9 29.1 + - - +
139O TYR* 3.3 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92O TYR 3.3 19.6 + - - +
93O GLU* 3.9 4.5 - - - +
94O SER 3.2 0.4 - - - -
95O ASP* 1.3 79.7 - - - +
97O ASP* 1.3 64.3 + - - +
100O ASP* 3.0 20.1 + - - +
136O LEU* 3.2 16.8 - - + +
139O TYR* 3.8 17.4 - - + +
140O GLU* 4.1 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93O GLU* 3.2 23.1 + - - +
94O SER* 3.2 10.9 + - - +
96O ALA* 1.3 79.3 - - - +
98O GLN* 1.3 51.7 + - - +
100O ASP* 3.0 8.1 + - - +
101O ALA* 2.7 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22O MET 4.4 3.6 + - - -
25O HIS* 3.1 39.8 + - - -
26O ALA* 3.4 26.5 - - - +
29O GLN* 4.0 11.4 - - - +
30O TYR* 3.6 17.9 + - - +
94O SER 2.8 21.3 + - - +
95O ASP* 3.7 5.3 - - - +
97O ASP* 1.3 72.9 - - - +
99O GLU* 1.3 59.4 + - - +
101O ALA* 3.2 7.1 + - - +
102O THR* 2.7 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O ALA* 5.0 1.7 - - - +
30O TYR* 2.3 29.2 + - - +
56O GLU* 3.3 5.6 - - - +
95O ASP 2.9 21.4 + - - +
96O ALA 3.9 3.1 - - - +
98O GLN* 1.3 78.3 + - - +
100O ASP* 1.3 58.6 + - - +
102O THR* 3.7 4.8 + - - -
103O ILE* 3.0 36.4 + - - +
132O GLU* 3.1 19.4 - - - +
135O HIS* 3.4 12.4 - - + +
136O LEU* 4.0 18.8 - - + +
139O TYR* 3.7 17.7 - - + -
200O FE 2.2 31.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96O ALA 3.0 18.8 + - - +
97O ASP* 3.5 7.6 - - - +
99O GLU* 1.3 75.2 - - - +
101O ALA* 1.3 65.2 + - - +
103O ILE* 3.6 9.6 + - - +
104O GLU* 3.3 28.6 + - - +
136O LEU* 4.1 19.4 - - + +
140O GLU* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22O MET* 4.4 5.0 - - + +
97O ASP 2.7 19.7 + - - +
98O GLN* 3.6 8.5 - - - +
100O ASP* 1.3 77.2 + - - +
102O THR* 1.3 58.1 + - - +
104O GLU* 3.3 8.3 - - - +
105O ALA* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22O MET* 3.4 23.6 + - + +
23O GLU* 5.6 0.2 - - - -
98O GLN* 2.7 31.8 + - - +
99O GLU* 3.7 8.2 + - - -
100O ASP 3.2 0.2 - - - -
101O ALA* 1.3 75.2 - - - +
103O ILE* 1.3 59.7 + - - +
105O ALA* 3.2 0.7 + - - +
106O TYR* 2.9 60.4 + - + +
132O GLU* 3.0 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 103 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O GLU 3.0 21.9 + - - +
100O ASP* 4.0 6.5 - - - +
102O THR* 1.3 77.0 - - - +
104O GLU* 1.3 63.4 + - - +
106O TYR* 3.9 6.2 - - - +
107O SER* 2.9 36.1 + - - +
129O ILE* 3.8 22.6 - - + +
132O GLU* 3.6 24.0 - - + +
133O GLN* 3.8 32.5 - - + +
136O LEU* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100O ASP* 3.3 21.8 + - - +
101O ALA* 3.3 13.0 - - - +
102O THR 3.2 0.2 - - - -
103O ILE* 1.3 78.4 - - - +
105O ALA* 1.3 68.4 + - - +
107O SER* 3.2 16.4 + - - -
108O GLN* 3.3 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22O MET* 3.8 27.4 - - + -
101O ALA 3.0 13.8 + - - +
102O THR 3.2 6.5 + - - +
104O GLU* 1.3 76.2 - - - +
106O TYR* 1.3 64.8 + - - +
108O GLN* 2.9 9.4 + - - +
109O PHE* 2.8 38.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19O ALA* 3.4 23.5 + - + -
22O MET* 3.9 13.3 - - - +
23O GLU* 2.8 37.0 + - - +
63O PHE* 4.0 7.9 - + - -
102O THR* 2.9 44.3 + - + +
103O ILE 4.1 1.3 - - - +
105O ALA* 1.3 74.2 - - + +
107O SER* 1.3 53.5 + - - +
109O PHE* 3.6 13.8 - + - +
110O LEU* 2.7 34.8 + - - +
125O PHE* 3.7 20.3 - + + -
128O ILE* 3.6 33.0 - - + -
129O ILE* 3.7 22.5 - - + +
132O GLU* 4.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 107 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O ILE* 2.9 29.7 + - - +
104O GLU* 3.6 12.1 + - - -
105O ALA 3.0 0.4 - - - -
106O TYR* 1.3 76.9 - - - +
108O GLN* 1.3 59.9 + - - +
110O LEU* 3.3 17.8 - - - +
111O LYS* 3.4 8.0 + - - +
129O ILE* 3.6 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 108 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104O GLU 3.3 7.6 + - - +
105O ALA* 2.9 10.3 + - - +
107O SER* 1.3 76.7 - - - +
109O PHE* 1.3 71.7 + - + +
110O LEU 3.1 1.3 - - - -
111O LYS* 2.9 31.4 + - - +
112O VAL* 3.1 22.9 + - + +
115O GLU* 5.0 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 109 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15O VAL* 3.8 36.3 - - + +
18O LYS* 3.8 34.3 - - + -
19O ALA* 3.9 21.1 - - + -
22O MET* 4.1 10.1 - - - -
105O ALA* 2.8 42.5 + - + -
106O TYR* 3.6 17.0 - + - +
108O GLN* 1.3 81.8 - - + +
110O LEU* 1.3 63.1 + - - +
112O VAL* 3.3 6.5 + - + +
113O CYS* 3.2 26.6 + - - -
125O PHE* 3.8 15.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106O TYR 2.7 16.1 + - - +
107O SER* 3.3 10.5 - - - +
109O PHE* 1.3 77.1 - - - +
111O LYS* 1.3 63.6 + - - +
113O CYS* 3.2 8.9 + - - +
114O LYS* 2.9 46.5 + - + +
122O ALA* 4.1 24.0 - - + +
125O PHE* 4.2 9.6 - - + -
126O GLU* 4.0 29.4 - - + +
129O ILE* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107O SER 3.4 7.8 + - - +
108O GLN* 2.9 31.8 + - - +
110O LEU* 1.3 80.8 - - - +
112O VAL* 1.3 50.0 + - - +
114O LYS* 2.7 33.5 + - - +
115O GLU* 2.7 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O LYS* 4.3 24.5 - - + +
12O VAL* 5.0 0.4 - - + -
15O VAL* 4.2 20.6 - - + -
108O GLN* 3.1 23.3 + - + +
109O PHE* 3.6 7.9 - - + +
110O LEU 3.3 0.2 - - - -
111O LYS* 1.3 76.4 - - - +
113O CYS* 1.3 52.0 + - - +
115O GLU* 2.7 22.2 + - - +
116O GLN* 2.6 53.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 113 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O VAL* 3.9 22.0 - - - -
15O VAL* 4.5 3.6 - - - -
109O PHE 3.2 15.5 + - - -
110O LEU 3.3 8.1 - - - +
112O VAL* 1.3 76.6 - - - +
114O LYS* 1.3 60.0 + - - +
116O GLN 3.5 0.4 + - - -
117O GLY 3.2 2.3 + - - -
118O ASP* 2.7 46.8 + - + +
121O THR* 3.5 33.4 - - - -
122O ALA* 3.8 9.6 - - + -
125O PHE* 4.0 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110O LEU* 2.9 36.2 + - + +
111O LYS* 2.7 23.3 + - - +
113O CYS* 1.3 72.2 - - - +
115O GLU* 1.3 56.1 + - + +
117O GLY* 2.9 20.8 + - - -
118O ASP 5.0 0.7 - - - +
119O ILE* 6.0 6.0 - - + +
122O ALA* 4.7 7.4 - - + -
126O GLU* 5.0 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108O GLN* 5.0 4.3 + - - -
111O LYS* 2.7 25.4 + - + +
112O VAL* 2.7 29.4 + - - +
114O LYS* 1.3 74.7 - - + +
116O GLN* 1.3 69.8 + - - +
117O GLY 3.2 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O ASP* 4.2 0.9 - - - +
8O ARG* 2.7 69.8 + - + +
11O LYS* 3.5 33.7 + - + +
12O VAL* 3.7 30.1 - - + -
112O VAL* 2.6 31.2 + - + +
113O CYS 4.1 1.8 - - - +
115O GLU* 1.3 86.3 + - - +
117O GLY* 1.3 61.1 + - - +
118O ASP* 3.3 3.2 + - + +
----------------------------------------------------------
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