Contacts of the helix formed by residues 92 - 121 (chain B) in PDB entry 2DPD
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 ASP 92 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLY 3.4 17.3 - - - +
69B ILE* 3.0 10.0 + - - +
91B LYS* 1.3 80.0 - - + +
93B TYR* 1.3 63.3 + - - +
94B GLU* 3.1 13.9 + - - +
95B ALA* 3.0 29.8 + - + +
96B ALA* 3.1 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 5.8 0.4 - - + -
28B GLU* 3.0 29.2 + - + +
90B PHE* 3.6 55.6 - + + +
91B LYS 3.8 2.6 + - - -
92B ASP* 1.3 72.6 + - - +
94B GLU* 1.3 61.4 + - + +
96B ALA* 3.2 6.1 + - + -
97B LYS* 2.9 56.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ASP* 3.1 9.6 + - - +
93B TYR* 1.3 72.7 - - + +
95B ALA* 1.3 69.3 + - - +
97B LYS* 2.9 20.8 + - - +
98B LEU* 2.9 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASP 5.3 2.0 - - - +
68B GLY 4.8 1.8 - - - +
69B ILE* 4.1 20.0 - - + +
92B ASP* 3.0 38.2 + - + +
94B GLU* 1.3 76.7 - - - +
96B ALA* 1.3 61.1 - - - +
98B LEU* 3.5 11.6 + - - +
99B TYR* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 4.2 14.2 - - + +
69B ILE* 3.8 19.0 - - + +
90B PHE* 3.6 31.0 - - + -
92B ASP 3.1 6.2 + - - +
93B TYR* 3.3 14.1 - - + +
94B GLU 3.0 0.6 - - - -
95B ALA* 1.3 73.7 - - - +
97B LYS* 1.3 67.9 + - - +
98B LEU 3.0 0.5 + - - -
99B TYR* 3.0 5.6 + - - +
100B LYS* 2.8 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU* 5.4 2.9 - - - +
93B TYR* 2.9 56.3 + - + +
94B GLU* 3.5 21.8 - - - +
96B ALA* 1.3 72.2 - - - +
98B LEU* 1.3 65.0 + - + +
100B LYS* 3.1 9.3 + - - +
101B LYS* 3.0 47.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU* 2.9 19.9 + - + +
95B ALA* 3.5 11.0 - - - +
97B LYS* 1.3 77.3 - - + +
99B TYR* 1.3 63.7 + - - +
101B LYS* 3.0 22.3 + - + +
102B GLN* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 5.5 0.2 - - - -
17B ALA* 3.9 16.8 - - - +
20B LYS* 3.2 50.5 + - + -
24B ILE* 3.4 21.3 - - + -
64B LEU* 4.4 7.2 - - + -
67B ASP* 5.9 1.3 - - - -
69B ILE* 5.2 9.6 - - + -
95B ALA 3.1 9.6 + - - +
96B ALA* 3.0 9.3 + - - +
98B LEU* 1.3 76.4 - - - +
100B LYS* 1.3 66.6 + - - +
102B GLN* 3.2 29.5 + - + +
103B LEU* 3.0 49.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASN 2.8 28.8 + - - -
122A PHE* 3.3 27.9 - - + +
21B LEU* 3.6 18.4 - - + -
24B ILE* 3.7 24.5 - - + -
25B THR* 3.4 23.7 - - - +
28B GLU* 3.3 29.4 + - - +
96B ALA 2.8 17.1 + - - +
97B LYS* 3.1 12.5 + - - +
99B TYR* 1.3 72.5 - - - +
101B LYS* 1.3 58.7 + - + +
103B LEU* 3.2 3.5 + - - +
104B LYS 3.0 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PHE* 5.2 1.3 - - + -
97B LYS* 3.0 32.9 + - - +
98B LEU* 3.0 14.9 + - + +
100B LYS* 1.3 75.6 - - + +
102B GLN* 1.3 65.9 + - - +
104B LYS* 3.0 18.2 + - - +
105B VAL* 3.0 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 3.0 20.4 + - - +
99B TYR* 3.5 33.0 + - + +
101B LYS* 1.3 75.9 - - + +
103B LEU* 1.3 50.6 + - + +
105B VAL* 2.8 15.3 + - - +
106B GLU* 2.8 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PHE* 4.0 2.0 - - - -
13B VAL* 4.7 2.7 - - + -
17B ALA* 3.4 36.8 - - + +
18B PHE* 5.6 0.2 - - - -
21B LEU* 3.9 42.0 - - + +
24B ILE* 4.8 0.2 - - + -
99B TYR* 3.0 57.7 + - + +
100B LYS* 3.6 7.0 - - - +
101B LYS 3.2 0.2 - - - -
102B GLN* 1.3 71.9 - - - +
104B LYS* 1.3 65.4 + - - +
106B GLU* 3.6 17.8 - - + +
107B LEU* 2.9 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.5 18.0 - - + +
122A PHE* 3.4 54.9 - - + -
100B LYS 3.0 7.6 + - - +
101B LYS* 3.0 12.1 + - - +
103B LEU* 1.3 75.0 - - - +
105B VAL* 1.3 55.9 + - + +
107B LEU* 3.2 4.0 + - - +
108B ASP* 2.7 71.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LYS 3.0 9.7 + - - +
102B GLN* 2.8 14.4 + - - +
104B LYS* 1.3 81.4 - - + +
106B GLU* 1.3 64.8 + - + +
108B ASP* 3.0 17.5 + - - +
109B ARG* 3.1 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE 5.1 1.4 - - - +
12B LEU 5.6 0.2 - - - -
13B VAL* 4.0 33.2 + - + +
14B LYS* 4.9 2.9 + - - +
17B ALA* 4.7 7.4 - - - +
102B GLN* 2.8 20.9 + - + +
103B LEU* 3.6 18.8 - - + +
105B VAL* 1.3 74.4 - - + +
107B LEU* 1.3 66.0 + - - +
108B ASP 3.2 0.2 + - - -
109B ARG* 3.3 21.6 + - - +
110B SER* 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ILE* 3.7 12.9 - - + +
117A ALA* 3.6 26.9 - - + -
118A LEU* 3.5 37.0 - - + +
122A PHE* 4.2 0.2 - - + -
13B VAL* 3.9 32.3 - - + -
18B PHE* 4.6 13.2 - - + -
21B LEU* 3.7 22.2 - - + -
103B LEU* 2.9 21.3 + - + +
104B LYS 3.6 0.4 - - - +
106B GLU* 1.3 77.7 - - - +
108B ASP* 1.3 57.6 + - - +
110B SER* 3.3 5.3 + - - -
111B LYS* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.7 13.0 - - - +
104B LYS* 2.7 50.0 + - - +
105B VAL* 3.0 11.6 + - - +
107B LEU* 1.3 77.8 - - - +
109B ARG* 1.3 62.7 + - - +
111B LYS* 3.4 10.9 + - - +
112B LYS* 3.0 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.1 39.4 + - + +
49A GLY* 3.5 15.2 + - - -
50A PHE 3.9 0.6 - - - +
10B GLY* 2.4 37.7 + - - -
11B PHE 2.7 20.2 + - - -
105B VAL* 3.1 20.8 + - + +
106B GLU* 3.6 20.4 + - - +
108B ASP* 1.3 74.4 - - - +
110B SER* 1.3 52.7 + - - +
112B LYS* 2.6 32.2 + - + +
113B LEU* 2.8 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ILE* 4.0 17.0 - - - -
11B PHE 4.6 1.6 + - - -
12B LEU* 3.3 19.9 - - - +
13B VAL* 3.0 34.9 + - - +
106B GLU* 2.9 18.5 + - - -
107B LEU* 3.3 8.5 + - - -
109B ARG* 1.3 77.0 + - - +
111B LYS* 1.3 65.3 + - - +
113B LEU* 3.4 1.9 + - - -
114B ILE* 3.2 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 5.8 4.3 - - + +
114A ILE* 3.6 24.0 - - + +
115A GLU* 3.4 36.1 + - + +
118A LEU* 5.3 12.6 - - + -
107B LEU 2.9 9.2 + - - +
108B ASP* 3.5 15.0 - - - +
110B SER* 1.3 77.5 - - - +
112B LYS* 1.3 64.3 + - - +
114B ILE* 3.1 4.3 + - - +
115B GLU* 2.8 56.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.7 34.3 - - + -
108B ASP* 3.0 17.9 + - - +
109B ARG* 2.6 20.8 + - + +
111B LYS* 1.3 71.6 - - - +
113B LEU* 1.3 51.5 + - - +
115B GLU* 3.2 7.0 + - - +
116B LYS* 2.7 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 4.2 12.2 - - + -
45A PHE* 3.6 25.6 - - + -
48A ILE* 3.5 26.9 - - + +
50A PHE* 3.9 14.1 - - + -
10B GLY 4.0 9.4 - - - +
11B PHE* 3.9 38.4 - - + +
12B LEU* 4.0 15.9 - - + -
109B ARG* 2.8 19.5 + - - +
110B SER* 3.6 8.3 - - - +
112B LYS* 1.3 71.3 - - - +
114B ILE* 1.3 65.7 + - + +
116B LYS* 3.0 5.3 + - - +
117B ALA* 2.8 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 5.6 0.7 - - + -
13A VAL* 4.6 4.3 - - + -
18A PHE* 4.9 5.6 - - + -
107A LEU* 3.8 15.9 - - + +
110A SER* 3.8 23.8 - - - +
111A LYS* 3.6 38.4 - - + +
114A ILE* 5.3 3.8 - - + -
12B LEU* 3.3 44.9 - - + -
110B SER 3.2 4.7 + - - +
111B LYS* 3.1 9.9 + - - +
113B LEU* 1.3 79.7 - - + +
115B GLU* 1.3 60.3 + - - +
117B ALA* 3.4 5.6 + - - +
118B LEU* 2.8 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 3.6 37.3 + - + +
115A GLU* 3.9 1.6 - - - +
111B LYS* 2.8 57.2 + - + +
112B LYS* 3.7 6.5 - - - +
114B ILE* 1.3 78.7 - - + +
116B LYS* 1.3 55.9 + - - +
118B LEU* 3.7 6.7 - - + +
119B SER* 3.1 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 4.0 2.6 + - - -
44A GLU* 2.9 47.2 + - - +
45A PHE* 3.5 25.0 - - + -
48A ILE* 4.1 19.3 - - + -
112B LYS 2.7 22.0 + - - +
113B LEU* 3.5 3.8 - - - +
115B GLU* 1.3 70.0 - - - +
117B ALA* 1.3 66.1 + - - +
119B SER* 3.0 5.2 + - - -
120B ASP* 2.8 54.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 3.3 38.3 - - + -
21A LEU* 5.3 1.8 - - + -
22A TYR* 3.2 19.9 + - + -
107A LEU* 3.8 15.8 - - + +
113B LEU 2.8 12.3 + - - +
114B ILE 3.7 4.0 - - - +
116B LYS* 1.3 73.1 - - - +
118B LEU* 1.3 62.8 + - - +
121B ASN* 3.1 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LYS* 3.7 27.4 - - + +
107A LEU* 3.5 31.6 - - + -
108A ASP* 3.8 9.9 - - - +
111A LYS* 5.1 13.0 - - + -
114B ILE* 2.8 25.3 + - + +
115B GLU* 3.7 9.0 - - + +
117B ALA* 1.3 76.5 - - - +
119B SER* 1.3 60.0 + - - +
122B PHE* 3.6 43.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU 3.1 16.3 + - - -
116B LYS* 3.0 8.4 + - - -
118B LEU* 1.3 76.5 - - - +
120B ASP* 1.3 66.7 + - - +
122B PHE* 2.9 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 2.5 27.4 + - + +
25A THR* 4.8 4.5 - - - +
26A MET* 6.2 1.6 - - + -
44A GLU* 2.9 13.0 - - - +
116B LYS* 2.8 34.8 + - - +
119B SER* 1.3 82.5 + - - +
121B ASN* 1.3 72.8 + - - +
122B PHE* 3.4 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.1 48.6 + - + +
22A TYR* 3.2 36.7 - - - +
25A THR* 2.5 34.8 + - - +
100A LYS* 2.8 29.3 + - - -
117B ALA 3.1 18.4 + - - +
120B ASP* 1.3 76.8 - - - +
122B PHE* 1.3 60.7 + - + +
----------------------------------------------------------
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