Contacts of the helix formed by residues 4 - 20 (chain B) in PDB entry 3DVA
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 THR 4 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B MET* 1.3 79.8 - - - +
5B MET* 1.3 63.2 + - - +
6B VAL* 3.2 11.2 - - - +
7B GLN* 3.2 27.9 + - - +
8B ALA 3.2 15.2 + - - -
150B PRO* 3.6 5.0 - - - +
176B TYR 3.5 10.8 - - - -
177B ARG* 4.2 18.8 - - + +
179B PHE 3.7 11.7 - - - +
180B ARG* 3.9 33.2 - - + +
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Residues in contact with MET 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B THR* 1.3 75.0 - - - +
6B VAL* 1.3 63.3 + - - +
8B ALA* 3.1 4.0 + - - +
9B ILE* 3.0 29.4 + - + +
147B PRO* 4.2 19.5 - - + +
148B SER 4.5 0.2 - - - -
149B THR 4.3 11.7 - - - +
150B PRO* 3.6 22.2 - - + +
153B ALA* 3.5 27.6 - - + -
171B GLU* 4.6 7.2 - - + -
172B HIS 3.8 24.9 - - - +
175B LEU* 3.3 48.3 + - + +
176B TYR* 3.1 18.2 + - + +
179B PHE 4.5 1.4 + - - -
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Residues in contact with VAL 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B THR* 3.2 13.7 - - - +
5B MET* 1.3 75.8 - - - +
7B GLN* 1.3 65.3 + - + +
9B ILE* 3.2 6.3 + - - +
10B THR* 3.0 32.3 + - - +
37B PHE 3.6 22.2 - - - +
38B ARG 4.3 3.4 - - - +
39B ALA* 3.8 22.9 - - + +
176B TYR* 3.0 40.4 + - + +
177B ARG* 3.8 27.6 - - + +
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Residues in contact with GLN 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLN 4.1 0.9 - - - +
3B MET* 3.5 17.0 - - + +
4B THR* 3.2 26.4 + - - +
6B VAL* 1.3 87.7 - - + +
8B ALA* 1.3 55.4 + - - +
10B THR* 3.4 7.4 + - - -
11B ASP* 2.9 28.6 + - - +
180B ARG* 3.0 40.3 + - - +
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Residues in contact with ALA 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B MET* 4.1 15.6 - - - -
4B THR 3.2 11.8 + - - +
5B MET 3.1 10.2 + - - +
7B GLN* 1.3 72.7 - - - +
9B ILE* 1.3 66.2 + - - +
11B ASP* 3.3 3.5 + - - +
12B ALA* 2.9 25.3 + - - +
150B PRO* 3.2 32.8 - - + +
153B ALA* 4.6 0.2 - - + -
154B LYS* 3.8 17.8 - - + +
183B VAL* 4.6 1.6 - - + -
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Residues in contact with ILE 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B MET* 3.0 22.5 + - + +
6B VAL* 3.3 11.4 - - - +
8B ALA* 1.3 75.9 - - - +
10B THR* 1.3 62.4 + - - +
12B ALA* 3.2 4.7 + - - +
13B LEU* 3.0 29.4 + - + +
39B ALA* 4.5 6.7 - - + -
115B ARG* 3.7 16.8 - - - +
147B PRO* 5.2 0.9 - - + -
153B ALA* 3.6 22.2 - - + +
154B LYS* 5.4 0.2 - - - +
157B LEU* 3.5 13.2 - - + +
169B PHE* 3.6 30.1 - - + -
171B GLU* 3.5 28.5 - - + +
176B TYR* 4.8 4.9 - - + -
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Residues in contact with THR 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 3.0 14.8 + - - +
7B GLN* 3.7 10.1 - - - -
8B ALA 3.3 0.2 - - - -
9B ILE* 1.3 75.5 - - - +
11B ASP* 1.3 57.6 + - - +
13B LEU* 3.2 5.7 + - - +
14B ARG* 2.8 53.6 + - - +
38B ARG 3.9 4.4 + - - +
39B ALA* 2.7 32.5 + - - +
41B GLU* 4.1 13.7 - - + +
43B LEU* 4.3 8.2 - - + +
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Residues in contact with ASP 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B MET* 3.6 20.9 - - + +
7B GLN 2.9 17.3 + - - +
8B ALA* 3.5 7.9 - - - +
10B THR* 1.3 76.6 - - - +
12B ALA* 1.3 58.9 + - - +
14B ARG* 3.1 18.6 + - - +
15B ILE* 2.9 43.7 + - - +
154B LYS* 2.5 33.5 + - + +
185B GLU* 4.2 7.3 - - - +
186B GLY 4.8 0.9 + - - -
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA 2.9 13.2 + - - +
9B ILE 3.2 9.6 + - - +
11B ASP* 1.3 77.0 - - - +
13B LEU* 1.3 61.1 + - - +
15B ILE* 3.4 3.7 + - - +
16B GLU* 3.2 28.6 + - - +
154B LYS* 3.7 29.7 - - + +
157B LEU* 3.7 19.3 - - + -
158B ILE* 3.8 15.4 - - + +
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.0 29.6 + - + +
10B THR 3.6 5.2 - - - +
12B ALA* 1.3 72.8 - - - +
14B ARG* 1.3 59.8 - - - +
16B GLU* 3.2 5.3 + - - +
17B LEU* 2.9 36.1 + - + +
23B VAL* 5.3 0.2 - - - +
25B ILE* 3.8 26.0 - - + -
39B ALA 3.9 20.4 - - - +
40B THR* 4.3 9.9 - - + -
43B LEU* 4.0 18.4 - - + -
77B VAL* 4.1 3.1 - - + -
115B ARG* 4.0 25.6 - - - +
157B LEU* 4.0 6.1 - - + -
161B ILE* 3.9 21.1 - - + -
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Residues in contact with ARG 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 2.8 39.5 + - - +
11B ASP* 3.4 16.8 + - - +
13B LEU* 1.3 76.7 - - - +
15B ILE* 1.3 57.2 + - + +
18B LYS* 3.1 26.1 + - + +
41B GLU 4.0 10.1 + - - -
42B GLY* 4.5 9.7 + - - -
43B LEU* 3.9 19.2 - - + +
46B GLU* 2.5 37.5 + - - +
47B PHE* 3.4 23.9 - - + -
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Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP* 2.9 25.6 + - - +
12B ALA* 3.7 4.9 - - - +
14B ARG* 1.3 78.4 - - + +
16B GLU* 1.3 64.8 + - - +
18B LYS* 3.8 5.6 - - - +
19B ASN* 2.8 49.6 + - - +
154B LYS* 3.7 21.3 - - - +
158B ILE* 4.5 4.5 - - + -
186B GLY* 3.4 36.8 - - - +
187B GLU* 3.8 18.8 - - + +
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Residues in contact with GLU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA 3.2 17.2 + - - +
13B LEU 3.2 3.3 + - - +
15B ILE* 1.3 82.5 - - - +
17B LEU* 1.3 61.7 + - - +
19B ASN* 4.8 5.1 + - - +
20B ASP* 2.8 43.1 + - - +
23B VAL* 3.7 14.9 - - + +
75B ARG* 5.3 1.2 - - - -
158B ILE* 3.2 35.7 - - - +
161B ILE* 3.7 36.2 - - + +
162B ARG* 4.0 23.0 + - - +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU 2.9 20.3 + - - +
14B ARG 3.7 4.3 - - - +
16B GLU* 1.3 75.9 - - - +
18B LYS* 1.3 61.6 + - - +
20B ASP 3.4 2.1 - - - +
23B VAL* 3.5 35.0 - - + +
25B ILE* 4.0 19.5 - - + -
43B LEU* 4.0 17.0 - - + -
47B PHE* 3.6 35.0 - - + -
51B ARG* 2.5 47.2 + - + +
52B VAL* 3.9 23.8 - - + -
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Residues in contact with LYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 3.1 18.2 + - + +
15B ILE* 3.8 5.6 - - - +
16B GLU 3.1 0.2 - - - -
17B LEU* 1.3 80.2 - - - +
19B ASN* 1.3 76.8 + - - +
20B ASP* 3.5 1.9 + - - -
21B PRO* 5.0 1.6 - - - +
46B GLU* 5.3 5.4 - - - +
47B PHE* 3.6 18.4 - - + -
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Residues in contact with ASN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 2.8 39.9 + - - +
16B GLU* 4.5 6.5 + - - +
18B LYS* 1.3 92.0 - - - +
20B ASP* 1.3 58.7 + - + +
21B PRO* 3.9 6.1 - - - +
162B ARG* 4.8 8.9 - - - +
187B GLU* 3.9 20.0 - - - +
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Residues in contact with ASP 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU* 2.8 25.1 + - - +
17B LEU 4.0 1.8 - - - -
18B LYS 3.4 0.4 - - - -
19B ASN* 1.3 79.1 - - + +
21B PRO* 1.3 60.2 - - - +
22B ASN* 2.9 29.6 + - - +
23B VAL* 3.3 15.8 + - + -
51B ARG* 2.6 27.4 + - - -
75B ARG* 3.3 27.0 + - - -
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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) + - + + + + + -
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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