Contacts of the helix formed by residues 31 - 43 (chain A) in PDB entry 1VH7
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 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A GLY 4.9 0.3 - - - +
16A ARG* 4.2 4.5 - - - +
17A VAL* 4.1 1.3 - - - -
28A ASP* 3.1 35.0 + - + +
29A SER 3.5 0.2 - - - -
30A GLY* 1.3 74.3 - - - +
32A PRO* 1.3 66.1 - - - +
33A VAL* 3.0 22.2 + - - +
34A GLU* 3.5 22.6 + - + +
35A LEU* 2.9 28.6 + - - +
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Residues in contact with PRO 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 3.6 9.7 - - + +
12A VAL* 3.7 27.1 - - + -
15A GLY 3.1 34.3 - - - +
16A ARG* 3.8 2.5 - - - -
17A VAL* 3.6 13.2 - - + +
30A GLY 3.1 10.3 - - - +
31A ASP* 1.3 89.1 - - - +
33A VAL* 1.3 58.2 + - + +
35A LEU* 3.9 0.7 - - + -
36A GLY* 3.0 22.7 + - - -
49A PHE* 3.8 16.2 - - + -
65A LEU* 4.0 15.9 - - + -
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ASP* 3.0 13.0 + - - +
32A PRO* 1.3 77.3 - - + +
34A GLU* 1.3 61.5 + - - +
36A GLY* 3.4 1.1 + - - -
37A LYS* 2.9 28.9 + - - +
65A LEU* 4.1 20.4 - - + -
68A LYS* 4.1 33.0 - - + +
69A VAL* 4.2 12.1 - - + -
72A GLN* 3.7 34.3 - - + -
73A ILE* 4.7 2.6 - - + +
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Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASN 5.0 0.2 - - - +
26A LEU* 3.5 22.1 - - + +
27A ARG* 2.9 29.9 + - - +
28A ASP* 2.9 34.7 + - - +
31A ASP* 3.3 21.5 + - + +
33A VAL* 1.3 78.8 - - - +
35A LEU* 1.3 58.7 + - - +
37A LYS* 3.3 7.2 + - + +
38A PHE* 2.9 28.5 + - - +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 3.7 23.6 - - + -
17A VAL* 4.0 11.7 - - + -
21A THR* 3.4 25.8 - - + -
23A PHE* 3.9 24.2 - - + -
26A LEU* 4.1 16.5 - - + +
29A SER 5.2 2.0 - - - +
31A ASP 2.9 17.3 + - - +
32A PRO 4.0 2.7 - - - +
34A GLU* 1.3 77.6 - - - +
36A GLY* 1.3 57.4 - - - +
38A PHE* 3.3 7.1 + - + +
39A TYR* 2.9 59.8 + - + -
228A HIS* 4.1 5.4 - - + +
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Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.3 3.8 - - - +
32A PRO 3.0 19.1 + - - -
33A VAL* 3.8 1.3 - - - -
35A LEU* 1.3 73.5 - - - +
37A LYS* 1.3 65.1 + - - +
39A TYR* 3.3 7.7 + - - +
40A SER* 3.0 23.9 + - - -
47A LEU* 3.7 30.2 - - - +
49A PHE* 4.9 1.6 - - - -
73A ILE* 4.0 3.6 - - - -
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Residues in contact with LYS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL 2.9 18.5 + - - +
34A GLU* 3.5 9.2 - - + +
36A GLY* 1.3 75.5 - - - +
38A PHE* 1.3 61.9 + - - +
40A SER* 2.7 25.1 + - - +
41A GLU* 3.0 28.7 - - + +
72A GLN* 3.9 26.9 - - + +
73A ILE* 3.8 11.7 - - + +
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Residues in contact with PHE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.4 42.4 - + - -
25A ASN* 3.4 27.8 - - - -
26A LEU* 4.0 17.5 - - + -
34A GLU 2.9 14.9 + - - +
35A LEU* 3.4 13.0 - - + +
37A LYS* 1.3 73.9 - - - +
39A TYR* 1.3 64.3 + + - +
41A GLU* 2.8 36.7 + - + +
42A ILE* 3.1 45.9 + - + +
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Residues in contact with TYR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ALA* 4.0 14.1 - - + -
10A LEU* 4.3 7.2 - - + -
23A PHE* 3.5 21.0 - + - -
35A LEU* 2.9 46.4 + - + +
36A GLY 3.6 5.2 - - - +
38A PHE* 1.3 78.0 - + - +
40A SER* 1.3 61.9 + - - +
42A ILE* 3.1 25.7 + - + +
43A GLY 3.3 0.5 + - - -
44A ILE* 3.0 47.8 + - + -
47A LEU* 4.2 7.6 - - + -
227A PHE* 3.3 18.3 + - + -
228A HIS* 2.7 52.2 + + - -
234A VAL* 4.6 4.5 - - + -
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Residues in contact with SER 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY 3.0 11.4 + - - -
37A LYS* 2.7 26.3 + - - +
39A TYR* 1.3 76.9 - - - +
41A GLU* 1.3 62.6 + - - +
42A ILE 3.8 0.2 + - - -
43A GLY* 4.1 5.2 + - - -
44A ILE* 4.2 6.7 - - - +
73A ILE* 4.6 10.0 - - - +
74A ASP 5.0 2.2 + - - -
75A ILE* 3.5 44.1 - - - +
249A ARG* 5.9 0.3 + - - -
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LYS* 3.0 29.6 - - + +
38A PHE* 2.8 24.9 + - + +
40A SER* 1.3 83.0 - - - +
42A ILE* 1.3 62.0 + - + +
43A GLY 3.5 0.4 + - - -
235A ARG* 4.8 5.2 + - - -
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Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 5.0 4.0 - - + -
38A PHE* 3.1 53.8 + - + +
39A TYR* 3.5 28.9 - - + +
41A GLU* 1.3 83.9 - - + +
43A GLY* 1.3 55.8 + - - +
233A ASP* 5.6 4.0 - - - +
234A VAL* 3.9 30.0 - - + +
235A ARG* 4.0 46.3 + - + +
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Residues in contact with GLY 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR 3.3 1.0 + - - -
40A SER 4.1 3.5 + - - -
41A GLU 3.5 3.2 + - - -
42A ILE* 1.3 80.6 - - - +
44A ILE* 1.3 64.9 + - - +
234A VAL* 3.8 9.8 - - - +
235A ARG* 6.0 0.2 - - - -
238A LYS* 2.6 41.3 + - - -
249A ARG* 4.2 2.6 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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