Contacts of the strand formed by residues 21 - 29 (chain A) in PDB entry 1VGX
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 TYR 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.0 2.8 - - - +
17A VAL* 3.4 42.8 - - + +
18A LYS 3.4 20.4 - - - -
19A ALA* 3.8 3.8 - - - -
20A PRO* 1.3 75.1 - - - +
22A VAL* 1.3 69.1 + - - +
23A ARG* 3.5 15.7 - - + -
40A ASP* 2.7 38.4 + - - +
41A LEU* 3.8 0.7 - - - -
42A ARG* 3.0 63.5 + - + +
103A PHE* 4.6 0.2 - - - -
148A LEU* 3.8 10.0 - - - +
149A LYS* 3.3 20.0 - - + +
151A GLN* 3.4 25.6 - - + -
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Residues in contact with VAL 22 (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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21A TYR* 1.3 76.1 - - - +
23A ARG* 1.3 63.6 + - - +
39A TYR* 4.2 12.1 - - + -
40A ASP 3.5 2.7 - - - -
41A LEU* 3.9 11.4 - - + -
96A GLU* 4.1 17.3 - - + +
99A VAL* 3.7 24.0 - - + -
100A MET* 3.9 28.7 - - + -
103A PHE* 3.6 31.2 - - + -
148A LEU* 4.6 1.3 - - + -
149A LYS 3.0 5.6 + - - +
150A VAL* 3.4 9.3 - - - +
151A GLN 3.0 22.5 + - - -
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Residues in contact with ARG 23 (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 PHE* 4.0 8.7 + - - +
12A LEU* 3.7 37.3 - - - +
21A TYR* 3.5 19.7 - - + -
22A VAL* 1.3 78.3 - - - +
24A LEU* 1.3 78.8 + - - +
25A ALA* 3.1 29.1 + - - +
39A TYR* 3.4 6.8 - - - -
40A ASP* 2.9 63.2 + - + +
42A ARG* 4.9 0.6 - - - +
87A TYR* 4.3 8.9 + - - -
96A GLU* 3.8 4.0 - - - +
151A GLN* 3.3 24.2 - - - +
153A THR* 2.9 38.8 + - - +
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Residues in contact with LEU 24 (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 PHE* 3.2 34.6 - - + -
23A ARG* 1.3 71.2 - - - +
25A ALA* 1.3 57.8 + - - +
26A GLY 3.6 19.1 - - - +
27A VAL* 5.1 2.7 - - + -
37A SER* 3.9 10.3 - - - -
38A LYS 3.5 14.8 - - - +
39A TYR* 3.9 15.7 - - + -
94A PRO* 3.7 38.4 - - + -
96A GLU* 2.7 33.5 + - + +
153A THR* 3.4 10.6 + - - -
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Residues in contact with ALA 25 (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 GLU 4.6 0.7 - - - -
9A SER* 3.6 4.9 + - - +
10A PHE* 2.9 31.7 + - - +
23A ARG* 3.1 29.1 + - - +
24A LEU* 1.3 72.8 - - - +
26A GLY* 1.3 59.1 + - - +
38A LYS* 2.7 20.4 + - + +
40A ASP 4.2 6.3 - - - +
87A TYR* 3.8 26.2 - - + +
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Residues in contact with GLY 26 (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 GLU 3.6 17.7 - - - -
10A PHE* 3.7 18.5 - - - -
24A LEU* 3.4 9.9 - - - +
25A ALA* 1.3 81.0 - - - +
27A VAL* 1.3 63.2 + - - +
38A LYS* 2.9 30.2 + - - +
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Residues in contact with VAL 27 (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 GLU* 3.7 22.3 + - - +
10A PHE* 4.7 10.4 - - + -
24A LEU* 5.1 2.9 - - + -
26A GLY* 1.3 77.4 - - - +
28A LYS* 1.3 65.3 + - - +
29A THR* 4.2 4.6 + - - +
35A GLN* 3.6 31.9 - - + +
36A ILE 3.3 10.5 - - - +
37A SER* 4.2 12.1 - - - +
38A LYS* 5.3 0.2 - - - -
94A PRO* 4.3 13.2 - - + -
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Residues in contact with LYS 28 (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 GLU* 3.2 44.9 + - + +
27A VAL* 1.3 77.0 - - - +
29A THR* 1.3 66.5 + - - +
30A THR 3.8 0.3 + - - -
35A GLN* 3.6 0.3 - - - -
36A ILE* 2.8 45.8 + - + +
38A LYS* 4.9 8.4 - - - +
73B GLY* 3.8 22.2 - - - +
74B VAL 3.4 23.7 + - - +
75B VAL* 4.4 10.3 - - + +
91B ILE* 3.4 31.2 - - + -
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Residues in contact with THR 29 (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 GLU* 5.4 0.6 + - - -
27A VAL* 4.2 4.5 + - - +
28A LYS* 1.3 84.5 + - - +
30A THR* 1.3 74.4 + - - +
31A PRO* 4.6 1.0 - - - +
33A GLY* 4.4 11.7 - - - +
34A ASP 3.4 12.6 - - - +
35A GLN* 4.5 11.4 + - + +
91B ILE* 4.3 2.1 - - - +
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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