Contacts of the strand formed by residues 5 - 13 (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 ARG 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ALA* 4.1 8.5 + - + +
4A LYS* 1.3 78.1 - - - +
6A ILE* 1.3 66.5 + - - +
7A ILE* 4.1 13.3 - - + +
45A ASP* 3.3 20.4 - - + +
46A GLU* 2.9 39.0 + - - -
99A LYS* 4.0 1.2 - - - +
167A GLU* 2.9 32.3 + - - -
197A PRO* 3.7 19.4 - - - +
199A ILE* 4.7 1.0 - - - +
214A PHE* 3.8 1.2 - - - -
219A ASP* 3.1 20.2 + - - +
220A ALA* 3.2 25.8 - - + +
221A ALA 3.0 25.6 + - - -
249A ARG* 6.3 0.2 - - - +
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Residues in contact with ILE 6 (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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5A ARG* 1.3 78.9 - - - +
7A ILE* 1.3 61.1 + - - +
43A GLY 5.1 0.4 - - - +
44A ILE* 3.8 14.7 - - + +
45A ASP* 2.7 46.9 + - - +
46A GLU 3.6 0.5 + - - -
210A PHE* 4.1 12.1 - - + -
214A PHE* 3.9 15.3 - - + -
221A ALA* 3.7 3.6 - - + +
227A PHE* 3.8 28.0 - - + -
234A VAL* 4.9 3.8 - - + -
237A LEU* 4.0 11.9 - - + -
238A LYS* 4.2 26.5 - - + -
241A LEU* 3.8 24.9 - - + -
248A VAL* 4.9 5.6 - - + -
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Residues in contact with ILE 7 (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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5A ARG* 4.1 11.9 - - + +
6A ILE* 1.3 79.5 - - - +
8A ALA* 1.4 65.5 + - - +
44A ILE* 4.6 0.2 - - - -
46A GLU* 3.4 42.6 - - + +
47A LEU 4.3 0.2 - - - -
48A VAL* 3.7 28.7 - - + -
199A ILE* 4.1 20.0 - - + -
220A ALA* 3.8 28.3 - - + -
221A ALA 2.9 14.5 + - - +
222A LEU* 3.3 10.7 - - + -
223A ALA 3.1 24.8 + - - +
227A PHE* 3.8 7.6 - - - -
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Residues in contact with ALA 8 (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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7A ILE* 1.4 74.8 - - - +
9A CYS* 1.3 59.4 + - - +
10A LEU* 3.8 4.4 - - + +
39A TYR* 4.0 19.7 - - + -
44A ILE* 3.8 21.6 - - + +
46A GLU 3.2 6.7 + - - -
47A LEU* 3.4 20.3 - - + -
48A VAL 2.9 24.4 + - - +
223A ALA 3.5 4.3 - - - +
227A PHE* 4.0 11.9 - - + -
228A HIS* 5.1 1.1 - - + -
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Residues in contact with CYS 9 (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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7A ILE 4.0 0.4 + - - -
8A ALA* 1.3 72.7 - - - +
10A LEU* 1.3 63.3 + - - +
11A ASP* 4.0 11.3 + - - -
48A VAL* 3.3 16.4 - - + -
50A LEU* 3.8 32.5 - - - -
222A LEU* 3.5 33.4 - - + -
223A ALA 2.9 9.2 + - - +
224A ALA* 3.4 13.9 - - + +
228A HIS* 2.8 23.4 + - - -
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Residues in contact with LEU 10 (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 3.8 15.7 - - - +
9A CYS* 1.3 79.9 - - - +
11A ASP* 1.3 64.5 + - - +
12A VAL* 3.5 7.7 + - + +
17A VAL* 4.5 4.7 - - + -
32A PRO* 3.6 31.0 - - + +
35A LEU* 3.7 29.6 - - + -
36A GLY* 4.3 4.9 - - - +
39A TYR* 4.3 6.3 - - + -
47A LEU* 4.1 16.2 - - + -
48A VAL 2.7 14.4 + - - +
49A PHE* 3.4 24.0 - - + -
50A LEU 3.0 24.6 + - - -
228A HIS* 4.1 11.7 - - + +
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Residues in contact with ASP 11 (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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9A CYS* 4.0 6.3 + - - -
10A LEU* 1.3 72.4 - - - +
12A VAL* 1.3 58.2 + - - +
17A VAL* 3.5 10.0 - - - +
18A VAL* 2.9 41.2 + - + +
50A LEU* 3.5 27.8 - - - +
52A ILE* 5.9 3.6 - - + -
224A ALA* 4.7 13.7 - - - +
228A HIS* 5.1 2.7 + - - -
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Residues in contact with VAL 12 (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* 3.9 13.2 - - + +
11A ASP* 1.3 78.8 - - - +
13A LYS* 1.3 63.0 + - - +
15A GLY 5.2 2.7 - - - +
16A ARG 3.2 14.8 - - - +
17A VAL* 4.4 1.1 - - - -
18A VAL* 3.9 1.8 - - - -
32A PRO* 3.7 31.6 - - + -
49A PHE* 4.3 9.0 - - + -
50A LEU 2.9 21.0 + - - +
51A ASP* 3.4 20.0 - - + +
52A ILE* 3.0 28.4 + - - +
65A LEU* 3.8 23.8 - - + -
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Residues in contact with LYS 13 (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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12A VAL* 1.3 77.3 - - - +
14A ASP* 1.3 104.0 + - - +
15A GLY 4.3 0.4 - - - +
16A ARG* 2.9 24.0 + - - +
18A VAL* 4.0 11.2 - - + +
51A ASP* 4.3 0.2 - - - -
52A ILE* 3.7 40.8 - - + +
53A THR* 3.7 8.1 - - - +
54A ALA* 5.2 5.9 - - - +
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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