Contacts of the strand formed by residues 28 - 32 (chain E) in PDB entry 1VCB
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 GLU 28 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D LYS* 2.8 14.2 + - - +
12D THR* 3.6 9.8 + - + +
13D THR* 3.1 26.9 + - - +
20E LYS* 2.7 46.4 + - + +
21E LEU 3.6 3.4 - - - -
22E ILE* 3.6 25.4 - - + +
26E GLY 3.7 11.2 - - - +
27E HIS* 1.3 76.3 - - - +
29E PHE* 1.3 62.3 + - - +
30E ILE* 3.8 5.7 - - + +
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Residues in contact with PHE 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D THR* 3.4 18.6 - - + +
15D PHE* 3.6 22.2 - + + -
93D PHE* 3.5 41.1 - + - -
19E VAL 3.4 4.0 - - - +
20E LYS* 3.5 0.4 - - - -
21E LEU* 2.9 45.6 + - + +
23E SER* 4.5 4.5 - - - -
27E HIS* 3.6 25.6 - - + -
28E GLU* 1.3 73.6 - - - +
30E ILE* 1.3 63.3 + - - +
31E VAL* 3.6 1.4 + - + -
67E SER* 4.2 11.7 - - - -
70E LEU* 4.0 28.0 - - + -
71E SER* 4.1 12.1 - - - -
74E CYS* 3.9 22.2 - - - -
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Residues in contact with ILE 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D THR* 4.0 21.3 - - + -
13D THR 3.1 6.8 + - - +
14D ILE* 3.8 15.8 - - + +
15D PHE* 3.2 26.9 + - - +
34D ILE* 3.9 19.7 - - + -
35D LEU* 5.1 4.9 - - + -
18E TYR* 3.4 37.4 - - + -
19E VAL 3.3 8.1 - - - +
20E LYS* 4.3 24.2 - - + -
28E GLU* 3.8 15.3 - - + +
29E PHE* 1.3 76.0 - - - +
31E VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PHE* 4.2 17.7 - - + -
18E TYR* 3.4 6.8 - - - -
19E VAL* 2.8 38.9 + - + +
21E LEU* 4.3 8.5 - - + -
29E PHE 4.1 7.9 - - - +
30E ILE* 1.3 80.0 - - - +
32E LYS* 1.3 73.8 + - - +
35E HIS* 3.7 22.0 - - + -
36E ALA* 4.4 4.5 - - + +
74E CYS* 3.6 36.8 - - + +
77E PHE* 4.7 10.1 - - + -
78E THR* 5.6 0.9 - - + -
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Residues in contact with LYS 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D PHE 4.9 3.5 + - - +
16D THR* 4.6 13.4 + - - +
17D ASP* 3.0 27.6 + - - -
17E MET* 3.5 21.2 - - + +
18E TYR* 3.6 35.6 - - + -
31E VAL* 1.3 79.7 - - - +
33E ARG* 1.3 64.4 + - - +
34E GLU* 3.0 24.2 - - - +
35E HIS* 3.2 34.2 + - + +
36E ALA* 3.1 18.9 + - - +
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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