Contacts of the strand formed by residues 68 - 75 (chain B) in PDB entry 1VCA
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 SER 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B THR* 3.3 23.2 - - - -
38B GLN* 3.4 31.3 + - - +
67B HIS* 1.3 74.0 + - - +
69B TYR* 1.3 60.9 + - - +
70B LEU* 3.8 7.1 + - - +
83B GLY* 5.9 0.7 - - - -
84B ILE 3.6 6.3 + - - -
85B GLN* 4.1 19.6 + - - +
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Residues in contact with TYR 69 (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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21B LEU* 4.1 13.9 - - + -
35B TRP* 4.2 13.2 - + + -
36B ARG 3.6 2.2 - - - -
37B THR* 3.8 19.7 - - + -
43B LEU* 2.7 41.1 + - + -
56B LEU* 3.4 24.0 - - + -
58B MET* 4.1 13.2 - - + -
64B GLY 3.8 2.3 + - - -
65B ASN* 3.0 43.7 + - - -
67B HIS* 3.8 17.5 - + + -
68B SER* 1.3 71.0 - - - +
70B LEU* 1.3 61.3 + - - +
71B CYS 3.9 1.1 + - - -
82B LYS 4.1 0.2 - - - +
83B GLY* 3.3 1.7 - - - -
84B ILE* 2.8 41.9 + - + +
86B VAL* 3.8 18.8 - - + -
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Residues in contact with LEU 70 (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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34B SER 3.8 0.5 - - - +
35B TRP* 3.4 7.2 - - - -
36B ARG* 2.8 83.4 + - + +
37B THR 4.4 6.7 - - - +
38B GLN* 3.6 34.1 - - + +
68B SER* 4.4 9.4 - - - +
69B TYR* 1.3 73.4 - - - +
71B CYS* 1.3 61.8 + - - +
72B THR* 3.9 0.5 + - - -
81B GLU* 3.9 17.0 - - - +
82B LYS 3.7 0.7 - - - -
83B GLY* 3.6 24.0 - - - +
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Residues in contact with CYS 71 (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 ILE* 3.9 1.9 - - + +
5B THR* 4.8 3.4 - - + -
23B CYS* 2.0 54.1 - - + -
33B PHE* 4.0 14.1 - - - -
34B SER 3.5 7.4 - - - -
35B TRP* 3.9 20.4 - - + -
69B TYR 3.9 1.6 + - - -
70B LEU* 1.3 73.5 - - - +
72B THR* 1.3 68.4 + - - +
80B LEU 3.8 0.5 - - - +
81B GLU* 3.3 5.9 - - - +
82B LYS 2.8 39.4 + - - +
84B ILE* 6.0 0.2 - - + -
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Residues in contact with THR 72 (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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32B PHE 3.6 1.6 - - - +
33B PHE* 3.4 4.5 - - - +
34B SER* 2.8 47.1 + - - -
36B ARG* 3.7 20.6 + - - -
70B LEU 3.9 0.5 + - - -
71B CYS* 1.3 76.3 + - - +
73B ALA* 1.3 60.4 + - - +
74B THR* 3.9 9.5 + - - +
79B LYS* 4.0 29.8 - - + -
80B LEU 3.3 11.2 - - - +
81B GLU* 3.9 7.4 + - + +
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Residues in contact with ALA 73 (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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1B PHE* 3.4 11.0 - - + -
3B ILE* 3.8 20.4 - - + +
25B THR* 3.4 33.0 - - + -
31B PRO* 5.4 0.7 - - + -
32B PHE 3.6 4.9 - - - +
33B PHE* 4.0 12.6 - - + -
72B THR* 1.3 71.9 - - - +
74B THR* 1.3 60.9 + - - +
79B LYS* 3.4 1.6 - - - -
80B LEU 2.9 31.7 + - - +
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Residues in contact with THR 74 (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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1B PHE* 4.5 0.4 - - - -
30B SER 4.3 1.7 - - - +
31B PRO* 3.5 4.8 - - - +
32B PHE* 2.9 50.8 + - + +
34B SER* 6.1 0.3 - - - -
72B THR* 4.1 8.5 + - - +
73B ALA* 1.3 72.1 - - - +
75B CYS* 1.3 60.4 + - - +
76B GLU 3.6 21.5 + - - +
77B SER 4.9 0.9 - - - -
78B ARG 3.3 9.9 - - - +
79B LYS* 3.4 31.8 + - + +
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Residues in contact with CYS 75 (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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1B PHE* 3.6 29.9 - - + -
27B GLY 4.6 2.7 - - - -
28B CYS* 2.0 53.2 - - - -
29B GLU 4.4 1.6 - - - -
31B PRO* 4.9 0.2 - - - -
74B THR* 1.3 70.9 - - - +
76B GLU* 1.3 73.1 + - - +
77B SER 2.9 9.7 + - - -
78B ARG* 2.8 39.0 + - - +
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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
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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