Contacts of the strand formed by residues 103 - 113 (chain B) in PDB entry 2VSC
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 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A PCA 3.5 22.9 + - + -
2A LEU* 3.5 22.9 - - + +
27A ASN* 2.8 47.9 + - - +
29A GLU* 3.3 39.7 + - - +
99A THR* 3.4 4.3 - - - +
100A GLU* 2.7 63.4 + - + +
35B GLU* 4.0 23.3 - - + -
101B LEU 3.9 8.5 - - - +
102B THR* 1.3 81.3 - - - +
104B GLU* 1.3 61.6 + - - +
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Residues in contact with GLU 104 (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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1A PCA 2.7 41.7 + - - +
2A LEU* 3.0 10.6 + - - -
97A GLU* 4.2 19.1 - - + +
98A VAL 3.4 12.1 - - - +
99A THR* 3.9 13.3 + - + +
102B THR* 5.3 2.9 - - + -
103B ARG* 1.3 76.2 - - - +
105B GLY* 1.3 60.8 + - - +
106B GLU* 4.5 8.1 - - - +
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Residues in contact with GLY 105 (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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2A LEU* 4.0 8.2 - - - +
4A PHE* 3.4 19.4 - - - -
97A GLU* 3.4 4.3 - - - +
98A VAL 3.1 29.3 + - - +
104B GLU* 1.3 80.5 - - - +
106B GLU* 1.3 66.1 + - - +
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Residues in contact with GLU 106 (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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4A PHE* 3.4 8.0 - - - -
6A LYS* 3.6 10.4 + - - -
41A LYS* 5.5 4.2 + - - -
95A THR* 3.9 23.0 - - + +
96A CYS 3.0 14.4 - - - +
97A GLU* 3.8 24.0 - - - +
104B GLU* 4.5 6.9 - - - +
105B GLY* 1.3 73.9 - - - +
107B THR* 1.3 63.3 + - - +
108B ILE* 5.8 3.2 - - + +
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Residues in contact with THR 107 (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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4A PHE* 3.4 30.3 - - + -
5A ASN 6.0 0.7 - - - +
6A LYS* 2.9 43.8 + - - +
7A THR 5.3 0.5 + - - -
22A PRO 5.1 0.2 - - - +
23A CYS* 4.0 16.2 - - + -
24A PHE 5.5 0.2 - - - +
94A TYR 3.9 0.3 - - - +
95A THR* 3.4 2.1 - - - -
96A CYS* 2.8 32.4 + - + +
106B GLU* 1.3 72.6 - - - +
108B ILE* 1.3 70.1 + - - +
109B ILE* 3.9 14.1 - - + +
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Residues in contact with ILE 108 (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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6A LYS* 5.9 0.5 - - - +
7A THR 3.6 12.0 - - - +
8A LYS* 4.3 4.2 - - - +
93A ASN* 4.0 31.2 - - + +
94A TYR 3.2 10.8 - - - +
95A THR* 3.6 21.5 - - + +
1119A NAG 5.7 0.4 - - - +
106B GLU* 5.8 2.7 - - + +
107B THR* 1.3 83.8 + - - +
109B ILE* 1.3 66.1 + - - +
110B GLU 4.3 0.2 - - - -
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Residues in contact with ILE 109 (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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7A THR* 3.7 19.1 - - - +
8A LYS 3.6 3.1 - - - -
9A SER* 4.0 9.2 - - - -
10A VAL* 4.1 12.1 - - + +
21A ILE* 3.8 16.8 - - + -
22A PRO* 3.3 35.2 - - + +
40A TRP* 3.9 24.0 - - + -
94A TYR* 2.8 33.7 + - - +
107B THR* 3.9 24.0 - - + +
108B ILE* 1.3 83.7 - - - +
110B GLU* 1.3 73.5 + - - +
111B LEU 3.8 0.5 + - - -
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Residues in contact with GLU 110 (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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8A LYS* 2.9 23.5 + - + +
9A SER* 3.0 11.4 - - - -
10A VAL 2.9 26.3 + - - +
92A GLY* 3.5 15.4 - - - +
93A ASN* 3.4 20.7 + - - +
1119A NAG 3.7 33.1 + - - +
108B ILE* 4.9 0.4 - - - +
109B ILE* 1.3 75.6 - - - +
111B LEU* 1.3 66.5 + - - +
112B LYS* 4.1 26.1 - - + +
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Residues in contact with LEU 111 (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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10A VAL* 3.6 21.8 - - + +
12A PHE* 3.8 25.6 - - + -
19A VAL* 3.5 27.8 - - + -
21A ILE* 4.3 9.9 - - + -
82A MET* 5.1 0.7 - - - -
87A ALA* 4.1 21.5 - - + +
90A HIS 3.7 21.8 - - - +
91A THR* 3.6 7.7 - - - -
92A GLY* 2.9 27.0 + - - +
94A TYR* 3.8 27.1 - - + +
1116A NAG 4.0 2.5 - - + -
109B ILE 3.8 0.8 + - - -
110B GLU* 1.3 72.5 - - - +
112B LYS* 1.3 60.7 + - - +
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Residues in contact with LYS 112 (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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8A LYS* 6.4 0.9 - - - +
9A SER* 3.6 31.5 + - - +
10A VAL 2.8 14.8 + - - +
11A GLU* 3.4 13.2 - - + +
12A PHE* 2.9 33.5 + - - +
91A THR* 5.1 0.9 - - - -
110B GLU* 4.1 25.4 - - - +
111B LEU* 1.3 76.2 - - - +
113B TYR* 1.3 62.3 + - - +
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Residues in contact with TYR 113 (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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12A PHE* 3.3 40.8 - + + -
13A THR* 3.7 23.1 - - - -
14A PHE* 3.8 22.3 - - - +
88A VAL* 4.2 24.5 - - + +
91A THR* 3.9 17.4 - - + +
112B LYS* 1.3 75.8 - - - +
114B ARG* 1.3 64.1 + - - +
115B VAL* 4.2 27.3 + - + +
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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