Contacts of the strand formed by residues 103 - 113 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLU* 3.6 32.6 + - + +
101A LEU* 3.6 7.6 - - + +
102A THR* 1.3 81.8 - - - +
104A GLU* 1.3 59.2 + - - +
1120A MG 4.3 6.3 - - - -
1B PCA 3.6 25.2 + - + -
2B LEU* 3.4 24.7 - - + +
27B ASN* 2.9 53.9 + - - +
29B GLU* 3.3 27.5 + - - +
99B THR* 3.3 4.0 - - - +
100B GLU* 2.7 73.4 + - - +
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Residues in contact with GLU 104 (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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102A THR* 5.1 3.1 - - + -
103A ARG* 1.3 75.8 - - - +
105A GLY* 1.3 61.4 + - - +
1B PCA 2.7 43.2 + - - +
2B LEU* 3.1 10.4 + - - +
97B GLU* 4.4 20.0 - - + +
98B VAL 3.3 11.4 - - - +
99B THR* 4.0 15.0 + - + +
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Residues in contact with GLY 105 (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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104A GLU* 1.3 81.3 - - - +
106A GLU* 1.3 61.2 + - - +
2B LEU* 4.0 7.7 - - - +
4B PHE* 3.4 20.2 - - - -
97B GLU* 3.4 5.3 - - - +
98B VAL 3.0 32.1 + - - +
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Residues in contact with GLU 106 (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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105A GLY* 1.3 75.2 - - - +
107A THR* 1.3 63.6 + - - +
108A ILE* 4.6 12.6 - - - +
4B PHE* 3.4 10.6 - - - -
41B LYS* 5.4 4.3 + - - -
95B THR* 3.6 25.2 + - + +
96B CYS 3.2 10.5 - - - +
97B GLU* 4.2 16.0 - - + +
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Residues in contact with THR 107 (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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106A GLU* 1.3 77.7 - - - +
108A ILE* 1.3 68.7 + - - +
109A ILE* 4.0 11.4 - - + +
4B PHE* 3.5 36.7 - - + +
5B ASN 5.8 0.9 - - - +
6B LYS* 3.1 31.7 - - - +
7B THR 5.1 0.6 + - - +
23B CYS* 4.1 16.4 - - + -
24B PHE 5.6 0.2 - - - +
94B TYR 3.8 0.2 - - - +
95B THR* 3.4 4.0 - - - +
96B CYS* 2.9 34.5 + - + +
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Residues in contact with ILE 108 (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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106A GLU* 4.6 12.3 - - - +
107A THR* 1.3 79.9 + - - +
109A ILE* 1.3 67.0 + - - +
6B LYS* 3.0 36.2 + - - +
7B THR 3.3 3.5 - - - +
8B LYS 4.1 1.7 - - - +
93B ASN* 3.9 29.4 - - + +
94B TYR 3.2 10.5 - - - +
95B THR* 4.0 16.2 - - - +
1117B NAG 5.6 4.7 - - - +
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Residues in contact with ILE 109 (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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107A THR* 4.0 24.0 - - + +
108A ILE* 1.3 82.4 - - - +
110A GLU* 1.3 71.3 + - - +
111A LEU 3.7 0.3 + - - -
7B THR* 3.9 14.4 - - - +
8B LYS 3.7 3.1 - - - -
9B SER* 3.9 13.9 - - - -
10B VAL* 4.1 7.0 - - + +
21B ILE* 3.8 18.6 - - + +
22B PRO* 3.4 38.8 - - + +
40B TRP* 3.8 25.6 - - + -
94B TYR* 2.8 36.1 + - - +
96B CYS* 4.4 0.4 - - + -
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Residues in contact with GLU 110 (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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108A ILE* 4.8 0.2 - - - +
109A ILE* 1.3 74.4 - - - +
111A LEU* 1.3 64.2 + - - +
112A LYS* 3.6 39.0 + - + +
8B LYS* 3.0 16.5 + - - +
9B SER* 3.0 16.6 - - - -
10B VAL 2.9 28.6 + - - +
92B GLY* 3.4 14.9 - - - +
93B ASN* 3.3 18.2 + - - +
1117B NAG 3.2 42.9 + - - +
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Residues in contact with LEU 111 (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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109A ILE* 3.7 2.4 + - - +
110A GLU* 1.3 71.3 - - - +
112A LYS* 1.3 60.1 + - - +
10B VAL* 3.6 22.0 - - + +
12B PHE* 3.6 38.4 - - + -
19B VAL* 4.4 5.4 - - + -
21B ILE* 4.0 10.5 - - + +
82B MET* 3.4 31.0 - - + -
87B ALA* 3.9 4.5 - - + +
90B HIS 3.6 17.3 - - - +
91B THR* 3.6 6.3 - - - -
92B GLY* 2.8 35.1 + - - +
94B TYR* 3.7 19.5 - - + -
1116B NAG 4.1 9.9 - - + -
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Residues in contact with LYS 112 (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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110A GLU* 3.6 43.5 + - + +
111A LEU* 1.3 73.9 - - - +
113A TYR* 1.3 61.5 + - - +
8B LYS* 5.3 9.1 - - - +
9B SER* 3.9 19.5 + - - +
10B VAL 2.8 14.8 + - - +
11B GLU* 3.2 15.6 - - + +
12B PHE* 3.0 30.9 + - - -
91B THR* 4.9 1.3 - - - -
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Residues in contact with TYR 113 (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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111A LEU 4.3 0.6 + - - -
112A LYS* 1.3 76.9 - - - +
114A ARG* 1.3 73.3 + - - +
115A VAL* 4.2 20.8 + - + +
11B GLU* 4.7 1.1 - - - -
12B PHE* 3.5 33.9 - + + -
13B THR* 3.7 21.5 - - - -
14B PHE* 3.5 26.0 + - - +
88B VAL* 4.6 12.3 - - + +
91B THR* 3.8 23.0 - - + +
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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