Contacts of the strand formed by residues 92 - 100 (chain D) 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 GLY 92 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C GLU* 4.0 14.8 - - - -
111C LEU 2.8 38.5 + - - -
42D PHE* 4.3 3.4 - - - -
43D LYS* 5.8 1.6 - - - -
91D THR* 1.3 75.7 - - - +
93D ASN* 1.3 63.0 + - - -
94D TYR* 3.3 9.4 - - - -
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Residues in contact with ASN 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ILE* 3.5 23.4 - - + +
109C ILE 3.9 1.3 - - - -
110C GLU* 3.8 27.2 + - - +
41D LYS 4.0 3.6 - - - +
42D PHE* 3.6 21.3 - - - -
43D LYS* 4.4 4.4 + - - +
92D GLY* 1.3 70.2 - - - -
94D TYR* 1.3 62.1 + - - +
95D THR* 5.4 0.6 + - - -
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Residues in contact with TYR 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C THR 3.9 0.3 - - - +
108C ILE* 3.3 6.4 - - - +
109C ILE* 2.8 40.7 + - - +
111C LEU* 3.8 14.2 - - + +
21D ILE* 3.6 32.8 - - + -
40D TRP* 3.8 22.2 - + + -
41D LYS 3.4 13.9 - - - -
42D PHE* 3.8 22.2 - + + -
47D ILE* 3.8 23.8 - - + -
63D PHE* 3.2 10.4 - + - -
80D LEU* 4.6 0.2 - - + -
82D MET* 4.0 5.9 - - + +
90D HIS* 2.7 44.7 + - - +
92D GLY 3.3 23.6 - - - -
93D ASN* 1.3 73.6 - - - +
95D THR* 1.3 61.5 + - - +
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Residues in contact with THR 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C GLU* 3.9 37.2 - - + +
107C THR 3.4 12.6 - - - +
108C ILE* 4.0 14.4 - - + +
39D LYS 3.6 1.7 - - - +
40D TRP* 3.2 9.1 - - - -
41D LYS* 2.8 59.6 + - - +
93D ASN 4.2 0.9 + - - -
94D TYR* 1.3 73.2 + - - +
96D CYS* 1.3 62.5 + - - +
97D GLU* 4.7 1.1 - - + +
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Residues in contact with CYS 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C GLU* 3.1 4.3 - - - -
107C THR* 2.9 37.1 + - + +
109C ILE* 5.8 0.2 - - + -
4D PHE* 4.2 1.6 - - - -
23D CYS* 2.0 48.7 - - + -
38D VAL* 4.7 1.3 - - - -
39D LYS 3.7 3.4 - - - -
40D TRP* 3.4 35.7 - - + -
78D ALA* 3.8 13.5 - - - -
95D THR* 1.3 73.1 - - - +
97D GLU* 1.3 61.2 + - - +
98D VAL* 4.0 6.3 - - - -
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Residues in contact with GLU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C GLU* 4.2 18.0 - - - +
105C GLY 3.4 12.8 - - - +
106C GLU* 3.9 20.4 - - + +
37D TYR* 3.8 5.4 - - - +
38D VAL* 3.4 5.2 - - - +
39D LYS* 2.8 78.5 + - + +
41D LYS* 4.6 11.2 + - - -
95D THR* 4.0 4.0 - - + -
96D CYS* 1.3 73.2 - - - +
98D VAL* 1.3 62.9 + - - +
99D THR* 3.9 11.9 + - - +
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Residues in contact with VAL 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C GLU* 3.3 1.7 - - - +
105C GLY 3.1 30.5 + - - +
2D LEU* 3.2 22.3 - - + +
4D PHE* 4.1 4.7 - - + -
25D VAL* 3.8 20.4 - - + -
28D MET* 3.8 25.6 - - + -
36D VAL* 4.1 13.5 - - + -
37D TYR 3.5 2.7 - - - +
38D VAL* 4.7 3.4 - - + -
73D LEU* 5.6 0.7 - - + -
78D ALA* 3.7 29.4 - - + -
96D CYS* 4.0 9.6 - - - -
97D GLU* 1.3 75.8 - - - +
99D THR* 1.3 66.5 + - - +
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Residues in contact with THR 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C THR* 3.3 34.1 - - + -
103C ARG 3.4 4.9 - - - +
104C GLU* 3.2 22.8 + - + +
35D GLU 3.7 0.2 - - - +
36D VAL* 3.4 8.3 - - - +
37D TYR* 2.9 48.6 + - - +
97D GLU* 3.9 11.6 + - - -
98D VAL* 1.3 76.1 - - - +
100D GLU* 1.3 64.9 + - - +
101D LEU* 3.9 12.0 + - + -
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Residues in contact with GLU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLU* 5.4 0.2 - - - +
101C LEU 4.6 0.5 - - - +
102C THR* 3.3 5.5 - - - +
103C ARG* 2.8 65.3 + - + +
1120C MG 4.3 8.7 - - - -
2D LEU* 4.1 13.0 - - + +
28D MET* 3.3 27.6 - - + +
29D GLU* 2.8 34.9 + - - +
30D ALA* 3.0 20.9 + - + -
35D GLU* 3.3 6.3 - - + +
36D VAL* 5.1 0.2 - - + -
99D THR* 1.3 74.4 - - - +
101D LEU* 1.3 66.0 + - - +
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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