Contacts of the strand formed by residues 83 - 89 (chain A) in PDB entry 3VAS
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 CYS 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.2 21.5 - - - +
70A VAL* 3.7 11.0 - - + -
73A ILE* 3.7 30.5 - - - -
74A GLN* 2.9 28.4 + - + +
81A PHE 4.0 3.2 - - - +
82A VAL* 1.3 86.2 - - - +
84A SER* 1.3 62.4 + - - +
107A LEU* 3.3 20.9 - - + +
108A VAL* 3.1 26.9 + - - +
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Residues in contact with SER 84 (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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7A GLY* 3.8 15.6 + - - -
9A VAL 2.7 13.2 + - - +
10A PHE* 3.4 20.5 - - - -
11A GLY* 2.7 30.9 + - - -
70A VAL* 3.8 4.5 - - - +
83A CYS* 1.3 75.4 + - - +
85A TYR* 1.3 57.4 + - - +
107A LEU* 4.1 1.8 - - - -
108A VAL* 3.2 13.4 - - - +
157A LEU* 3.7 31.5 + - - +
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Residues in contact with TYR 85 (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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11A GLY* 3.2 17.5 - - - -
13A GLY* 3.2 37.0 + - - -
14A ASN 3.5 2.6 + - - -
15A PRO* 3.3 19.8 - - + +
66A THR* 4.1 7.2 - - + -
67A LEU* 3.7 47.8 + - + +
70A VAL* 4.6 5.4 - - + -
84A SER* 1.3 75.3 - - - +
86A VAL* 1.3 79.1 + - - +
87A GLY* 3.8 1.8 - - - -
107A LEU* 4.1 20.4 - - + -
108A VAL 2.9 9.5 + - - -
109A THR* 3.2 10.9 - - + -
110A GLU 3.1 24.6 + - - -
111A PHE* 3.8 29.6 - + - -
157A LEU* 5.3 0.9 - - - +
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Residues in contact with VAL 86 (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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10A PHE* 3.6 33.0 - - + -
11A GLY 2.9 6.8 + - - +
12A MET* 3.1 7.6 - - + +
13A GLY 2.9 24.8 + - - -
85A TYR* 1.3 83.3 - - - +
87A GLY* 1.3 61.2 + - - +
110A GLU* 3.8 22.7 - - + +
144A LEU* 4.0 12.8 - - + +
148A HIS* 3.8 21.8 - - + -
149A ILE* 4.5 10.5 - - + -
154A VAL* 3.8 19.3 - - + -
157A LEU* 4.8 3.1 - - + -
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Residues in contact with GLY 87 (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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13A GLY 3.5 15.3 - - - -
15A PRO* 3.9 7.2 - - - -
85A TYR* 3.8 8.7 - - - -
86A VAL* 1.3 77.7 - - - +
88A CYS* 1.3 59.2 + - - -
110A GLU 4.2 1.4 + - - -
111A PHE* 3.3 14.4 - - - -
112A GLN* 2.8 23.8 + - - +
144A LEU* 4.3 9.4 - - - -
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Residues in contact with CYS 88 (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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13A GLY 4.3 1.2 + - - -
15A PRO* 3.6 15.0 - - - +
87A GLY* 1.3 72.4 - - - -
89A ILE* 1.3 63.0 + - - +
112A GLN* 3.2 29.2 - - + +
114A ALA* 3.8 18.2 - - - -
120A THR* 5.6 0.2 - - - +
140A ALA* 3.2 24.6 - - - +
141A ALA* 3.3 24.4 + - - +
143A ASP* 3.9 15.0 - - - -
144A LEU* 3.8 24.1 - - + +
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Residues in contact with ILE 89 (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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15A PRO* 3.6 28.3 - - + -
87A GLY 4.1 0.4 + - - -
88A CYS* 1.3 72.5 - - - +
90A GLY* 1.3 60.9 + - - +
95A GLY* 3.3 38.6 - - - +
96A LYS* 4.4 0.4 - - - +
98A ILE* 4.8 4.3 - - + -
99A LYS* 4.3 16.6 - - + -
111A PHE* 3.9 29.6 - - + -
112A GLN 3.0 7.8 + - - +
113A ILE* 3.3 16.0 - - + -
114A ALA* 2.8 30.3 + - - +
120A THR* 3.7 16.6 - - + +
140A ALA* 3.5 7.2 - - - -
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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