Contacts of the strand formed by residues 78 - 89 (chain A) 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 ARG 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A PHE* 3.7 40.4 - - + +
27A GLY 5.0 3.2 + - - -
73A ALA 3.9 0.2 - - - +
74A THR* 3.3 4.9 - - - +
75A CYS* 2.8 53.0 + - - +
76A GLU* 3.5 24.4 + - - +
77A SER* 1.3 86.6 - - - +
79A LYS* 1.3 62.0 + - - +
80A LEU* 6.0 0.7 - - + -
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Residues in contact with LYS 79 (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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1A PHE* 4.4 0.2 - - - -
72A THR* 4.2 18.3 - - + +
73A ALA 3.3 4.9 - - - +
74A THR* 3.5 31.6 + - + +
77A SER 4.2 5.1 + - - +
78A ARG* 1.3 80.2 - - - +
80A LEU* 1.3 73.0 + - - +
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Residues in contact with LEU 80 (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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1A PHE* 3.5 56.1 - - + +
2A LYS* 4.3 0.9 - - - -
3A ILE* 3.8 30.9 - - + +
72A THR* 3.3 5.4 - - - +
73A ALA 2.7 31.3 + - - -
78A ARG* 6.3 0.4 - - + -
79A LYS* 1.3 81.3 - - - +
81A GLU* 1.3 61.8 + - - +
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Residues in contact with GLU 81 (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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3A ILE* 3.9 7.7 - - - +
36A ARG* 3.6 29.4 + - - -
70A LEU* 4.7 11.9 - - + -
71A CYS 3.1 13.5 - - - +
72A THR* 3.9 11.9 + - + +
80A LEU* 1.3 77.6 - - - +
82A LYS* 1.3 62.0 + - - +
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Residues in contact with LYS 82 (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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3A ILE* 3.7 33.1 - - + +
4A GLU* 4.9 0.7 - - - +
5A THR* 3.6 33.7 + - + +
8A GLU* 2.8 46.2 + - - -
9A SER* 5.2 1.4 - - - -
35A TRP* 5.5 0.2 - - - -
69A TYR 4.2 0.3 - - - +
70A LEU* 4.4 4.0 - - - -
71A CYS* 2.9 33.3 + - - +
81A GLU* 1.3 75.4 - - - +
83A GLY* 1.3 65.0 + - - +
84A ILE* 5.2 0.5 - - - +
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Residues in contact with GLY 83 (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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8A GLU 4.4 3.3 - - - +
9A SER* 4.3 14.4 - - - +
68A SER* 5.2 4.9 - - - -
69A TYR 3.2 9.9 - - - -
70A LEU* 4.1 14.9 - - - +
82A LYS* 1.3 81.2 + - - +
84A ILE* 1.3 66.3 + - - +
85A GLN 4.2 0.2 - - - -
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Residues in contact with ILE 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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5A THR* 3.7 35.9 - - + +
6A THR 4.2 7.4 - - - +
7A PRO* 3.9 30.5 - - + +
8A GLU 5.1 0.7 - - - +
9A SER 3.9 2.9 - - - -
10A ARG 4.2 6.1 - - - +
11A TYR 4.6 1.1 - - - +
21A LEU* 3.8 40.2 - - + -
22A THR 4.4 0.7 - - - +
35A TRP* 4.4 11.4 - - + -
68A SER* 4.4 2.2 + - - -
69A TYR* 2.7 44.4 + - + +
82A LYS 5.2 0.4 - - - +
83A GLY* 1.3 76.9 - - - +
85A GLN* 1.3 71.9 + - - +
86A VAL* 3.6 3.5 + - + -
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Residues in contact with GLN 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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9A SER 3.1 15.9 + - - +
10A ARG* 3.2 10.9 - - + +
11A TYR 3.0 24.8 + - - +
67A HIS 3.9 2.7 - - - +
68A SER* 4.2 19.3 - - - +
83A GLY 4.2 0.4 - - - -
84A ILE* 1.3 72.5 - - - +
86A VAL* 1.3 64.3 + - - +
87A GLU* 3.5 29.3 - - - +
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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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11A TYR* 3.7 9.6 - - + +
13A ALA* 4.0 24.9 - - + -
21A LEU* 4.0 28.3 - - + -
58A MET* 4.4 11.7 - - + -
65A ASN* 3.5 22.0 - - + +
66A GLU* 3.8 9.8 - - - +
67A HIS 2.9 27.8 + - - +
69A TYR* 3.8 21.3 - - + -
84A ILE* 4.5 3.1 - - + +
85A GLN* 1.3 76.3 - - - +
87A GLU* 1.3 63.1 + - - +
88A ILE* 4.4 6.1 - - + -
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Residues in contact with GLU 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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10A ARG* 2.8 40.0 + - + +
11A TYR 2.9 11.1 + - - +
12A LEU* 3.4 16.5 - - + +
13A ALA* 2.7 33.3 + - - +
66A GLU* 4.8 5.4 - - - +
85A GLN* 3.5 25.2 - - - +
86A VAL* 1.3 76.1 - - - +
88A ILE* 1.3 59.5 + - - +
177A ILE* 6.2 0.5 - - - +
178A ASP* 5.4 7.4 + - - +
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Residues in contact with ILE 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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12A LEU* 4.8 2.4 - - - +
13A ALA 3.3 9.2 - - - +
15A ILE* 4.3 8.1 - - + -
61A VAL* 4.0 20.2 - - + -
62A SER 4.1 5.4 - - - +
63A PHE* 3.4 50.3 - - + -
65A ASN 4.4 0.7 - - - -
66A GLU* 3.8 47.8 + - + +
86A VAL* 4.2 9.4 + - + -
87A GLU* 1.3 81.2 - - - +
89A TYR* 1.3 65.2 + - - +
119A TYR* 4.1 14.6 - - + -
120A PRO* 4.6 3.5 - - - +
177A ILE* 5.5 1.4 - - - +
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Residues in contact with TYR 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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12A LEU* 3.4 29.7 + - + -
13A ALA 3.2 23.7 + - - -
14A GLN* 3.4 36.9 + - + +
15A ILE* 2.9 31.2 + - - +
88A ILE* 1.3 75.9 - - - +
90A SER* 1.3 69.2 + - - +
91A PHE* 4.0 15.3 - + + -
119A TYR* 3.2 18.6 - - - +
120A PRO* 4.2 5.6 - - + -
175A LEU* 4.1 7.9 - - + -
177A ILE* 3.9 16.6 - - + -
183A VAL* 3.0 38.5 - - + +
184A PRO* 5.5 0.6 - - - +
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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