Contacts of the strand formed by residues 75 - 80 (chain A) in PDB entry 1VJ3
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 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.8 6.1 - - - -
37A LYS* 3.9 13.7 - - - +
40A THR* 2.6 63.6 + - - +
41A SER* 4.1 7.8 + - - +
52A MET* 4.3 4.4 - - - -
53A ASN* 3.5 12.8 - - + +
55A VAL* 4.0 15.7 - - + -
71A PRO* 5.7 0.7 - - - +
72A LEU* 3.2 22.7 - - - +
73A LYS* 2.9 41.1 + - - +
74A GLY* 1.3 88.2 - - - +
76A ILE* 1.3 64.9 + - - +
77A ASN* 3.1 21.8 + - - +
92A ILE* 5.7 1.6 - - - +
300A TAB 3.7 30.5 + - - +
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Residues in contact with ILE 76 (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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52A MET* 3.3 40.4 - - + -
53A ASN 2.7 14.9 + - - +
54A VAL* 3.2 6.5 - - + +
55A VAL 2.7 33.6 + - - +
75A ARG* 1.3 72.7 - - - +
77A ASN* 1.3 56.4 + - - +
78A VAL* 4.1 2.2 - - + -
93A HIS* 3.6 32.3 - - + +
105A LEU* 3.9 18.4 - - + -
109A TYR* 3.9 12.3 - - + +
115A VAL* 3.9 9.4 - - + -
117A ILE* 3.4 32.3 - - + -
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Residues in contact with ASN 77 (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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55A VAL* 3.6 21.7 - - - +
57A MET* 3.7 18.0 - - + +
62A TRP* 3.8 5.7 - - + -
65A ILE* 5.9 0.2 - - - +
70A ARG* 5.1 0.2 - - - +
71A PRO* 3.6 10.8 - - - +
72A LEU* 2.7 50.9 + - - +
75A ARG 3.1 16.0 + - - -
76A ILE* 1.3 70.2 - - - +
78A VAL* 1.3 68.1 + - - +
91A GLY 4.9 0.2 - - - +
92A ILE* 3.9 26.6 - - + +
93A HIS* 3.5 24.2 + - - +
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Residues in contact with VAL 78 (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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54A VAL* 4.5 4.3 - - + -
55A VAL 3.0 12.9 + - - +
56A LEU* 3.6 7.4 - - + -
57A MET* 3.1 27.7 + - - +
76A ILE* 4.1 12.1 - - + +
77A ASN* 1.3 82.2 - - - +
79A VAL* 1.3 62.9 + - - +
80A ILE* 4.1 8.3 - - + -
93A HIS* 3.2 33.4 - - + +
95A ALA* 4.7 5.2 - - + -
101A ALA* 3.9 31.9 - - + +
104A LEU* 5.6 1.8 - - + -
105A LEU* 4.1 15.9 - - + -
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Residues in contact with VAL 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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57A MET* 3.2 7.4 - - + +
59A ARG* 3.4 42.2 - - + +
62A TRP* 3.6 45.1 - - + -
78A VAL* 1.3 75.0 - - - +
80A ILE* 1.3 62.6 + - - +
81A THR* 3.4 5.1 + - + +
87A ASP* 4.3 15.0 - - - +
92A ILE* 4.3 4.3 - - + -
93A HIS 3.0 13.0 + - - +
94A SER* 3.1 10.4 - - - -
95A ALA 3.0 22.9 + - - -
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Residues in contact with ILE 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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56A LEU* 5.1 5.8 - - + -
57A MET 2.8 21.8 + - - +
58A GLY* 3.8 0.8 - - - -
59A ARG 3.4 9.7 + - - -
78A VAL* 4.1 9.0 - - + +
79A VAL* 1.3 72.9 - - - +
81A THR* 1.3 54.2 + - - +
95A ALA* 3.4 6.1 - - + +
97A SER* 3.7 31.9 - - - +
98A LEU* 4.6 1.6 - - - +
101A ALA* 3.4 33.7 - - + -
128A LEU* 3.9 28.5 - - + -
207A NDP 2.8 57.3 - - + +
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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