Contacts of the strand formed by residues 78 - 83 (chain N) in PDB entry 5VAI
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 THR 78 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N SER* 2.5 30.2 + - - -
22N CYS 3.0 10.6 + - - -
23N ALA* 4.8 3.1 - - - -
29N PHE* 3.8 5.6 - - - -
72N ARG* 3.8 1.6 - - - -
73N ASP* 2.9 38.9 + - + +
76N LYS* 3.7 22.2 - - + -
77N ASN* 1.3 78.5 - - - +
79N LEU* 1.3 62.5 + - - +
80N TYR* 3.0 29.6 - - + +
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Residues in contact with LEU 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N SER* 2.8 28.1 - - - -
22N CYS* 2.8 21.0 + - + +
29N PHE* 4.3 6.7 - - + -
34N MET* 3.5 41.3 - - + -
35N ASN* 4.2 9.0 - - - +
36N TRP* 3.1 46.4 - - + +
51N ILE* 4.3 1.3 - - + -
70N ILE* 4.2 10.8 - - + -
71N SER 3.8 9.6 - - - +
72N ARG* 3.9 18.2 - - + -
78N THR* 1.3 73.2 + - - +
80N TYR* 1.3 69.7 + - - +
96N CYS* 4.3 4.9 - - + -
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Residues in contact with TYR 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N ARG* 3.1 55.9 - - + +
20N LEU 2.4 22.7 - - - +
21N SER* 4.0 16.4 + - - -
36N TRP* 3.1 13.6 + - - -
69N THR 4.1 0.2 - - - -
70N ILE* 3.3 1.6 - - - -
71N SER* 2.9 59.0 + - - +
72N ARG 4.6 0.2 - - - -
73N ASP* 3.5 18.7 + - + -
76N LYS* 4.2 12.1 + - - +
78N THR* 3.0 39.4 + - + +
79N LEU* 1.3 75.8 - - - +
81N LEU* 1.3 61.1 + - - +
82N GLN* 5.2 0.7 - - + +
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Residues in contact with LEU 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18N LEU 2.7 16.6 - - - +
19N ARG* 4.3 0.2 - - - -
20N LEU* 2.9 53.9 + - + +
36N TRP* 3.7 28.9 - - + -
48N VAL* 5.5 8.1 - - + -
49N SER* 5.7 3.1 - - - -
60N TYR* 5.4 1.8 - - + -
68N PHE* 4.3 20.4 - - + -
69N THR 3.2 29.8 - - - +
70N ILE* 4.0 8.3 - - + +
80N TYR* 1.3 73.0 - - - +
82N GLN* 1.3 55.1 + - - +
83N MET* 3.7 15.3 + - + +
94N TYR* 4.7 15.3 - - + -
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Residues in contact with GLN 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N SER* 3.4 17.4 + - - -
18N LEU* 2.4 53.0 - - - +
19N ARG* 3.0 36.8 + - + +
67N ARG 4.8 0.2 - - - +
68N PHE* 3.8 4.0 - - - -
69N THR* 2.8 55.6 + - + +
71N SER* 5.8 1.1 - - - +
80N TYR* 4.1 1.0 - - - +
81N LEU* 1.3 64.3 - - - +
83N MET* 1.3 58.9 + - - +
84N ASN* 3.8 9.0 + - - +
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Residues in contact with MET 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N VAL* 4.9 4.7 - - + -
16N GLY 3.0 0.2 - - - +
17N SER* 2.5 39.8 - - - -
18N LEU* 2.8 44.2 + - + +
20N LEU* 4.8 7.0 - - + -
68N PHE* 4.9 15.7 - - + -
81N LEU* 4.3 21.8 - - + +
82N GLN* 1.3 75.0 - - - +
84N ASN* 1.3 57.6 - - - +
86N LEU* 3.4 35.2 - - + -
94N TYR* 4.5 12.3 - - - -
124N VAL* 3.9 29.6 - - + -
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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