Contacts of the strand formed by residues 80 - 86 (chain W) in PDB entry 4JPB
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 SER 80 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33W VAL* 4.5 13.2 - - - -
34W ILE 3.7 7.9 - - - -
35W GLU* 4.7 0.6 - - - +
79W LYS* 1.3 84.0 + - - +
81W ILE* 1.3 66.3 + - - +
82W ILE 4.2 0.2 - - - -
94W LEU* 3.4 7.8 - - - +
95W VAL* 2.9 45.0 + - - +
96W ASP 3.4 11.1 + - - -
97W ARG* 3.8 8.3 - - - -
98W VAL* 4.0 9.3 + - - +
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Residues in contact with ILE 81 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32W MET 3.8 0.3 - - - +
33W VAL* 3.4 4.8 - - - -
34W ILE* 2.9 54.6 + - + +
35W GLU 4.9 0.2 - - - +
36W LYS* 4.2 18.4 - - - -
37W SER 5.2 0.9 - - - +
39W ILE* 4.6 6.7 - - + -
53W ILE* 4.5 7.0 - - + -
62W VAL* 3.9 28.3 - - + -
80W SER* 1.3 79.8 - - - +
82W ILE* 1.3 63.8 + - - +
83W VAL* 3.5 13.8 + - + +
92W GLY* 3.7 31.0 - - - -
93W PHE 3.3 2.5 - - - +
94W LEU* 3.8 17.0 - - + -
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Residues in contact with ILE 82 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14W LEU* 4.5 8.1 - - + -
16W PHE* 3.5 42.6 - - + -
25W PHE* 3.7 15.5 - - + -
30W ILE* 3.5 38.4 - - + -
32W MET 4.1 2.5 - - - -
33W VAL* 4.2 18.6 - - + -
80W SER 4.2 0.4 - - - -
81W ILE* 1.3 72.2 - - - +
83W VAL* 1.3 62.0 + - - +
84W ALA* 3.7 1.8 + - + +
91W VAL 3.6 1.2 - - - +
92W GLY* 3.4 0.3 - - - -
93W PHE* 2.7 42.9 + - + +
95W VAL* 3.8 25.1 - - + -
98W VAL* 5.7 2.2 - - + -
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Residues in contact with VAL 83 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W ILE* 3.7 2.8 - - - +
31W GLU* 2.8 31.7 + - + +
32W MET* 3.0 27.0 + - + +
34W ILE* 4.6 17.5 - - + -
53W ILE* 5.2 1.6 - - + -
55W LEU* 4.9 8.7 - - + -
58W ARG* 5.0 0.2 - - - +
60W ILE* 3.9 30.1 - - + -
81W ILE* 3.9 19.5 - - + +
82W ILE* 1.3 73.4 - - - +
84W ALA* 1.3 60.2 + - - +
90W GLU* 4.1 15.7 - - + +
91W VAL 3.4 9.4 - - - +
92W GLY* 4.5 2.9 - - - -
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Residues in contact with ALA 84 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29W ASN* 3.2 19.1 - - + +
30W ILE* 4.3 11.0 - - + -
31W GLU* 4.8 1.8 - - - -
82W ILE* 3.7 2.6 + - + -
83W VAL* 1.3 75.2 - - - +
85W ARG* 1.3 62.1 + - - +
90W GLU* 3.6 3.5 - - - +
91W VAL* 2.9 33.3 + - - +
93W PHE* 4.5 7.4 - - + -
138W ILE* 4.2 29.8 - - + -
142W ILE* 4.8 2.7 - - + -
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Residues in contact with ARG 85 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29W ASN* 2.9 33.2 + - - +
31W GLU* 3.3 37.8 + - - +
58W ARG* 5.1 4.6 - - - +
84W ALA* 1.3 76.7 - - - +
86W THR* 1.3 63.8 + - - +
87W LYS 4.0 15.8 + - - +
88W ASP* 3.8 18.8 + - - +
89W VAL 3.3 13.0 - - - +
90W GLU* 3.7 29.2 + - + +
142W ILE* 4.6 1.3 - - - -
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Residues in contact with THR 86 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29W ASN* 3.6 8.1 - - - +
85W ARG* 1.3 78.4 - - - +
87W LYS* 1.3 77.6 + - - +
88W ASP* 4.1 0.2 - - - +
89W VAL* 3.0 22.6 + - - +
138W ILE* 4.4 2.9 - - + +
139W ASP* 3.3 38.0 + - - +
142W ILE* 3.7 38.9 - - + +
143W GLU* 5.5 2.6 + - - +
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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