Contacts of the strand formed by residues 89 - 95 (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 VAL 89 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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642A LYS* 3.3 48.5 - - + +
643A VAL* 5.2 3.8 - - + -
85W ARG* 3.3 4.7 - - - +
86W THR* 3.0 34.6 + - - +
88W ASP* 1.3 82.8 - - - +
90W GLU* 1.3 63.5 + - - +
91W VAL* 3.9 14.5 + - + -
142W ILE* 3.7 25.6 - - + +
146W THR* 4.3 13.9 - - + -
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Residues in contact with GLU 90 (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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31W GLU* 3.5 21.7 - - - +
58W ARG* 2.9 45.9 + - - -
59W ILE 5.2 0.5 - - - +
60W ILE* 3.2 24.1 - - + +
61W PRO* 3.5 19.3 - - - +
83W VAL* 4.1 4.7 - - + +
84W ALA 3.6 12.8 - - - +
85W ARG* 3.7 27.4 + - + +
88W ASP 3.6 1.9 + - - +
89W VAL* 1.3 76.3 - - - +
91W VAL* 1.3 70.8 + - - +
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Residues in contact with VAL 91 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A VAL* 4.2 17.7 - - + -
60W ILE* 4.1 5.2 - - - -
61W PRO* 3.8 9.2 - - + +
63W VAL* 3.9 24.9 - - + -
82W ILE 3.6 1.0 - - - +
83W VAL* 3.4 1.8 - - - -
84W ALA* 2.9 34.4 + - - +
89W VAL* 3.9 18.4 - - + -
90W GLU* 1.3 81.2 - - - +
92W GLY* 1.3 63.3 + - - +
93W PHE* 3.8 30.9 + - + -
142W ILE* 4.2 15.0 - - + -
145W ILE* 4.7 5.8 - - + -
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Residues in contact with GLY 92 (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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60W ILE* 3.7 7.8 - - - +
61W PRO 2.7 16.6 + - - -
62W VAL* 3.1 6.6 - - - +
63W VAL* 2.7 34.0 + - - +
81W ILE* 3.7 17.9 - - - -
82W ILE 3.4 6.3 - - - -
83W VAL* 4.1 4.3 - - - -
91W VAL* 1.3 72.6 - - - +
93W PHE* 1.3 60.8 + - - -
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Residues in contact with PHE 93 (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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25W PHE* 4.4 9.6 - + + -
63W VAL* 3.6 23.3 - - + -
65W LEU* 3.7 33.9 - - + -
68W ILE* 4.4 2.0 - - + -
81W ILE* 3.3 2.9 - - - -
82W ILE* 2.7 51.6 + - + +
84W ALA* 4.5 4.9 - - + -
91W VAL* 3.8 27.4 - - + -
92W GLY* 1.3 71.8 - - - -
94W LEU* 1.3 64.4 + - - +
95W VAL* 3.5 3.9 + - + +
138W ILE* 3.7 28.0 - - + -
141W ILE* 3.7 32.1 - - + -
142W ILE* 4.2 16.2 - - + -
145W ILE* 4.8 2.5 - - + -
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Residues in contact with LEU 94 (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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18W ILE* 5.4 0.5 - - - +
36W LYS* 3.7 31.2 - - + +
39W ILE* 4.4 2.7 - - + -
50W GLU* 3.9 28.7 - - + +
62W VAL* 4.3 11.0 - - + -
63W VAL 2.9 19.7 + - - +
64W ASN* 4.3 4.9 - - - -
65W LEU* 3.7 16.7 + - - +
66W ALA 4.9 0.2 + - - -
78W MET* 3.7 45.8 - - + +
80W SER 3.4 13.2 - - - +
81W ILE* 3.8 16.4 - - + +
92W GLY 3.8 1.0 + - - -
93W PHE* 1.3 71.6 - - - +
95W VAL* 1.3 63.1 + - - +
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Residues in contact with VAL 95 (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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16W PHE* 3.6 42.8 - - + -
17W GLU 4.2 2.5 - - - +
18W ILE* 4.6 5.6 - - + -
65W LEU* 4.1 12.8 - - + -
78W MET* 3.6 9.2 - - - -
79W LYS 3.1 6.6 + - - -
80W SER* 2.9 49.1 + - - +
82W ILE* 3.8 27.1 - - + -
93W PHE* 3.5 4.9 + - + +
94W LEU* 1.3 79.9 - - - +
96W ASP* 1.3 62.7 + - - +
97W ARG 4.2 5.6 - - - +
98W VAL* 4.9 0.7 - - - +
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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