Contacts of the strand formed by residues 136 - 142 (chain W) in PDB entry 5GJQ
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 136 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94W HIS* 5.0 5.4 - - + -
97W LEU* 3.5 25.1 - - + -
107W MET* 3.1 22.0 - - + +
109W ILE* 3.7 14.1 - - + -
131W LEU* 3.1 38.5 + - + +
132W LYS* 4.7 0.2 - - - +
134W GLU* 3.9 12.8 - - + -
135W LYS* 1.3 77.1 - - - +
137W ASN* 1.3 69.4 + - - +
138W VAL* 3.7 6.0 - - + +
160W LEU* 4.3 3.5 - - - +
166W THR 3.0 10.0 - - - +
167W GLY* 2.7 24.8 - - - +
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Residues in contact with ASN 137 (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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4W GLU* 3.5 22.0 - - - +
106W LYS* 4.8 0.6 - - + +
107W MET 2.2 28.9 + - - +
108W ARG* 2.9 18.4 - - + +
109W ILE 2.6 32.5 + - - -
136W VAL* 1.3 69.0 - - - +
138W VAL* 1.3 54.1 + - - +
139W ASP 4.2 0.2 - - - -
165W GLY* 3.1 26.7 - - - +
166W THR* 3.8 1.9 + - - -
167W GLY 3.1 4.9 - - - -
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Residues in contact with VAL 138 (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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90W ILE* 6.1 0.4 - - + -
109W ILE* 3.6 15.5 - - + +
131W LEU* 3.6 29.2 - - + -
136W VAL* 3.7 16.6 - - + +
137W ASN* 1.3 77.6 - - - +
139W ASP* 1.3 74.9 + - - +
140W ILE* 4.2 13.9 - - + -
156W PHE* 3.5 28.0 - - + -
157W VAL* 5.4 0.4 - - + -
160W LEU* 4.5 0.2 - - + -
165W GLY* 6.0 0.2 - - - -
167W GLY 2.4 24.3 + - - +
168W SER* 2.9 13.7 - - - +
169W HIS 2.8 20.5 + - - +
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Residues in contact with ASP 139 (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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108W ARG* 3.3 24.6 + - - +
109W ILE 2.9 20.6 + - - +
110W ILE* 3.2 5.1 - - + -
111W ALA* 3.2 13.9 + - - +
137W ASN 4.2 0.2 - - - -
138W VAL* 1.3 93.8 + - - +
140W ILE* 1.3 64.6 + - - +
165W GLY* 5.7 2.6 - - - -
168W SER* 4.3 0.2 - - - -
169W HIS* 2.7 27.7 + - - +
187W PRO 2.2 31.3 - - - +
188W ILE* 3.6 23.8 - - + +
192W GLU 5.1 2.6 - - - +
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Residues in contact with ILE 140 (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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111W ALA* 3.3 22.2 - - + +
113W VAL* 3.8 24.0 - - + -
138W VAL* 4.2 10.3 - - + -
139W ASP* 1.3 80.2 - - - +
141W ILE* 1.3 65.3 + - - +
142W ASN* 4.2 6.7 - - + +
153W LEU* 3.8 22.2 - - + +
156W PHE* 3.8 30.7 - - + -
157W VAL* 4.0 13.2 - - + -
169W HIS 3.9 4.0 + - - -
170W LEU* 3.7 14.1 - - + +
171W VAL 2.6 25.5 + - - +
188W ILE* 3.1 12.6 - - - +
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Residues in contact with ILE 141 (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 ARG* 5.0 6.3 - - - +
32W ALA* 5.8 3.1 - - + -
36W VAL* 5.5 7.9 - - + -
110W ILE* 3.8 25.4 - - + -
111W ALA 2.3 27.9 + - - +
112W PHE* 3.1 50.6 - - + +
113W VAL* 2.3 37.6 + - - +
140W ILE* 1.3 66.0 - - - +
142W ASN* 1.3 53.4 + - - +
171W VAL 4.1 0.9 - - - -
173W VAL* 3.4 21.8 - - + -
179W LEU* 5.2 9.2 - - + -
188W ILE* 3.6 23.6 - - + -
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Residues in contact with ASN 142 (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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113W VAL* 3.0 28.2 - - + +
140W ILE* 4.2 5.4 - - + -
141W ILE* 1.3 74.8 - - - +
143W PHE* 1.3 55.4 + - - +
144W GLY 2.9 16.5 + - - -
148W VAL* 2.1 46.2 + - - +
153W LEU* 3.3 13.0 - - + +
170W LEU* 5.5 0.7 - - + -
171W VAL 3.6 5.0 + - - +
172W THR* 2.8 28.9 + - + +
173W VAL* 2.1 38.0 + - - +
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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