Contacts of the strand formed by residues 130 - 140 (chain J) in PDB entry 2WQT
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 ILE 130 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110J LEU* 4.4 19.7 - - + -
111J VAL 3.7 4.7 - - - +
112J LEU* 4.7 3.4 - - + +
113J ASN* 3.6 9.6 + - - +
126J LEU* 3.5 18.2 - - + +
127J TYR* 3.3 20.2 + - + +
128J ASN 3.5 1.1 - - - +
129J ALA* 1.3 79.1 - - - +
131J GLU* 1.3 59.9 + - - +
132J TRP 3.6 24.9 - - - +
133J VAL* 4.2 5.4 - - + -
173J PRO* 3.5 36.4 - - + +
178J LEU* 5.1 2.7 - - + -
205J LEU* 3.6 39.0 - - + -
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Residues in contact with GLU 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G ASN* 3.0 33.3 + - - +
111J VAL* 2.7 28.5 + - - +
112J LEU 3.9 11.5 - - - +
113J ASN* 3.9 23.2 - - - +
129J ALA 3.6 1.8 + - - -
130J ILE* 1.3 73.9 - - - +
132J TRP* 1.3 71.2 - - + +
172J ARG* 3.2 38.7 + - - +
173J PRO* 3.8 6.7 - - - +
225J GLY* 5.3 2.6 - - - -
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Residues in contact with TRP 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G ASP 5.6 2.2 - - - -
127G TYR* 4.7 17.9 - + + -
128G ASN* 3.0 36.8 - - + +
173G PRO* 5.1 8.5 - - + -
174G ALA* 3.7 34.8 - - + -
109J ALA 3.9 0.2 - - - +
110J LEU* 3.5 4.2 - - - -
111J VAL* 3.0 43.4 + - + -
130J ILE* 3.6 5.7 - - - +
131J GLU* 1.3 100.9 - - + +
133J VAL* 1.3 64.0 + - - +
134J LEU* 4.2 15.8 - - + +
170J ALA* 3.6 29.8 - - + -
171J GLN 3.4 21.1 - - - -
172J ARG* 3.3 39.5 - - - -
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Residues in contact with VAL 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J ILE* 4.1 11.0 - - + -
109J ALA 3.4 3.1 - - - -
110J LEU* 3.8 15.0 - - + -
130J ILE* 4.2 9.2 - - + -
132J TRP* 1.3 75.1 - - - +
134J LEU* 1.3 62.8 + - - +
171J GLN* 2.8 39.1 + - - +
173J PRO* 4.0 18.4 - - + -
176J LEU* 3.6 33.4 - - + -
178J LEU* 4.0 22.4 - - + -
252J ILE* 4.4 11.6 - - + +
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Residues in contact with LEU 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G ASP* 5.0 5.6 - - + -
127G TYR* 4.0 18.2 - - + -
108J ILE* 3.8 2.3 - - - +
109J ALA* 2.8 58.0 + - + +
111J VAL* 3.9 26.2 - - + -
132J TRP* 4.2 8.7 - - + -
133J VAL* 1.3 78.5 - - - +
135J PRO* 1.4 75.0 - - + +
166J ILE* 4.0 26.9 - - + -
167J GLY 4.4 2.0 - - - +
169J PRO 4.3 4.3 - - - +
170J ALA* 3.8 24.7 - - + -
227J ILE* 5.0 3.1 - - + -
252J ILE* 4.2 5.4 - - - -
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Residues in contact with PRO 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J GLU 3.9 5.6 - - - +
108J ILE* 5.0 0.2 - - - -
134J LEU* 1.4 91.7 - - + +
136J ALA* 1.3 60.4 + - - +
166J ILE* 3.8 1.9 - - - +
167J GLY* 2.9 27.5 + - - -
168J GLY 3.6 24.0 - - - +
169J PRO 3.9 13.0 - - - +
249J ILE* 3.7 21.5 - - + -
252J ILE* 3.8 16.3 - - + -
253J GLY* 3.9 2.9 - - - -
254J SER 3.6 24.5 - - - +
255J VAL* 3.8 10.8 - - + -
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Residues in contact with ALA 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J ALA* 3.6 4.5 - - - +
107J GLU* 2.8 36.4 + - + +
109J ALA* 4.1 11.4 - - + -
135J PRO* 1.3 77.0 - - - +
137J LEU* 1.3 62.9 + - - +
164J TYR* 5.6 0.7 - - + -
165J VAL 3.2 13.0 - - - +
166J ILE* 4.4 4.9 - - + -
229J LEU* 3.9 27.8 - - + -
249J ILE* 4.4 0.7 - - - +
255J VAL* 3.7 12.1 - - - +
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Residues in contact with LEU 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104J ILE* 4.2 14.1 - - + -
105J GLU 3.4 9.2 - - - +
106J ALA* 4.3 1.3 - - - -
107J GLU* 5.3 0.2 - - - -
136J ALA* 1.3 77.3 - - - +
138J GLU* 1.3 58.9 + - - +
139J VAL 4.1 0.4 - - - -
164J TYR* 3.3 6.3 - - - +
165J VAL* 2.9 43.8 + - + +
185J MET* 3.9 20.6 - - - -
245J PHE* 4.4 11.7 - - + +
246J GLU 5.2 0.2 - - - -
247J ALA* 3.8 28.3 - - + +
255J VAL* 3.8 23.1 - - + +
256J ALA* 4.1 1.8 - - - -
257J ALA* 3.9 35.9 - - + +
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Residues in contact with GLU 138 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60J LYS* 3.1 49.6 + - - +
82J LEU* 5.0 1.4 - - + +
86J MET* 5.7 0.3 - - - +
103J ARG 3.6 0.2 - - - +
104J ILE* 3.2 3.4 - - - -
105J GLU* 2.8 41.5 + - + +
107J GLU* 3.1 34.6 - - + +
137J LEU* 1.3 74.3 - - - +
139J VAL* 1.3 63.2 + - - +
140J VAL* 3.5 15.7 + - - +
161J CYS* 3.7 15.2 - - - -
162J GLY 4.7 1.4 + - - -
163J VAL 3.8 10.0 - - - +
164J TYR* 4.2 1.6 - - + -
229J LEU* 3.8 17.9 - - + -
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Residues in contact with VAL 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94J ILE* 4.3 7.9 - - + -
99J VAL* 4.1 13.7 - - + -
102J PRO* 4.0 23.8 - - + -
103J ARG 3.2 11.4 - - - +
104J ILE* 3.5 18.8 - - + -
138J GLU* 1.3 70.2 - - - +
140J VAL* 1.3 60.3 + - - +
162J GLY* 3.2 8.3 + - - -
163J VAL* 2.9 53.0 + - + +
165J VAL* 4.7 8.1 - - + -
239J VAL* 4.9 0.2 - - + -
259J PHE* 3.9 26.5 - - + -
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Residues in contact with VAL 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J LYS* 4.1 2.9 - - - +
99J VAL* 3.7 2.7 - - - +
101J GLN 4.0 0.2 - - - +
102J PRO* 3.3 5.2 - - - +
103J ARG* 2.7 54.9 + - + +
105J GLU* 3.8 17.9 - - - +
138J GLU* 3.5 20.8 + - + +
139J VAL* 1.3 75.8 - - - +
141J GLY* 1.3 58.0 + - - +
147J TRP* 3.6 23.3 - - + -
160J SER 3.2 15.9 - - - +
162J GLY 4.2 0.7 - - - +
236J MET* 3.9 12.3 - - + -
1263J PO4 3.5 20.4 - - - +
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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