Contacts of the strand formed by residues 130 - 140 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110O LEU* 4.4 19.1 - - + -
111O VAL 3.7 4.7 - - - +
112O LEU* 4.7 3.8 - - + +
113O ASN* 3.2 9.1 + - - +
126O LEU* 3.5 19.3 - - + +
127O TYR* 3.3 20.2 + - + +
128O ASN 4.8 1.0 - - - +
129O ALA* 1.3 75.1 - - - +
131O GLU* 1.3 61.7 + - - +
132O TRP 3.6 24.5 - - - +
133O VAL* 4.2 5.6 - - + -
173O PRO* 3.5 33.7 - - + +
178O LEU* 5.1 2.9 - - + -
205O LEU* 3.5 39.5 - - + -
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Residues in contact with GLU 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128L ASN* 3.0 31.5 + - - +
111O VAL* 2.7 28.7 + - - +
112O LEU 3.9 11.6 - - - +
113O ASN* 3.2 23.8 + - - +
129O ALA 3.6 0.8 + - - -
130O ILE* 1.3 75.0 - - - +
132O TRP* 1.3 71.5 + - + +
172O ARG* 3.3 39.0 + - - +
173O PRO* 3.8 6.3 - - - +
225O GLY* 5.3 2.4 - - - -
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Residues in contact with TRP 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124L ASP 5.6 2.2 - - - -
127L TYR* 4.8 16.8 - + + -
128L ASN* 3.0 37.9 - - + +
173L PRO* 5.1 7.9 - - + -
174L ALA* 3.8 33.4 - - + -
110O LEU* 3.5 4.2 - - - -
111O VAL* 3.0 45.5 + - + -
130O ILE* 3.6 5.7 - - - +
131O GLU* 1.3 99.0 - - + +
133O VAL* 1.3 63.5 + - - +
134O LEU* 4.2 12.6 - - + -
170O ALA* 3.6 29.6 - - + -
171O GLN 3.4 23.1 - - - -
172O ARG* 3.3 39.0 - - - -
173O PRO* 5.0 0.2 - - - -
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Residues in contact with VAL 133 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108O ILE* 4.2 10.5 - - + -
109O ALA 3.4 3.1 - - - -
110O LEU* 3.8 14.4 - - + -
130O ILE* 4.2 8.7 - - + -
132O TRP* 1.3 75.5 - - - +
134O LEU* 1.3 65.2 + - - +
171O GLN* 2.8 39.2 + - - +
173O PRO* 4.0 18.4 - - + -
176O LEU* 3.6 33.9 - - + -
178O LEU* 4.0 21.8 - - + -
252O ILE* 4.3 11.7 - - + -
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Residues in contact with LEU 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124L ASP* 5.0 5.8 - - + -
127L TYR* 4.1 16.6 - - + -
108O ILE* 3.8 2.4 - - - +
109O ALA* 2.8 58.4 + - + +
111O VAL* 3.9 26.5 - - + -
132O TRP* 4.2 8.3 - - + -
133O VAL* 1.3 79.0 - - - +
135O PRO* 1.4 74.3 - - + +
166O ILE* 4.0 27.6 - - + -
167O GLY 4.4 2.9 - - - +
169O PRO 4.3 4.0 - - - +
170O ALA* 3.9 24.9 - - + -
227O ILE* 5.0 3.4 - - + -
252O ILE* 4.1 5.2 - - - -
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Residues in contact with PRO 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107O GLU 3.9 4.7 - - - +
108O ILE* 5.0 0.4 - - - -
134O LEU* 1.4 90.9 - - + +
136O ALA* 1.3 60.5 + - - +
166O ILE* 3.8 1.9 - - - +
167O GLY 2.9 26.5 + - - -
168O GLY 3.6 30.1 - - - +
169O PRO 3.8 12.1 - - - +
249O ILE* 3.8 17.0 - - + -
252O ILE* 3.8 17.2 - - + -
253O GLY 3.9 2.5 - - - -
254O SER 3.7 16.8 - - - +
255O VAL* 3.8 13.7 - - + -
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Residues in contact with ALA 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106O ALA* 3.6 4.9 - - - +
107O GLU* 2.8 38.5 + - + +
109O ALA* 4.1 10.8 - - + -
135O PRO* 1.3 77.3 - - - +
137O LEU* 1.3 63.5 + - - +
164O TYR* 5.6 0.4 - - + -
165O VAL 3.2 13.0 - - - +
166O ILE* 4.4 5.4 - - + -
229O LEU* 3.9 27.4 - - + -
249O ILE* 4.7 0.2 - - - +
255O VAL* 3.8 10.8 - - - +
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Residues in contact with LEU 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104O ILE* 4.2 13.7 - - + -
105O GLU 3.4 9.0 - - - +
106O ALA* 4.3 1.3 - - - -
136O ALA* 1.3 79.3 - - - +
138O GLU* 1.3 60.6 + - - +
139O VAL 4.0 0.2 - - - -
164O TYR* 3.3 5.7 - - - +
165O VAL* 2.9 43.1 + - + +
185O MET* 3.9 20.0 - - - -
229O LEU* 5.7 0.2 - - - -
245O PHE* 4.4 11.2 - - + +
246O GLU 5.2 0.2 - - - -
247O ALA* 3.8 28.5 - - + +
255O VAL* 3.8 23.1 - - + +
256O ALA* 4.1 2.2 - - - -
257O ALA* 3.9 35.0 - - + +
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Residues in contact with GLU 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O LYS* 3.1 48.3 + - - +
82O LEU* 5.0 1.5 - - + +
86O MET* 5.6 0.3 - - - +
103O ARG 3.6 0.2 - - - +
104O ILE* 3.2 3.8 - - - -
105O GLU* 2.8 41.3 + - + +
107O GLU* 3.1 34.7 - - + +
136O ALA 4.2 0.2 - - - -
137O LEU* 1.3 73.0 - - - +
139O VAL* 1.3 63.3 + - - +
140O VAL* 3.5 15.7 + - - +
161O CYS* 3.6 17.5 - - - -
162O GLY 4.6 1.0 + - - -
163O VAL 3.8 9.6 - - - +
164O TYR* 4.2 1.6 - - + -
229O LEU* 3.8 17.3 - - + -
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Residues in contact with VAL 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94O ILE* 4.3 7.9 - - + -
99O VAL* 4.1 15.7 - - + -
102O PRO* 4.1 23.6 - - + -
103O ARG 3.2 11.4 - - - +
104O ILE* 3.5 18.6 - - + -
138O GLU* 1.3 70.7 - - - +
140O VAL* 1.3 59.0 + - - +
162O GLY* 3.2 8.5 + - - -
163O VAL* 2.9 52.5 + - + +
165O VAL* 4.7 8.7 - - + -
259O PHE* 3.9 24.9 - - + -
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Residues in contact with VAL 140 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O LYS* 4.1 2.2 - - - +
99O VAL* 3.6 2.3 - - - +
101O GLN 4.0 0.2 - - - +
102O PRO* 3.4 4.7 - - - +
103O ARG* 2.7 55.2 + - + +
105O GLU* 3.7 12.3 - - - +
138O GLU* 3.5 19.4 + - - +
139O VAL* 1.3 74.9 - - - +
141O GLY* 1.3 60.6 + - - +
147O TRP* 3.6 22.0 - - + -
160O SER* 3.2 17.0 - - - +
162O GLY 4.2 0.9 - - - +
236O MET* 3.9 13.0 - - + -
1262O PO4 3.2 26.0 - - - +
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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