Contacts of the strand formed by residues 140 - 148 (chain B) in PDB entry 2OPL
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 GLU 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A VAL* 4.3 1.8 - - - -
178A PRO* 3.4 26.5 - - + +
180A ALA* 5.2 8.0 - - - +
120B GLY* 3.2 19.9 - - - -
121B ASP* 3.3 7.8 + - - +
138B TYR* 3.4 2.2 - - - -
139B ARG* 1.3 102.9 + - - +
141B ILE* 1.3 76.0 + - - +
142B ARG* 2.9 43.5 + - - +
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A THR* 4.9 1.1 - - + -
177A VAL* 4.7 0.9 - - + -
178A PRO 3.0 7.0 + - - +
179A VAL* 3.2 12.3 - - + -
180A ALA 2.9 24.4 + - - +
88B LEU* 4.9 5.6 - - + -
89B LEU* 4.0 20.9 - - + -
92B LEU* 3.8 27.6 - - + -
118B TYR* 5.0 0.7 - - + -
119B GLU 3.4 10.5 - - - +
120B GLY* 4.2 2.7 - - - -
138B TYR* 3.8 36.8 - - + -
140B GLU* 1.3 79.5 - - - +
142B ARG* 1.3 66.9 + - - +
143B VAL* 4.2 9.2 - - + -
173B VAL* 4.1 26.0 - - + -
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Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 5.2 1.2 - - - +
180A ALA* 3.4 14.4 - - + +
182A LEU* 5.8 1.8 - - + -
117B ARG 3.9 0.5 - - - +
118B TYR* 3.4 3.6 - - - -
119B GLU* 2.8 78.6 + - + +
121B ASP* 2.9 37.8 + - - +
139B ARG* 3.5 8.2 - - - +
140B GLU* 2.9 44.0 + - - +
141B ILE* 1.3 75.6 - - - +
143B VAL* 1.3 61.9 + - - +
144B PHE* 4.7 16.9 - - + -
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL* 4.2 19.5 - - + -
180A ALA 2.7 15.8 + - - +
181A VAL* 3.4 11.1 - - + -
182A LEU* 2.8 30.3 + - - +
92B LEU* 4.2 2.9 - - + -
96B LEU* 4.3 2.7 - - + -
117B ARG 3.3 4.5 - - - +
118B TYR* 3.3 47.6 - - + -
141B ILE* 4.2 5.8 - - + -
142B ARG* 1.3 79.6 - - - +
144B PHE* 1.3 68.7 + - - +
145B PHE* 3.7 25.6 - - + -
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Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LEU* 3.3 49.4 - - + -
183A LEU 4.2 10.8 - - - -
184A ASP* 4.3 7.6 - - + -
116B SER* 3.2 4.4 - - - -
117B ARG* 2.9 79.4 + - + +
142B ARG* 4.7 16.6 - - + -
143B VAL* 1.3 79.9 - - - +
145B PHE* 1.3 62.5 + - - +
146B SER* 5.2 0.5 + - - -
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Residues in contact with PHE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A VAL* 3.8 23.8 - - + -
182A LEU 2.9 6.9 + - - -
183A LEU* 3.5 8.0 - - - +
184A ASP 2.8 28.6 + - - -
96B LEU* 3.9 23.3 - - + -
97B THR* 3.7 20.0 - - - -
100B LEU* 3.9 19.7 - - + -
114B VAL* 3.7 23.6 - - + -
115B LYS 3.5 11.9 - - - -
116B SER* 3.7 10.5 - - - -
118B TYR* 3.6 15.3 - - - -
143B VAL* 3.7 21.1 - - + -
144B PHE* 1.3 73.2 - - - +
146B SER* 1.3 58.9 + - - +
147B ILE* 4.1 4.7 - - + -
160B ILE* 3.9 21.3 - - + -
163B ALA* 5.8 1.1 - - + -
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ASP* 3.5 33.7 + - - +
113B GLY 4.2 0.5 - - - +
114B VAL* 3.5 3.5 - - - +
115B LYS* 2.9 60.5 + - - +
116B SER* 6.0 0.2 - - - -
117B ARG* 4.8 3.5 + - - -
144B PHE 4.2 0.5 + - - -
145B PHE* 1.3 71.7 - - - +
147B ILE* 1.3 62.4 + - - +
148B ASP 4.3 0.2 + - - -
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LEU* 4.7 5.1 - - + +
184A ASP 5.3 0.4 + - - -
100B LEU* 4.0 29.6 - - + -
111B LEU* 3.9 16.2 - - + -
113B GLY 3.6 7.6 - - - +
114B VAL* 4.6 10.8 - - + -
145B PHE* 4.3 8.7 + - + -
146B SER* 1.3 78.8 - - - +
148B ASP* 1.3 59.3 + - - +
149B ALA* 3.9 20.9 - - + -
156B LYS* 2.8 64.9 + - + +
159B LEU* 4.6 4.9 - - + -
160B ILE* 4.1 19.5 - - + -
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Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LEU* 4.1 0.3 - - - -
112B ARG* 2.8 67.3 + - - +
113B GLY* 2.9 25.0 + - - +
146B SER 4.2 0.8 - - - -
147B ILE* 1.3 68.0 - - - +
149B ALA* 1.3 60.7 + - - +
156B LYS* 5.0 0.4 - - - +
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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