Contacts of the strand formed by residues 142 - 149 (chain B) in PDB entry 2OR0
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 TRP 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B VAL* 4.5 1.1 - - + -
98B GLU* 4.0 28.8 + - + -
99B ILE* 3.5 30.0 + - + +
106B THR* 3.8 23.3 - - + +
107B TRP 3.4 1.8 + - - -
108B MSE 3.1 20.8 - - + -
109B ALA* 2.7 29.0 + - - -
140B CYS* 3.7 3.1 - - - +
141B GLN* 1.3 88.5 + - + +
143B ALA* 1.3 54.4 + - - +
165B ILE* 3.6 22.2 - - + -
166B LEU 3.2 22.4 - - - -
167B PRO* 3.7 30.7 - - + +
171B TYR* 3.3 11.3 + - - -
202B ARG* 4.0 31.2 - - - -
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Residues in contact with ALA 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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108B MSE 5.0 1.8 - - - -
109B ALA* 3.3 12.8 - - + +
142B TRP* 1.3 75.9 - - - +
144B PHE* 1.3 58.6 + - - +
145B LEU* 3.9 14.4 - - + -
164B VAL 3.6 1.2 - - - +
165B ILE* 3.4 7.1 - - - +
166B LEU* 2.9 32.4 + - + +
171B TYR* 3.5 25.3 + - + +
191B LEU* 3.9 20.2 - - + -
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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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84B HIS* 3.8 24.9 - - + -
87B GLU* 3.6 35.4 - - + -
88B LEU* 4.0 21.8 - - + -
108B MSE 3.9 17.5 - - + +
109B ALA 2.8 12.4 + - - +
110B SER* 3.1 34.9 + - - +
111B PRO 3.3 1.9 - - - +
112B TYR* 3.8 22.0 - + + -
143B ALA* 1.3 72.3 - - - +
145B LEU* 1.3 59.8 + - - +
163B HIS* 4.0 15.7 - - + -
164B VAL 3.3 10.5 - - - -
165B ILE* 3.5 28.7 - - + -
204B LEU* 4.6 6.5 - - + -
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Residues in contact with LEU 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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110B SER 3.8 15.9 - - - +
111B PRO* 3.4 17.9 - - + +
112B TYR* 4.7 2.0 - - - -
127B LEU* 4.4 1.3 - - + -
131B TRP* 3.9 32.5 - - + +
143B ALA* 4.0 11.0 - - + -
144B PHE* 1.3 82.4 - - - +
146B GLY* 1.3 62.7 + - - +
163B HIS* 3.4 4.7 - - - -
164B VAL* 2.7 50.7 + - + +
166B LEU* 3.4 26.0 - - + -
171B TYR* 5.4 1.1 - - + -
191B LEU* 4.0 14.8 - - + -
193B VAL* 4.0 21.1 - - + -
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Residues in contact with GLY 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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111B PRO 3.5 10.9 + - - -
112B TYR* 3.2 26.2 + - - -
113B ALA 3.9 0.8 + - - -
114B PRO* 3.5 10.5 - - - +
115B MSE 3.8 0.2 + - - -
131B TRP* 2.9 25.8 + - - -
145B LEU* 1.3 72.2 - - - +
147B ALA* 1.3 64.2 + - - +
162B LEU 3.4 8.5 - - - -
163B HIS* 4.5 4.0 - - - -
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Residues in contact with ALA 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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114B PRO* 3.8 7.3 - - - +
116B GLY 3.5 12.3 - - - +
118B ALA* 4.3 6.3 - - + -
127B LEU* 3.6 31.2 - - + -
131B TRP* 4.5 0.4 - - + -
145B LEU 4.9 0.2 - - - +
146B GLY* 1.3 76.2 - - - +
148B MSE 1.3 62.3 + - - +
161B SER* 3.3 6.0 + - - -
162B LEU* 2.7 40.9 + - + +
164B VAL* 4.7 10.1 - - + -
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Residues in contact with MSE 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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114B PRO* 3.8 30.9 - - - +
116B GLY 3.1 9.6 + - - +
117B VAL* 3.4 6.9 - - + +
118B ALA* 2.8 25.2 + - - -
147B ALA* 1.3 73.1 - - - +
149B VAL* 1.3 61.4 + - - +
150B GLY 3.6 7.1 + - - +
151B ASP 5.4 0.2 - - - -
152B GLY* 3.6 29.8 - - - +
160B SER* 3.3 29.4 - - - +
161B SER* 3.4 23.3 - - - +
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Residues in contact with VAL 149 (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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118B ALA* 3.2 12.1 - - + +
120B PRO* 3.7 29.2 - - + -
125B TYR* 4.3 11.4 - - + -
148B MSE 1.3 70.1 - - - +
150B GLY* 1.3 60.8 + - - +
151B ASP* 3.3 1.4 + - - +
152B GLY* 3.0 19.8 + - - -
153B GLU 4.6 2.9 + - - +
158B THR* 4.6 10.5 - - - +
159B PRO* 2.9 33.7 - - + +
160B SER 3.1 13.7 + - - +
161B SER 3.8 2.7 - - - +
162B LEU* 4.0 19.5 - - + -
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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