Contacts of the strand formed by residues 161 - 167 (chain A) 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 SER 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A PRO* 5.6 2.9 - - - -
147A ALA 3.4 10.1 - - - -
148A MSE 4.2 16.6 - - - -
149A VAL* 4.6 0.4 - - - -
159A PRO* 3.9 1.6 - - - +
160A SER* 1.3 83.2 + - - +
162A LEU* 1.3 67.7 + - - +
205A ASN* 3.7 9.8 + - - +
206A ALA* 3.0 36.2 + - - +
207A ALA* 4.1 10.6 + - - +
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PRO* 5.7 0.3 - - - +
118A ALA* 3.8 25.1 - - + -
125A TYR* 3.8 27.8 - - + +
146A GLY* 3.3 5.9 - - - -
147A ALA* 2.8 32.8 + - + +
149A VAL* 3.6 15.3 - - + -
159A PRO* 3.8 26.2 - - + -
161A SER* 1.3 79.4 - - - +
163A HIS* 1.3 66.8 + - - +
164A VAL* 3.8 27.8 - - + -
203A THR* 4.3 11.2 - - - +
204A LEU 3.3 17.0 - - - +
206A ALA* 3.9 3.3 - - - +
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Residues in contact with HIS 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLU* 2.5 32.2 + - - +
112A TYR* 3.7 32.7 + + - +
144A PHE* 3.6 22.3 - - + -
145A LEU 3.3 3.8 - - - +
146A GLY* 4.5 7.0 - - - -
162A LEU* 1.3 81.9 - - - +
164A VAL* 1.3 60.1 + - - +
203A THR* 3.2 4.7 - - - -
204A LEU* 2.9 38.4 + - + +
206A ALA* 3.8 19.0 - - + +
209A VAL* 3.9 21.4 - - + +
210A MSE 6.1 1.9 - - + +
229A TYR* 3.7 16.7 + + - -
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ALA* 5.2 0.7 - - + -
125A TYR* 5.7 0.9 - - + -
127A LEU* 3.9 28.3 - - + -
143A ALA 3.4 1.6 - - - +
144A PHE* 3.4 5.0 - - - -
145A LEU* 2.8 46.3 + - + +
147A ALA* 4.8 4.5 - - + -
162A LEU* 3.8 31.0 - - + -
163A HIS* 1.3 79.1 - - - +
165A ILE* 1.3 63.0 + - - +
166A LEU* 3.6 18.7 - - + +
198A VAL* 4.2 15.5 - - + -
202A ARG 3.5 4.3 - - - -
203A THR* 4.0 9.9 - - + -
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Residues in contact with ILE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 3.9 22.4 - - + -
91A ALA* 4.7 4.9 - - + -
95A VAL* 3.8 19.5 - - + -
99A ILE* 3.6 18.2 - - + -
108A MSE 5.3 1.6 - - - -
142A TRP* 3.4 27.4 - - + -
143A ALA 3.3 7.2 - - - +
144A PHE* 3.8 33.2 - - + -
164A VAL* 1.3 76.0 - - - +
166A LEU* 1.3 67.5 + - - +
167A PRO* 4.5 0.2 - - - +
198A VAL* 3.8 8.1 - - - +
202A ARG* 2.8 54.5 + - + +
203A THR* 5.0 3.6 - - - -
204A LEU* 5.8 0.7 - - + -
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 3.8 19.7 - - + -
142A TRP* 3.2 8.1 - - - -
143A ALA* 2.8 34.7 + - + +
145A LEU* 4.3 7.6 - - + -
164A VAL* 3.6 30.3 - - + +
165A ILE* 1.3 79.9 - - - +
167A PRO* 1.3 73.6 - - + +
170A ASP* 4.0 11.2 - - + +
171A TYR* 3.6 11.1 - - + -
193A VAL* 3.9 19.7 - - + -
196A ALA* 4.0 19.5 - - + -
198A VAL* 3.7 17.0 - - + -
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Residues in contact with PRO 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLN 3.7 4.0 - - - +
142A TRP* 3.4 35.4 - - + -
166A LEU* 1.3 88.7 - - + +
168A ARG* 1.3 57.1 + - - +
169A THR* 3.1 19.1 - - + +
170A ASP* 2.8 46.8 + - - +
171A TYR* 3.3 7.9 - - - -
202A ARG* 3.8 16.6 - - - +
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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