Contacts of the strand formed by residues 156 - 160 (chain A) in PDB entry 2OHI
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 MET 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ILE* 3.7 18.2 - - + -
81A GLN 3.8 12.8 - - - +
82A ASN* 2.7 59.0 + - - +
105A TYR 3.8 9.4 - - - +
106A CYS* 4.1 0.7 - - - -
107A THR* 3.7 21.3 - - + -
129A VAL* 3.5 27.4 - - + -
144A PHE* 3.7 28.3 - - + -
145A LEU 3.2 14.1 - - - +
146A GLU* 4.0 4.3 - - - -
147A THR* 3.6 4.0 - - - -
155A SER* 1.3 78.2 - - - +
157A PHE* 1.3 64.8 + - - +
169A ASN* 4.5 4.0 - - - +
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Residues in contact with PHE 157 (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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82A ASN* 3.6 3.3 + - - -
143A THR 4.5 0.2 - - - -
144A PHE* 3.5 5.5 - - - +
145A LEU* 2.6 62.8 + - + +
147A THR* 3.8 27.3 + - + -
150A LEU* 4.3 13.5 - - + -
156A MET* 1.3 79.9 - - - +
158A THR* 1.3 61.1 + - - +
159A LEU* 4.3 0.7 - - + -
166A LEU* 3.9 34.1 - - + -
167A PHE 3.5 5.8 - - - +
168A SER* 3.1 34.5 - - - -
169A ASN* 5.4 0.7 - - + -
171A ALA* 3.8 19.5 - - + -
172A PHE* 4.7 6.5 - + - -
213A LYS* 4.9 6.5 - - + -
214A PHE* 6.4 1.6 - + - -
217A VAL* 5.7 2.9 - - + -
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Residues in contact with THR 158 (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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49A ILE* 3.9 13.7 - - + -
80A ILE* 3.7 7.1 - - - +
82A ASN* 3.1 20.1 + - - +
142A LEU* 3.5 42.0 - - + -
143A THR 3.5 4.0 - - - +
144A PHE* 3.5 19.3 - - + -
157A PHE* 1.3 72.1 - - - +
159A LEU* 1.3 62.1 + - - +
166A LEU* 3.8 2.8 - - - +
167A PHE* 2.8 49.1 + - + +
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Residues in contact with LEU 159 (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 THR 3.7 0.2 - - - +
142A LEU* 3.3 11.4 - - - +
143A THR* 2.8 49.3 + - + +
145A LEU* 4.0 27.8 - - + -
157A PHE* 4.3 2.9 - - + -
158A THR* 1.3 76.2 - - - +
160A LEU* 1.3 63.5 + - - +
161A ASP* 4.0 23.1 - - - +
165A ILE 3.6 6.3 - - - +
166A LEU* 3.7 26.9 - - + -
167A PHE* 4.9 1.8 - - - -
217A VAL* 5.4 4.5 - - + -
222A LEU* 4.2 30.1 - - + +
226A ILE* 6.0 4.5 - - + -
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Residues in contact with LEU 160 (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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12A VAL* 3.8 28.7 - - + -
40A VAL* 4.3 10.8 - - + -
140A LYS* 4.1 15.9 - - + -
141A THR 3.4 20.9 - - - +
142A LEU* 3.8 24.0 - - + -
159A LEU* 1.3 75.3 - - - +
161A ASP* 1.3 55.7 + - - +
163A ASP* 3.6 31.6 - - + +
164A GLY* 2.6 29.5 + - - -
165A ILE* 2.9 29.0 + - + +
167A PHE* 4.3 10.5 - - + -
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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