Contacts of the strand formed by residues 137 - 142 (chain B) in PDB entry 1WOH
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 LEU 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU* 4.4 20.2 - - + +
131B PHE* 3.9 29.4 - - + +
134B VAL* 3.7 31.4 - - + +
135B PRO 3.2 3.4 - - - -
136B ASP* 1.3 75.4 - - - +
138B HIS* 1.3 77.7 + - - +
139B VAL* 4.9 0.7 - - + -
170B LEU* 5.5 2.2 - - + -
172B ASN* 2.9 19.0 + - - +
173B LEU* 3.6 19.9 - - + +
174B VAL* 3.0 25.3 + - - +
175B HIS 3.6 3.3 + - - +
223B ASN 3.8 7.9 - - - +
225B TYR* 4.1 3.8 - - + -
268B VAL* 3.9 20.6 - - + -
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Residues in contact with HIS 138 (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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136B ASP* 2.9 28.5 + - - +
137B LEU* 1.3 79.3 - - - +
139B VAL* 1.3 64.4 + - - +
140B VAL* 5.8 0.2 - - + -
174B VAL* 3.6 17.6 - - + +
175B HIS* 3.3 32.1 + + + +
219B PRO* 3.9 19.7 - - + +
222B GLN* 3.3 35.9 + - + -
223B ASN 2.8 13.7 + - - +
224B VAL* 3.2 14.5 - - + -
225B TYR 2.8 24.9 + - - -
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 4.2 18.2 - - + -
137B LEU* 4.9 1.8 - - + -
138B HIS* 1.3 78.4 - - - +
140B VAL* 1.3 72.2 + - - +
141B GLN* 4.1 7.6 - - + -
163B PHE* 3.8 24.9 - - + -
173B LEU* 4.3 18.8 - - + -
175B HIS* 3.0 7.5 + - - -
176B ILE* 3.3 15.9 - - + +
177B THR* 2.9 25.8 + - - -
225B TYR* 3.2 28.3 - - + +
227B SER* 4.4 5.4 - - - -
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Residues in contact with VAL 140 (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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138B HIS* 5.7 0.4 - - + -
139B VAL* 1.3 74.1 - - - +
141B GLN* 1.3 64.6 + - - +
142B LEU* 4.2 3.7 + - + +
177B THR* 3.5 10.1 - - - +
179B VAL* 5.6 2.0 - - + -
218B LEU* 4.4 17.7 - - + -
219B PRO* 3.9 30.7 - - + -
224B VAL* 3.7 19.4 - - + +
225B TYR 3.1 5.7 + - - -
226B PHE* 3.6 29.3 - - + -
227B SER 3.1 21.7 + - - +
228B VAL* 5.9 0.2 - - - +
257B ILE* 4.7 12.1 - - + -
258B LEU* 5.1 4.2 - - + +
261B ALA* 4.5 5.6 - - + -
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Residues in contact with GLN 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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121B HIS* 5.0 1.1 - - + -
139B VAL* 3.8 13.2 - - + -
140B VAL* 1.3 73.8 - - - +
142B LEU* 1.3 65.5 + - - +
143B ASP* 3.0 31.9 + - + +
145B HIS 3.8 0.4 + - - -
146B LEU* 3.2 19.0 + - - +
147B ASP* 4.3 0.2 - - - +
163B PHE* 3.1 34.2 - - + +
176B ILE* 3.5 11.9 - - + +
177B THR 2.9 11.3 + - - +
178B THR* 2.7 31.9 + - + -
179B VAL* 2.9 26.2 + - - +
227B SER 3.3 9.0 - - - +
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Residues in contact with LEU 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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140B VAL* 4.2 4.0 + - + -
141B GLN* 1.3 71.7 - - - +
143B ASP* 1.3 63.3 + - - +
179B VAL* 3.4 22.2 - - + +
227B SER 3.0 9.6 + - - +
228B VAL* 4.4 14.8 - - + -
229B ASP* 3.0 32.0 + - - +
232B GLY* 4.8 1.8 - - - -
233B PHE* 4.4 11.7 - - + -
249B LEU* 4.2 15.3 - - + -
254B GLY* 3.8 29.6 - - - +
257B ILE* 4.0 30.7 - - + -
258B LEU* 4.0 26.5 - - + -
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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