Contacts of the strand formed by residues 137 - 142 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E LEU* 4.2 17.7 - - + +
131E PHE* 3.8 31.0 - - + +
134E VAL* 4.0 18.2 - - + +
135E PRO 3.2 3.8 + - - -
136E ASP* 1.3 71.4 - - - +
138E HIS* 1.3 72.2 + - - +
139E VAL* 4.8 1.1 - - + -
170E LEU* 5.1 2.7 - - + -
172E ASN* 2.8 27.4 + - - +
173E LEU* 3.3 28.3 - - + +
174E VAL* 3.0 22.3 + - - +
175E HIS 3.7 1.7 + - - -
223E ASN 3.8 10.3 - - - +
225E TYR* 4.2 4.5 - - + -
268E VAL* 4.1 21.3 - - + -
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Residues in contact with HIS 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E ASP* 3.0 25.0 + - - +
137E LEU* 1.3 76.1 - - - +
139E VAL* 1.3 65.1 + - - +
140E VAL 4.3 0.2 - - - -
174E VAL* 3.6 13.7 - - + +
175E HIS* 3.4 41.0 + + + +
219E PRO* 4.4 14.2 - - + +
222E GLN* 3.1 42.4 + - + -
223E ASN 2.8 12.1 + - - +
224E VAL* 3.2 15.8 - - + -
225E TYR 2.9 23.4 + - - -
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Residues in contact with VAL 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E LEU* 4.3 12.3 - - + -
137E LEU* 4.8 1.8 - - + -
138E HIS* 1.3 79.6 - - - +
140E VAL* 1.3 73.2 + - - +
141E GLN* 4.2 4.3 - - + +
163E PHE* 4.0 22.9 - - + -
173E LEU* 3.9 29.2 - - + -
175E HIS* 3.0 7.5 + - - -
176E ILE* 3.4 17.9 - - + +
177E THR* 2.9 28.6 + - - +
225E TYR* 3.4 28.3 - - + +
227E SER* 4.4 2.0 - - - -
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Residues in contact with VAL 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E VAL* 1.3 73.7 - - - +
141E GLN* 1.3 62.4 + - - +
142E LEU* 4.0 5.5 + - + +
177E THR* 3.6 9.9 - - + +
179E VAL* 5.6 2.0 - - + -
218E LEU* 4.4 17.3 - - + -
219E PRO* 4.0 28.5 - - + -
224E VAL* 3.5 19.7 - - + +
225E TYR 3.0 6.9 + - - -
226E PHE* 3.6 28.3 - - + -
227E SER 3.0 23.6 + - - +
257E ILE* 4.6 14.4 - - + -
258E LEU* 5.2 3.6 - - + +
261E ALA* 4.5 6.3 - - + -
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Residues in contact with GLN 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E HIS* 4.8 1.1 - - + -
139E VAL* 3.8 7.8 - - + -
140E VAL* 1.3 71.8 - - - +
142E LEU* 1.3 63.9 + - - +
143E ASP* 2.9 35.9 + - + +
145E HIS 3.4 2.4 + - - -
146E LEU* 3.1 23.0 + - - +
147E ASP* 4.2 0.2 - - - +
163E PHE* 3.2 32.0 - - + +
176E ILE* 3.6 16.3 - - + +
177E THR 2.9 13.8 + - - +
178E THR* 2.7 28.2 + - - +
179E VAL* 2.8 27.2 + - - +
227E SER* 3.4 7.2 - - - +
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Residues in contact with LEU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E VAL* 4.0 4.4 + - + +
141E GLN* 1.3 71.4 - - - +
143E ASP* 1.3 62.1 + - - +
179E VAL* 3.5 15.9 - - + +
227E SER 2.9 11.7 + - - +
228E VAL* 4.3 20.9 - - + -
229E ASP* 3.0 27.9 + - - +
232E GLY* 4.8 1.6 - - - -
233E PHE* 4.4 7.6 - - + -
249E LEU* 4.3 10.8 - - + -
254E GLY* 3.9 28.3 - - - +
257E ILE* 3.9 38.6 - - + -
258E LEU* 3.9 28.7 - - + -
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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