Contacts of the strand formed by residues 173 - 181 (chain B) in PDB entry 1WOI
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 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B LEU* 4.1 15.7 - - + -
137B LEU* 3.6 25.1 - - + +
139B VAL* 4.2 8.1 - - + -
166B ALA* 3.9 32.1 - - + +
167B CYS* 4.0 18.3 - - - -
170B LEU* 3.0 26.8 + - + +
171B PRO 4.3 2.3 - - - +
172B ASN* 1.3 78.3 - - - +
174B VAL* 1.3 58.5 + - - +
175B HIS 3.8 11.4 - - - +
176B ILE* 3.7 32.5 - - + -
197B ARG* 4.4 13.3 + - - -
199B HIS* 5.2 1.3 - - + -
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Residues in contact with VAL 174 (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* 3.5 44.4 - - + +
137B LEU 3.1 3.2 + - - +
138B HIS* 3.6 17.0 - - - +
171B PRO 4.1 11.7 - - - +
172B ASN* 3.0 13.9 + - - +
173B LEU* 1.3 73.4 - - - +
175B HIS* 1.3 65.7 + - + +
197B ARG 4.5 11.8 - - - +
199B HIS* 4.5 4.6 - - - -
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Residues in contact with HIS 175 (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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137B LEU 3.5 1.0 + - - -
138B HIS* 3.3 36.9 + + + +
139B VAL 3.0 22.3 + - - -
173B LEU* 3.6 4.2 + - - +
174B VAL* 1.3 84.6 - - + +
176B ILE* 1.3 78.4 + - - +
177B THR* 3.0 28.4 + - - -
197B ARG 5.4 0.2 - - - -
198B GLY 3.1 26.0 + - - -
199B HIS* 3.9 7.2 - - - -
200B THR* 2.9 27.7 + - - -
217B GLN 5.6 2.2 - - - -
219B PRO* 5.8 1.7 - - + +
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Residues in contact with ILE 176 (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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139B VAL* 3.3 22.9 - - + +
141B GLN* 3.7 11.4 - - - +
148B PHE* 4.6 0.9 - - + -
163B PHE* 3.9 35.0 - - + -
167B CYS* 4.0 11.9 - - - -
173B LEU* 3.7 15.7 - - + -
175B HIS* 1.3 84.5 - - - +
177B THR* 1.3 61.2 + - - +
178B THR* 3.7 19.3 - - - +
199B HIS* 3.5 37.4 + - + +
200B THR 2.8 31.9 + - - +
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Residues in contact with THR 177 (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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139B VAL 2.9 10.4 + - - -
140B VAL* 3.5 8.4 - - + +
141B GLN* 2.8 27.7 + - - +
175B HIS* 3.0 24.4 + - - -
176B ILE* 1.3 70.7 - - - +
178B THR* 1.3 62.0 + - - +
179B VAL* 4.1 7.9 + - + +
200B THR* 3.4 14.0 - - + -
202B ILE* 3.8 27.8 - - + -
217B GLN 4.5 6.5 + - - +
218B LEU* 4.2 13.5 - - + -
219B PRO* 4.3 16.5 - - - +
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Residues in contact with THR 178 (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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141B GLN* 2.8 45.5 + - + +
143B ASP* 4.3 3.8 - - + +
145B HIS 4.1 1.6 - - - +
146B LEU* 4.1 19.0 - - + +
176B ILE* 3.7 7.8 - - - +
177B THR* 1.3 72.4 - - - +
179B VAL* 1.3 63.8 + - - +
181B LEU* 3.6 32.8 - - + +
199B HIS* 6.0 1.0 - - - +
200B THR 2.9 12.1 + - - +
201B ILE* 4.9 0.6 - - - +
202B ILE* 2.8 31.2 + - - +
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Residues in contact with VAL 179 (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* 5.5 2.5 - - + -
141B GLN 2.8 10.3 + - - +
142B LEU* 3.5 21.1 - - + +
143B ASP 3.0 25.0 + - - -
177B THR* 4.1 11.7 - - + +
178B THR* 1.3 80.2 - - - +
180B GLY* 1.3 64.1 - - - +
181B LEU 3.6 1.3 - - - -
202B ILE* 3.4 27.1 - - + +
207B VAL* 3.6 26.9 - - + -
214B VAL* 4.1 8.5 - - + -
218B LEU* 4.6 11.0 - - + -
249B LEU* 4.6 3.0 - - + +
257B ILE* 3.7 20.9 - - + -
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Residues in contact with GLY 180 (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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143B ASP 3.0 10.7 - - - +
144B ALA* 3.5 0.7 - - - -
179B VAL* 1.3 79.3 - - - +
181B LEU* 1.3 65.9 + - - +
182B ARG* 3.0 28.8 + - - +
202B ILE 2.9 8.6 + - - -
203B PRO 4.4 0.2 - - - -
204B MET* 3.7 25.3 - - - +
249B LEU* 4.7 7.4 - - - -
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Residues in contact with LEU 181 (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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69A LEU* 4.8 6.7 - - + -
143B ASP 3.2 7.5 + - - +
144B ALA 3.4 6.1 - - - +
145B HIS 3.2 38.6 - - - +
146B LEU* 3.5 19.3 - - + +
178B THR* 3.6 17.9 - - + +
180B GLY* 1.3 76.7 - - - +
182B ARG* 1.3 59.3 + - - +
186B PHE* 4.1 19.5 - - + -
201B ILE* 3.2 33.0 - - + -
202B ILE 3.6 6.0 + - - +
203B PRO* 3.3 16.8 - - + +
204B MET* 2.8 23.6 + - - +
205B ASP* 6.0 0.3 - - - -
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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