Contacts of the strand formed by residues 178 - 183 (chain B) in PDB entry 6WCZ
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 ALA 178 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 3.8 14.8 - - + -
72B GLN* 5.3 10.3 - - + +
74B TYR* 4.5 3.8 - - + -
141B ASP 3.3 7.1 + - - +
142B THR* 3.3 27.6 - - - +
143B LEU* 3.3 3.6 + - - +
176B PRO* 3.8 5.4 - - - +
177B GLY* 1.3 77.4 + - - +
179B PHE* 1.3 68.1 + - - +
223B SER* 3.3 18.4 - - - +
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Residues in contact with PHE 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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71B LEU* 3.3 14.2 - - - +
142B THR* 4.7 1.8 - - - -
143B LEU* 3.3 20.6 - - + +
172B LEU* 6.1 7.4 - - + -
176B PRO* 5.9 6.1 - - + -
177B GLY 5.5 1.1 - - - -
178B ALA* 1.3 82.0 - - - +
180B CYS* 1.3 60.6 + - - +
181B ILE* 3.5 26.7 - - + -
202B HIS* 4.0 21.1 - - + -
203B GLY 3.6 10.1 - - - -
221B TRP* 3.5 45.8 - + - -
222B VAL* 3.2 21.2 - - - +
223B SER* 3.1 39.0 + - - -
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Residues in contact with CYS 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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62B LEU* 4.9 18.4 - - - -
65B LEU* 5.0 5.4 - - - -
71B LEU* 3.7 22.4 - - + -
143B LEU 2.8 10.0 + - - +
144B LEU* 3.3 32.1 - - + +
145B CYS 3.5 4.9 + - - +
146B ASP* 5.2 3.9 - - - +
179B PHE* 1.3 77.8 - - - +
181B ILE* 1.3 60.8 + - - +
220B TYR* 4.9 15.0 - - - -
221B TRP 4.1 3.8 - - - -
222B VAL* 4.2 20.2 - - - +
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Residues in contact with ILE 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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143B LEU* 3.7 37.2 - - + +
144B LEU* 4.4 2.0 - - - -
145B CYS* 4.2 13.7 - - + +
164B VAL* 5.8 2.7 - - + -
165B LEU* 5.5 3.4 - - + -
168B VAL* 3.9 34.1 - - + -
172B LEU* 6.3 0.2 - - + -
179B PHE* 3.5 27.1 - - + -
180B CYS* 1.3 83.1 - - - +
182B LYS* 1.3 66.0 + - - +
183B VAL* 5.6 0.4 - - + -
220B TYR* 3.2 7.0 - - - +
221B TRP* 2.6 59.2 + - + +
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Residues in contact with LYS 182 (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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145B CYS* 3.3 24.0 + - - +
146B ASP* 3.4 22.1 + - - +
147B ILE 3.2 27.6 - - - +
148B GLY* 3.2 22.6 - - - +
164B VAL* 4.8 14.8 - - - +
165B LEU* 5.8 1.2 - - - +
181B ILE* 1.3 83.0 - - - +
183B VAL* 1.3 70.8 + - - +
184B LEU* 3.7 9.3 + - + +
218B GLU* 3.3 25.6 + - + +
220B TYR* 3.4 31.9 - - + -
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Residues in contact with VAL 183 (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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161B THR* 4.1 16.2 - - + -
164B VAL* 6.1 0.7 - - - -
165B LEU* 5.1 11.7 - - + -
181B ILE* 5.0 1.3 - - + -
182B LYS* 1.3 84.1 - - - +
184B LEU* 1.3 65.3 + - - +
185B CYS 3.9 5.8 - - - +
186B PRO* 3.7 29.1 - - + +
191B MET* 4.1 21.3 - - + -
206B LEU* 4.7 2.7 - - + -
218B GLU* 3.3 4.7 - - - +
219B MET 2.9 36.4 + - - +
221B TRP* 3.7 31.6 - - + +
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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