Contacts of the strand formed by residues 179 - 186 (chain B) in PDB entry 2WA2
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 CYS 179 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LYS* 6.5 0.2 - - - +
141B ALA 3.8 16.4 - - - +
142B ASP* 3.3 17.5 - - - +
143B THR 4.5 0.4 - - - +
144B VAL* 4.1 7.6 - - + -
173B LEU* 3.6 31.6 - - - -
176B ASN* 3.1 32.0 + - + +
177B GLN 3.2 2.0 + - - -
178B GLY* 1.3 81.0 - - - +
180B GLY* 1.3 70.8 + - - +
181B PHE* 3.6 13.0 - - - -
225B SER* 4.3 2.6 - - - -
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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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72B VAL* 4.2 4.5 - - - -
73B GLU* 4.3 19.7 + - - -
75B LYS* 5.8 3.6 - - - +
142B ASP 3.0 11.2 + - - -
143B THR* 3.3 3.2 - - - -
144B VAL 2.8 23.0 + - - -
178B GLY 3.6 1.4 + - - -
179B CYS* 1.3 77.0 - - - +
181B PHE* 1.3 61.5 + - - +
225B SER* 3.3 12.6 - - - -
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Residues in contact with PHE 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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72B VAL* 3.5 9.6 - - - +
144B VAL* 3.2 14.1 - - + +
173B LEU* 3.7 35.4 - - + -
179B CYS* 3.6 13.7 - - - -
180B GLY* 1.3 73.6 - - - +
182B CYS* 1.3 64.3 + - - +
183B VAL* 4.6 6.1 - - + -
204B PHE* 3.9 20.2 - - + -
205B GLY 4.0 11.4 - - - -
223B PHE* 3.4 52.5 - + - -
224B VAL* 3.3 19.5 - - - -
225B SER* 2.8 51.3 + - - -
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Residues in contact with CYS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 4.1 8.5 - - - -
66B ILE* 3.5 33.9 - - - -
72B VAL* 4.1 11.7 - - + -
88B TRP* 3.6 19.4 - - - -
144B VAL 3.0 6.7 + - - -
145B LEU* 3.4 19.1 - - + +
146B CYS 3.0 23.7 + - - +
181B PHE* 1.3 77.0 - - - +
183B VAL* 1.3 60.9 + - - +
222B TYR* 4.1 3.8 - - - -
223B PHE 3.3 5.8 - - - -
224B VAL* 3.8 11.4 - - + -
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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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144B VAL* 4.3 5.8 - - + +
146B CYS* 3.2 8.3 - - + -
165B VAL* 3.9 11.9 - - + -
166B LEU* 4.5 10.8 - - + -
169B ILE* 3.8 52.9 - - + -
181B PHE* 4.6 7.6 - - + -
182B CYS* 1.3 86.2 - - - +
184B LYS* 1.3 74.4 + - - +
185B VAL* 3.5 1.7 + - - +
222B TYR* 3.4 5.0 - - - -
223B PHE* 2.8 44.4 + - + +
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Residues in contact with LYS 184 (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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146B CYS 2.7 10.1 + - - +
147B ASP* 3.3 38.2 + - - +
148B ILE 3.6 22.3 - - - +
149B GLY* 2.6 27.8 + - - +
151B SER* 5.3 2.4 + - - +
162B THR* 5.1 1.7 - - - +
165B VAL* 4.1 12.1 - - - +
166B LEU* 5.1 0.9 - - - +
183B VAL* 1.3 83.4 - - - +
185B VAL* 1.3 63.7 + - - +
186B LEU* 3.8 21.7 + - - +
220B GLU* 2.9 38.7 + - + +
221B MET 4.3 1.3 - - - +
222B TYR* 3.6 20.5 + - + +
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Residues in contact with VAL 185 (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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162B THR* 3.5 22.9 - - + -
166B LEU* 4.4 8.1 - - + -
183B VAL 3.7 10.1 - - - +
184B LYS* 1.3 77.2 - - - +
186B LEU* 1.3 65.6 + - - +
187B ASN 3.5 0.2 + - - -
188B PRO* 3.7 29.6 - - + +
193B VAL* 3.7 9.9 - - + -
197B LEU* 4.0 14.4 - - + -
208B LEU* 3.6 24.9 - - + -
220B GLU* 3.4 0.2 - - - -
221B MET 2.7 35.1 + - - +
223B PHE* 3.9 10.1 - - + -
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Residues in contact with LEU 186 (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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148B ILE 5.0 1.1 + - - +
149B GLY* 3.9 21.5 - - - +
150B GLU 3.3 25.1 - - - +
151B SER* 3.9 21.5 - - - +
158B GLU* 3.6 41.1 - - + +
161B ARG* 4.8 5.8 - - + -
162B THR* 3.5 13.8 + - - +
184B LYS* 3.8 32.6 + - - +
185B VAL* 1.3 74.2 - - - +
187B ASN* 1.3 59.2 + - - +
188B PRO* 3.5 3.5 - - - +
218B THR* 4.1 8.3 + - - +
219B HIS* 3.8 4.2 + - - +
220B GLU* 3.5 17.9 + - - -
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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
------------------------------------------------------------
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