Contacts of the strand formed by residues 220 - 225 (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 GLU 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B LYS* 3.7 12.3 - - - -
184B LYS* 2.9 43.5 + - + -
185B VAL 3.4 10.5 - - - +
186B LEU 3.5 4.9 + - - +
210B ARG* 2.8 27.4 + - - +
211B VAL 5.2 0.2 + - - -
214B SER* 2.6 30.0 + - - +
218B THR* 3.0 29.9 + - + +
219B HIS* 1.3 78.6 - - - +
221B MET* 1.3 62.2 + - - +
222B TYR* 3.7 22.1 + - + -
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Residues in contact with MET 221 (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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184B LYS* 3.7 1.2 - - - +
185B VAL* 2.7 38.2 + - - +
188B PRO* 3.7 21.3 - - + -
208B LEU* 3.7 33.0 - - + +
209B ILE 3.3 16.2 - - - +
210B ARG* 4.2 9.9 - - - +
219B HIS* 3.4 6.5 + - - +
220B GLU* 1.3 80.1 - - - +
222B TYR* 1.3 67.6 + - - +
223B PHE 4.2 0.2 - - - -
234B ASN* 3.3 38.8 - - - +
235B VAL* 4.0 9.6 - - - -
238B VAL* 3.6 26.0 - - + -
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Residues in contact with TYR 222 (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 LYS* 4.2 13.4 - - + +
66B ILE* 3.9 10.8 - - + -
88B TRP* 3.6 24.5 - + - -
147B ASP* 3.0 30.7 + - - -
182B CYS* 4.1 5.4 - - - -
183B VAL 3.4 2.9 - - - -
184B LYS* 3.6 27.8 - - + +
207B GLY 3.6 0.3 - - - +
208B LEU* 3.3 4.8 - - - -
209B ILE* 2.8 43.4 + - + +
211B VAL* 3.6 27.4 - - + -
214B SER* 4.4 2.2 - - - -
220B GLU* 3.7 35.6 + - + -
221B MET* 1.3 80.5 - - - +
223B PHE* 1.3 61.8 - - - +
224B VAL* 3.5 17.5 + - + -
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Residues in contact with PHE 223 (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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166B LEU* 5.1 0.9 - - + -
173B LEU* 4.0 8.7 - - + -
181B PHE* 3.4 36.4 - + - -
182B CYS* 3.3 3.1 - - - -
183B VAL* 2.8 50.0 + - + +
185B VAL* 3.9 15.7 - - + -
197B LEU* 4.0 15.0 - - + -
200B MET* 3.8 47.3 - - + -
201B GLN* 4.1 14.8 - - + -
204B PHE* 4.9 0.2 - - + -
205B GLY 3.5 23.3 - - - -
206B GLY 4.4 0.2 - - - -
207B GLY 3.3 22.9 - - - -
208B LEU* 3.7 6.5 - - + +
222B TYR* 1.3 68.9 - - - +
224B VAL* 1.3 59.9 + - - +
231B ILE* 4.6 5.4 - - + -
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Residues in contact with VAL 224 (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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66B ILE* 4.0 13.5 - - + -
71B GLY* 3.2 23.6 - - - +
181B PHE* 3.3 10.9 - - - +
182B CYS* 3.8 27.1 - - + -
206B GLY* 3.1 3.1 - - - -
207B GLY 2.9 38.4 + - - +
209B ILE* 4.1 29.2 - - + -
222B TYR* 3.8 14.8 - - + +
223B PHE* 1.3 79.5 - - - +
225B SER* 1.3 57.4 + - - +
227B ILE* 3.7 11.3 - - + +
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Residues in contact with SER 225 (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 GLY 3.9 2.6 + - - -
72B VAL* 4.0 6.2 - - - +
73B GLU* 4.6 1.7 + - - +
179B CYS 4.3 2.0 - - - -
180B GLY* 3.3 11.3 - - - -
181B PHE* 2.8 58.1 + - - -
206B GLY* 4.0 12.7 + - - +
224B VAL* 1.3 72.8 - - - +
226B GLY* 1.3 62.2 + - - +
227B ILE 3.5 1.3 + - - -
228B LYS* 5.2 2.9 - - - +
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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
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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