Contacts of the strand formed by residues 204 - 209 (chain B) in PDB entry 2W77
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 ARG 204 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B TYR* 3.4 25.2 + - + +
201B ASP* 2.5 68.1 + - - +
202B THR 4.0 0.2 + - - -
203B ASP* 1.3 79.5 - - - +
205B ASN* 1.3 68.5 + - - +
229B VAL* 3.3 23.8 + - + -
232B SER* 3.5 20.2 - - - +
236B THR* 4.2 5.6 - - + -
362B TRP* 3.4 7.7 - - - -
391B TRP* 2.9 33.9 - - + -
795B PHE* 4.0 6.5 - - - -
1C PVE 2.5 34.2 + - - -
6C FHO 3.5 3.6 + - - -
11C FH7 2.9 21.0 + - - -
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Residues in contact with ASN 205 (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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186B ASP* 2.8 37.6 - - - +
190B ARG* 4.5 6.9 + - - +
197B VAL* 4.2 14.2 - - + +
198B SER 3.0 21.8 + - - +
199B ALA* 3.2 21.0 - - - +
200B TYR* 3.7 14.0 - - - +
201B ASP 5.1 1.8 + - - +
202B THR 5.5 2.3 - - - +
203B ASP 5.8 0.2 - - - -
204B ARG* 1.3 79.3 + - - +
206B ASN* 1.3 60.7 + - - +
207B TYR* 4.4 6.4 + - + -
229B VAL* 4.9 7.6 - - - +
236B THR* 3.5 15.8 + - - +
791B THR* 5.8 0.4 - - - -
1817B PO4 3.5 11.6 + - - -
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Residues in contact with ASN 206 (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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197B VAL* 3.4 5.9 - - - +
198B SER* 2.8 58.3 + - - +
199B ALA 5.3 0.2 - - - +
200B TYR* 3.4 30.5 + - + -
205B ASN* 1.3 76.0 - - - +
207B TYR* 1.3 70.3 + - - +
208B TYR* 3.4 37.6 + - - -
213B SER* 3.0 24.0 + - - -
214B ILE 5.1 1.0 - - - +
1C PVE 3.6 5.2 + - - +
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Residues in contact with TYR 207 (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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185B ILE* 3.4 6.2 - - + +
186B ASP* 2.3 41.9 + - - -
189B MET* 3.6 30.7 - - + -
195B ILE* 4.4 7.6 - - + -
196B THR 3.7 2.2 - - - -
197B VAL* 3.9 19.7 - - + -
205B ASN* 4.4 7.6 - - + -
206B ASN* 1.3 88.5 + - - +
208B TYR* 1.3 55.9 + - - +
213B SER* 3.4 4.9 - - - -
214B ILE* 2.6 54.7 + - + -
217B PHE* 3.8 29.4 - + - -
236B THR* 3.1 21.1 + - - -
266B ILE* 3.8 18.4 - - + -
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Residues in contact with TYR 208 (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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194B GLY 3.7 1.2 - - - +
195B ILE* 3.5 12.5 - - - +
196B THR* 2.9 48.9 + - + +
198B SER* 3.5 13.1 + - - -
206B ASN* 3.4 25.9 + - - -
207B TYR* 1.3 73.6 - - - +
209B ALA* 1.3 60.2 + - - +
212B PHE 3.1 21.5 - - - -
213B SER* 4.0 9.2 - - - -
214B ILE* 4.1 3.1 - - - -
705B SER* 4.3 21.5 - - - -
707B TRP* 4.0 28.5 - + - +
708B GLU* 3.5 43.6 - - + +
742B GLN* 5.1 2.3 + - - -
1C PVE 3.1 20.7 + - - -
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Residues in contact with ALA 209 (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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194B GLY 4.3 9.6 - - - +
195B ILE* 4.9 4.3 - - + -
208B TYR* 1.3 74.7 - - - +
210B ARG* 1.3 76.1 + - + +
211B GLY 3.2 2.0 - - - -
212B PHE 2.9 19.3 + - - -
214B ILE* 3.9 16.8 - - + +
250B LYS* 4.9 7.6 - - + -
263B GLY* 3.5 35.2 - - - +
264B ALA* 4.0 3.8 - - + -
708B GLU* 4.0 0.7 - - - -
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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