Contacts of the strand formed by residues 204 - 209 (chain B) in PDB entry 1V40
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 TYR 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B PRO* 3.5 48.4 + - + +
203B ASN* 1.3 71.2 - - - +
205B LYS* 1.3 61.0 + - - +
222B PHE* 3.9 17.0 - + + -
227B ILE* 3.8 35.9 - - + +
228B GLN 4.1 5.3 + - - -
229B TYR* 3.3 19.4 - - + +
230B GLU* 2.8 27.1 + - - +
254B LEU* 4.0 6.7 - - + -
255B GLU 3.4 0.7 - - - -
256B VAL* 3.8 37.4 - - + +
270B TYR* 4.8 8.9 + + - -
271B LEU* 4.2 24.1 - - + +
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Residues in contact with LYS 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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203B ASN 4.1 0.6 + - - +
204B TYR* 1.3 74.4 - - - +
206B LEU* 1.3 60.4 + - - +
207B THR* 3.9 8.5 + - - +
230B GLU* 3.6 43.8 + - + +
232B HIS* 4.0 28.8 + - + -
253B ILE 4.0 0.3 - - - +
254B LEU* 3.5 4.6 - - - +
255B GLU* 2.8 67.4 + - + +
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Residues in contact with LEU 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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204B TYR 4.2 0.8 - - - -
205B LYS* 1.3 71.2 - - - +
207B THR* 1.3 63.3 + - - +
208B TYR* 5.0 1.3 - - + -
215B ALA* 4.3 8.7 - - + +
218B ILE* 4.1 30.5 - - + -
219B ARG* 3.7 34.3 - - + +
222B PHE* 4.9 0.2 - - + -
229B TYR* 4.0 16.5 - - + -
230B GLU 2.9 11.3 + - - +
231B ASP* 3.9 12.1 - - - +
232B HIS* 2.8 33.9 + - - +
252B PRO* 4.0 20.9 - - + -
253B ILE 3.5 17.9 - - - +
254B LEU* 3.9 11.3 - - + +
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Residues in contact with THR 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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205B LYS* 3.9 12.4 + - - +
206B LEU* 1.3 74.5 - - - +
208B TYR* 1.3 69.8 + - - +
232B HIS* 3.3 29.1 - - + -
234B ILE* 4.2 13.5 - - + -
242B ILE* 4.8 11.7 - - + -
251B ILE* 3.9 11.4 - - + +
252B PRO* 3.2 22.3 - - - +
253B ILE* 3.1 37.1 + - + +
255B GLU* 4.3 4.7 + - - -
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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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206B LEU* 5.0 2.2 - - + -
207B THR* 1.3 77.9 - - - +
209B PHE* 1.3 85.9 + + - +
211B MET* 3.7 24.2 - - + -
212B ARG 3.6 18.2 - - - -
213B GLY* 3.7 7.7 - - - -
214B ARG* 3.1 20.3 + - - +
215B ALA* 3.3 26.5 - - + -
219B ARG* 3.7 6.7 - - - +
232B HIS 3.1 5.8 + - - +
233B ARG* 3.2 3.1 - - - -
234B ILE* 2.8 31.6 + - - +
251B ILE* 3.9 19.3 - - + -
252B PRO* 3.5 34.3 - - + -
3400B GSH 3.1 31.4 - - + -
3401B O16 4.7 2.3 + - - -
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Residues in contact with PHE 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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208B TYR* 1.3 103.7 - + + +
210B ASN* 1.3 62.8 + - - +
211B MET* 2.9 38.1 + - + -
219B ARG* 3.6 8.1 + - - -
233B ARG* 4.0 2.8 - - - +
234B ILE* 3.6 29.8 - - + -
235B GLU* 4.9 1.8 - - - -
236B GLN* 3.8 39.5 - - - -
239B TRP* 4.3 19.3 - + + -
251B ILE* 3.9 25.7 - - + +
3400B GSH 4.3 5.2 - - + -
3401B O16 2.8 31.2 - + - -
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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