Contacts of the strand formed by residues 203 - 211 (chain B) in PDB entry 6XAV
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 VAL 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B ASP 4.7 5.6 - - - +
202B CYS* 1.3 68.7 - - - +
204B LEU* 1.3 59.0 + - - +
205B MET* 3.8 19.7 + - + -
226B GLU* 5.4 4.0 - - + +
249B LYS* 6.4 0.7 - - - -
253B LEU* 4.4 24.2 - - + -
258B LYS* 5.1 12.1 - - + -
259B ASP 2.9 20.0 + - - +
260B VAL* 3.7 6.9 - - + +
261B ILE* 2.8 34.2 + - - +
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Residues in contact with LEU 204 (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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192B ALA* 3.8 34.1 - - + +
195B ILE* 4.4 17.9 - - + -
196B ALA* 4.7 5.4 - - + -
202B CYS 3.4 7.4 + - - +
203B VAL* 1.3 73.8 - - - +
205B MET* 1.3 68.6 + - - +
206B VAL* 4.3 10.8 - - + -
223B VAL* 5.0 7.2 - - + -
224B LYS 4.5 15.0 - - - +
225B GLY* 4.3 9.9 - - - -
226B GLU* 3.4 23.3 + - - +
261B ILE* 3.6 17.3 - - + +
263B LEU* 3.7 32.5 - - + -
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Residues in contact with MET 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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72B TYR* 5.3 1.6 - - - +
203B VAL* 4.2 15.3 - - + +
204B LEU* 1.3 80.0 - - - +
206B VAL* 1.3 63.1 + - - +
207B LEU* 4.0 1.1 + - - -
226B GLU* 3.7 32.1 - - + +
228B VAL* 5.2 5.8 - - + -
246B VAL* 3.8 37.5 - - + +
249B LYS* 4.5 20.6 - - + -
250B ALA* 5.0 5.4 - - - -
253B LEU* 5.2 4.0 - - - -
260B VAL* 4.1 20.4 - - - -
261B ILE 2.8 14.6 + - - +
262B ILE* 3.3 13.5 - - + +
263B LEU* 3.0 25.1 + - - +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 4.6 13.5 - - + -
192B ALA* 5.0 4.3 - - + -
204B LEU* 4.5 15.0 - - + -
205B MET* 1.3 76.3 - - - +
207B LEU* 1.3 61.0 + - - +
208B LEU* 4.0 29.7 + - + -
219B MET* 5.0 6.7 - - + -
223B VAL* 4.5 20.4 - - + -
226B GLU 3.2 13.9 + - - +
227B VAL* 3.9 11.0 - - + +
228B VAL* 3.1 28.6 + - - +
263B LEU* 3.9 23.1 - - + +
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Residues in contact with LEU 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 MET 4.0 1.8 + - - +
206B VAL* 1.3 73.3 - - - +
208B LEU* 1.3 69.8 + - - +
209B ILE* 3.8 33.4 + - + -
228B VAL 3.3 15.0 - - - +
242B VAL* 3.9 15.7 - - + -
243B ALA* 4.6 12.6 - - + -
246B VAL* 4.2 21.5 - - + -
262B ILE* 4.9 9.6 - - + -
263B LEU 3.5 7.4 + - - +
264B LEU* 3.8 26.5 - - + +
265B ASP 3.6 18.5 + - - -
266B SER* 4.4 0.2 + - - -
270B LEU* 5.4 1.8 - - + -
300B PHE* 4.1 22.0 - - + -
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Residues in contact with LEU 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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188B LEU* 5.5 3.8 - - + -
206B VAL* 4.0 19.5 - - + +
207B LEU* 1.3 81.7 - - - +
209B ILE* 1.3 56.8 + - - +
211B GLU* 4.0 23.4 - - + +
215B GLU* 4.4 9.6 - - + +
216B VAL* 4.7 6.7 - - + -
219B MET* 3.8 34.3 - - + -
227B VAL* 5.1 3.6 - - + -
228B VAL 3.5 7.7 + - - -
229B ALA* 3.2 17.0 - - + +
230B SER 2.7 34.3 + - - +
263B LEU 5.2 0.2 - - - +
265B ASP* 3.7 28.3 - - + +
266B SER* 4.6 1.1 - - - -
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Residues in contact with ILE 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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207B LEU* 3.8 33.7 - - + -
208B LEU* 1.3 74.1 - - - +
210B ASP* 1.3 77.7 + - + +
211B GLU* 3.7 3.5 - - - +
230B SER* 3.6 22.2 - - - +
239B HIS* 3.5 42.4 - - + +
242B VAL* 4.1 15.7 - - + -
243B ALA* 5.2 0.9 - - + +
266B SER* 3.2 37.8 + - - +
269B ARG* 3.9 7.1 - - + +
270B LEU* 4.9 16.6 - - + -
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Residues in contact with ASP 210 (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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298A LYS* 4.3 11.0 + - - -
209B ILE* 1.3 82.4 - - + +
211B GLU* 1.3 62.8 + - - +
230B SER 2.7 14.8 + - - -
231B THR 4.1 0.9 - - - -
232B PHE* 3.2 35.5 - - - +
239B HIS* 4.1 17.8 + - + +
269B ARG* 3.8 38.3 + - + +
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Residues in contact with GLU 211 (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 LEU* 4.0 30.9 - - + +
209B ILE 3.7 10.7 - - - +
210B ASP* 1.3 84.1 - - - +
212B ARG* 1.3 74.0 + - - +
215B GLU* 3.6 21.0 - - + +
216B VAL* 4.8 6.7 - - + -
230B SER 3.7 3.2 + - - -
231B THR* 3.3 7.7 - - - -
232B PHE* 3.1 25.9 + - - -
265B ASP* 3.8 33.6 - - - +
266B SER* 4.9 0.8 - - - -
269B ARG* 5.8 2.8 - - - +
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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