Contacts of the strand formed by residues 203 - 209 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201D ASP 4.3 7.4 - - - +
202D CYS* 1.3 69.4 - - - +
204D LEU* 1.3 61.1 + - - +
205D MET* 3.6 30.0 + - + -
226D GLU* 6.1 0.7 - - - +
253D LEU* 4.1 11.4 - - + -
258D LYS* 4.5 16.8 - - + -
259D ASP 2.6 19.6 + - - +
260D VAL* 3.5 16.5 - - + +
261D ILE* 2.8 27.6 + - - +
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Residues in contact with LEU 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D ALA* 3.3 38.6 - - + +
195D ILE* 4.3 24.5 - - + -
196D ALA* 4.4 15.7 - - + +
202D CYS 3.3 7.0 + - - +
203D VAL* 1.3 74.3 - - - +
205D MET* 1.3 70.4 + - - +
206D VAL* 4.7 8.1 - - + -
223D VAL* 5.4 6.1 - - + -
224D LYS 5.1 7.9 - - - +
225D GLY* 5.2 4.8 - - - -
226D GLU* 4.1 19.5 + - - +
261D ILE* 3.4 12.6 - - + +
263D LEU* 3.7 29.4 - - + -
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Residues in contact with MET 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D VAL* 3.8 27.8 - - + +
204D LEU* 1.3 80.3 - - - +
206D VAL* 1.3 61.0 + - - +
207D LEU* 4.1 1.1 + - + -
226D GLU* 4.1 16.8 - - - +
228D VAL* 5.6 5.6 - - + -
246D VAL* 4.5 16.8 - - + +
249D LYS* 4.6 20.4 - - + +
250D ALA* 4.6 8.3 - - - +
253D LEU* 3.8 19.5 - - + -
260D VAL* 3.7 18.8 - - + -
261D ILE 2.8 13.6 + - - +
262D ILE* 3.5 22.5 - - + +
263D LEU* 2.8 35.5 + - - +
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Residues in contact with VAL 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D LEU* 4.5 13.0 - - + -
192D ALA* 4.8 10.1 - - + -
204D LEU* 4.7 13.9 - - + -
205D MET* 1.3 78.1 - - - +
207D LEU* 1.3 60.4 + - - +
208D LEU* 3.8 28.4 + - + -
219D MET* 4.0 18.4 - - + -
223D VAL* 4.9 7.2 - - + -
226D GLU 3.5 11.1 + - - +
227D VAL* 3.8 17.4 - - + +
228D VAL* 2.9 31.2 + - - +
263D LEU* 3.8 14.4 - - + +
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Residues in contact with LEU 207 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205D MET* 4.1 1.2 + - + -
206D VAL* 1.3 72.3 - - - +
208D LEU* 1.3 60.6 + - - +
209D ILE* 3.5 39.2 + - + -
228D VAL* 3.3 17.5 - - + +
229D ALA* 5.1 0.4 - - - -
242D VAL* 3.9 10.8 - - + -
243D ALA* 4.5 5.2 - - + -
246D VAL* 3.8 35.7 - - + -
262D ILE* 4.9 8.7 - - + -
263D LEU 3.4 10.3 + - - +
264D LEU* 3.7 26.4 - - + +
265D ASP 3.8 10.4 + - - -
266D SER* 3.8 1.6 + - - -
270D LEU* 5.9 0.2 - - + -
300D PHE* 3.9 28.7 - - + -
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Residues in contact with LEU 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D VAL* 3.8 16.1 + - + -
207D LEU* 1.3 72.4 - - - +
209D ILE* 1.3 61.5 + - - +
211D GLU* 3.8 28.5 - - + +
215D GLU* 4.4 12.6 - - + +
216D VAL* 4.8 7.1 - - + +
219D MET* 4.0 42.2 - - + -
227D VAL* 4.9 3.8 - - + -
228D VAL 3.5 6.7 + - - -
229D ALA* 3.2 12.4 - - + +
230D SER 2.9 23.5 + - - +
265D ASP* 3.7 37.2 - - + +
266D SER* 5.2 0.9 - - - -
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Residues in contact with ILE 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D LEU* 3.5 45.8 + - + -
208D LEU* 1.3 72.1 - - - +
210D ASP* 1.3 75.4 + - + +
211D GLU* 3.6 4.5 + - - +
230D SER* 3.4 11.2 - - - +
239D HIS* 3.5 55.0 - - + +
242D VAL* 4.7 2.0 - - + -
243D ALA* 4.0 12.3 - - + +
266D SER* 3.2 32.1 + - - +
269D ARG* 4.0 5.7 - - + +
270D LEU* 4.3 14.1 - - + +
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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