Contacts of the strand formed by residues 203 - 208 (chain B) in PDB entry 1Q6X
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 GLN 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B VAL 3.5 1.2 - - - +
199B ALA* 3.3 5.4 - - - -
200B CYS 2.8 37.4 + - - +
201B CYS* 3.4 22.9 + - + +
202B ASN* 1.3 87.4 + - - +
204B PHE* 1.3 60.8 + - - +
205B PHE* 3.7 19.4 - - + -
232B ALA* 4.5 6.1 - - + +
238B ARG* 3.5 12.7 - - + +
239B LEU* 2.9 52.3 + - - +
374B ARG* 3.0 32.5 + - + +
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Residues in contact with PHE 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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197B ILE* 3.8 20.4 - - + -
198B VAL 3.4 1.8 - - - -
199B ALA* 3.8 24.7 - - + -
202B ASN 3.7 16.8 - - - -
203B GLN* 1.3 74.2 - - - +
205B PHE* 1.3 64.1 + - - +
242B ILE 4.8 2.7 - - - -
243B GLY* 3.9 20.0 - - - -
273B ILE* 4.9 4.3 - - + -
279B LEU* 4.5 6.5 - - + -
310B ALA 4.2 7.9 - - - -
312B ARG 3.4 29.8 - - - -
313B TRP* 3.7 19.1 - + + -
374B ARG* 3.6 6.1 - - - +
375B LEU* 3.0 50.6 + - + +
377B TRP* 4.4 22.4 - + - +
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Residues in contact with PHE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ILE* 3.4 9.7 - - - +
198B VAL* 3.0 36.9 + - - +
200B CYS* 4.9 0.9 - - + -
203B GLN* 3.7 24.5 - - + -
204B PHE* 1.3 79.3 - - - +
206B VAL* 1.3 65.5 + - - +
207B LEU 3.6 0.5 + - - -
228B ILE* 3.9 36.1 - - + -
231B MET* 3.9 30.3 - - + -
232B ALA* 3.9 32.3 - - + -
372B PRO* 4.1 8.1 - - + -
373B ARG 3.3 7.2 - - - +
374B ARG* 3.6 44.9 - - + -
375B LEU 4.7 0.2 - - - +
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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
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195B HIS* 3.9 11.4 - - + -
196B VAL 4.0 2.9 - - - -
197B ILE* 4.3 8.7 - - + -
205B PHE* 1.3 72.5 - - - +
207B LEU* 1.3 61.7 + - - +
208B ASP* 3.8 21.9 + - - +
272B MET* 3.6 27.8 - - + -
372B PRO* 3.4 10.3 - - - +
373B ARG* 2.7 63.6 + - + +
375B LEU* 3.5 26.5 - - + -
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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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131B ILE* 4.1 16.2 - - + -
195B HIS* 3.3 2.7 - - - +
196B VAL* 3.0 58.1 + - + +
198B VAL* 4.0 20.6 - - + -
205B PHE 3.6 0.2 + - - -
206B VAL* 1.3 72.9 - - - +
208B ASP* 1.3 74.6 + - - +
209B VAL* 3.4 2.3 + - + +
216B LEU* 4.7 0.4 - - + -
221B LEU* 4.2 18.8 - - + -
224B GLN* 3.5 36.6 - - + +
225B LEU* 4.3 11.9 - - + -
228B ILE* 4.7 4.3 - - + -
372B PRO* 4.3 9.6 - - + -
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Residues in contact with ASP 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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193B PRO* 3.9 20.5 - - - +
194B GLU 3.5 6.5 - - - +
195B HIS* 3.8 13.5 + - - +
206B VAL* 3.8 14.4 + - - +
207B LEU* 1.3 76.6 - - - +
209B VAL* 1.3 60.0 + - - +
210B VAL 3.4 13.2 - - - +
211B ILE* 4.6 13.7 - - + +
216B LEU* 3.2 24.8 - - - +
224B GLN* 5.6 1.5 + - - +
272B MET* 5.4 1.6 - - - +
370B PRO* 6.2 0.2 - - - +
373B ARG* 5.7 5.5 - - - +
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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