Contacts of the strand formed by residues 202 - 207 (chain B) in PDB entry 6S6A
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 GLU 202 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B ALA* 3.3 2.8 - - - +
201B ASP* 1.3 79.7 - - + +
203B VAL* 1.3 70.7 + - - +
204B LEU* 4.0 16.4 - - + -
217B TYR* 3.2 13.9 - - - +
218B GLN* 3.9 12.3 - - + +
220B LYS 5.0 0.2 - - - +
222B GLN* 3.1 23.8 + - - +
227B ARG* 2.6 34.3 + - - -
228B PHE* 3.8 5.5 - - + -
273B MET 3.9 0.6 - - - +
274B VAL* 3.5 0.5 - - - -
275B VAL* 3.0 42.7 + - + +
299D TYR* 2.6 28.4 + - - +
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU* 3.9 15.2 - - + +
194B PHE* 3.8 18.6 - - + -
195B ALA* 3.4 38.8 - - + +
198B ILE* 5.0 0.2 - - + -
200B ALA* 4.0 9.9 - - + -
202B GLU* 1.3 79.7 - - - +
204B LEU* 1.3 63.3 - - - +
216B HIS* 3.0 7.6 - - - +
217B TYR 2.9 31.4 + - - +
272B VAL* 3.7 24.0 - - + -
273B MET 3.2 11.0 - - - +
274B VAL* 4.0 8.3 - - + -
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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
----------------------------------------------------------
191B LEU* 4.8 0.2 - - - -
202B GLU* 4.0 11.0 - - + -
203B VAL* 1.3 77.5 - - - +
205B LEU* 1.3 61.8 + - - +
206B PHE* 3.7 32.1 - - + -
213B VAL* 4.6 4.9 - - + -
215B SER 3.5 6.1 - - - +
216B HIS* 3.5 16.6 - - + -
228B PHE* 3.3 42.6 - - + -
231B ILE* 4.7 7.6 - - + -
272B VAL* 3.5 5.9 - - - +
273B MET* 2.8 49.1 + - - +
299D TYR* 3.6 20.0 - - - +
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU* 3.8 32.5 - - + -
191B LEU* 4.2 17.5 - - + -
204B LEU* 1.3 75.9 - - - +
206B PHE* 1.3 59.9 + - - +
213B VAL* 3.7 3.3 - - - -
214B ILE* 3.0 45.7 + - + +
215B SER* 3.0 17.6 + - - +
266B PHE* 3.7 34.1 - - + -
270B THR* 3.9 18.4 - - + +
271B TYR 3.3 16.8 - - - +
272B VAL* 4.4 5.8 - - + -
297B PHE* 5.3 1.6 - - + -
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Residues in contact with PHE 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 LEU* 3.7 30.3 - - + -
205B LEU* 1.3 76.0 - - - +
207B GLU* 1.3 60.6 + - - +
211B PHE* 3.4 50.7 - + + -
212B LEU 3.5 6.1 - - - +
213B VAL* 3.4 28.0 - - + -
214B ILE* 4.3 3.1 - - - -
231B ILE* 3.4 32.8 - - + -
232B SER* 3.8 8.1 - - - -
235B ILE* 4.7 1.3 - - + -
263B ILE* 5.7 0.9 - - + -
270B THR* 3.2 6.6 - - - -
271B TYR* 2.7 46.9 + - + +
272B VAL 4.9 0.2 - - - -
273B MET* 3.9 19.3 - - + -
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Residues in contact with GLU 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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50B VAL* 6.1 0.2 - - - -
51B ARG 4.4 9.8 - - - +
52B PHE* 3.2 42.4 - - + -
53B LEU* 3.6 29.7 + - + +
206B PHE* 1.3 72.4 - - - +
208B ARG* 1.3 70.7 + - - +
209B ALA* 3.3 14.6 + - - +
210B THR* 2.7 44.7 + - - +
211B PHE* 2.8 33.1 + - - -
212B LEU 3.2 8.2 + - - +
214B ILE* 4.2 5.5 - - + +
269B ASN* 3.4 10.2 - - - +
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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