Contacts of the strand formed by residues 293 - 299 (chain B) in PDB entry 6F0X
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 293 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171B TRP* 5.4 0.2 - - - -
173B ARG* 2.9 30.0 - - + +
240B ILE* 3.5 44.9 - - + -
247B VAL* 3.7 17.5 - - + -
249B VAL* 4.7 3.6 - - + -
287B ILE* 4.9 13.5 - - + +
288B LYS* 6.2 0.2 - - - -
290B HIS* 3.7 13.9 - - + +
291B SER 2.8 5.1 + - - +
292B ASN* 1.3 82.0 - - - +
294B VAL* 1.3 83.1 + - - +
295B ILE* 4.3 14.4 - - + -
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Residues in contact with VAL 294 (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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152B TYR* 4.8 5.4 - - + -
153B VAL* 3.7 35.9 - - + -
156B THR* 6.3 2.9 - - + -
171B TRP* 6.4 0.7 - - + -
173B ARG* 3.3 10.5 - - + +
175B VAL* 4.6 9.4 - - + -
192B LEU* 5.6 1.6 - - + -
246B LEU* 6.1 3.4 - - + -
247B VAL 2.9 11.0 + - - +
248B PHE* 3.2 22.6 - - + -
249B VAL* 2.8 22.9 + - - +
292B ASN 5.6 1.1 - - - -
293B VAL* 1.3 81.1 - - - +
295B ILE* 1.3 77.0 + - - +
296B LEU* 4.3 16.8 - - + -
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Residues in contact with ILE 295 (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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173B ARG* 2.5 18.4 + - + +
174B VAL* 3.6 25.4 - - + -
175B VAL* 2.8 28.2 + - - +
233B PHE* 6.0 1.8 - - + -
249B VAL* 3.2 45.5 - - + +
251B ILE* 4.2 9.2 - - + -
284B ILE* 4.9 9.2 - - + -
287B ILE* 3.9 27.6 - - + -
293B VAL* 4.3 6.1 - - + -
294B VAL* 1.3 76.9 - - - +
296B LEU* 1.3 65.8 + - - +
297B THR* 4.1 19.3 - - + -
309B PHE* 5.6 0.7 - - + -
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Residues in contact with LEU 296 (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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149B LEU* 4.9 0.7 - - + -
175B VAL* 3.6 26.7 - - + +
177B LEU* 4.7 4.7 - - + -
189B CYS* 3.5 46.4 - - + +
192B LEU* 3.5 32.8 - - + -
248B PHE* 4.2 19.1 - - + -
249B VAL 2.8 10.1 + - - +
250B LEU* 3.4 11.4 - - + +
251B ILE 2.9 26.7 + - - +
294B VAL* 4.3 9.4 - - + -
295B ILE* 1.3 81.8 - - - +
297B THR* 1.3 63.5 + - - +
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Residues in contact with THR 297 (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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174B VAL* 4.5 2.5 - - + +
175B VAL 2.9 17.0 + - - +
176B LEU* 3.2 18.8 - - - +
177B LEU* 2.9 29.1 + - - +
189B CYS* 5.0 0.2 - - - -
251B ILE* 3.3 17.5 - - + -
254B VAL* 3.4 20.9 - - + -
295B ILE* 4.1 11.2 - - + -
296B LEU* 1.3 81.9 - - - +
298B THR* 1.3 65.7 + - - +
309B PHE* 3.6 29.3 - - + -
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Residues in contact with THR 298 (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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176B LEU* 4.3 2.5 - - - -
177B LEU* 3.2 6.5 - - + +
185B LYS* 3.7 46.9 - - + +
186B THR* 4.0 9.5 + - - +
189B CYS* 4.0 12.1 - - - -
250B LEU* 5.1 5.2 - - + -
251B ILE 3.5 1.5 + - - +
252B ASP* 2.1 54.5 + - - +
253B GLN* 3.7 12.7 - - - +
254B VAL* 3.8 6.4 + - - +
297B THR* 1.3 80.3 - - - +
299B SER* 1.3 61.9 + - - +
300B ASN* 4.1 2.5 + - - -
901B AGS 5.9 0.4 - - - -
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Residues in contact with SER 299 (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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176B LEU* 4.6 3.8 - - - -
177B LEU 3.0 8.9 + - - -
178B HIS* 3.4 23.2 - - - +
179B GLY 3.5 4.9 + - - -
185B LYS* 4.1 3.8 - - - +
253B GLN* 5.7 1.8 - - - +
254B VAL* 5.9 1.8 - - - -
255B GLU* 5.3 8.6 + - - +
298B THR* 1.3 75.7 - - - +
300B ASN* 1.3 60.8 + - - +
301B ILE* 3.0 10.6 + - - +
302B THR* 2.8 26.4 + - - -
305B ILE* 3.3 29.1 - - - +
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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