Contacts of the strand formed by residues 282 - 291 (chain B) in PDB entry 6BAA
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 282 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B ALA 4.6 1.2 - - - +
34B ARG* 3.6 4.4 - - - -
35B PHE* 2.6 35.4 + - - +
36B VAL 3.1 18.7 + - - +
219B VAL* 3.7 2.3 - - - +
220B VAL* 2.8 47.4 + - + +
281B LEU* 1.3 78.6 - - - +
283B ILE* 1.3 66.3 + - - +
284B ILE* 3.3 9.9 + - + +
303B SER* 3.0 34.1 + - - -
304B TYR 3.6 6.1 - - - +
305B LEU* 4.1 20.0 - - + +
326C TYR* 5.2 1.9 + - - -
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Residues in contact with ILE 283 (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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198B PHE* 4.0 33.2 - - + -
217B MET* 4.0 25.6 - - + -
218B GLN 3.7 2.5 - - - +
219B VAL* 3.7 31.0 - - + -
267B LEU* 4.6 17.7 - - + -
281B LEU* 5.8 3.1 - - + -
282B GLU* 1.3 77.4 - - - +
284B ILE* 1.3 63.2 + - - +
285B VAL* 3.8 9.3 + - + -
303B SER* 3.1 7.4 - - - -
304B TYR* 3.0 46.8 + - + +
309B ILE* 5.0 4.0 - - + -
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Residues in contact with ILE 284 (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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35B PHE* 3.8 13.9 - - + -
36B VAL* 3.5 17.5 - - + -
216B HIS 4.0 0.3 - - - +
217B MET* 3.4 6.9 - - - +
218B GLN* 2.7 50.5 + - + +
220B VAL* 3.4 25.6 - - + -
282B GLU* 3.3 34.8 - - + +
283B ILE* 1.3 74.9 - - - +
285B VAL* 1.3 63.1 + - - +
286B ILE* 3.7 26.7 - - + +
301B ARG* 6.2 0.4 - - + -
302B THR 3.8 4.9 - - - +
250C PHE* 4.0 18.8 - - + -
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Residues in contact with VAL 285 (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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183B PHE* 3.4 25.3 - - + -
200B LEU* 3.4 32.1 - - + -
215B ILE* 4.7 10.5 - - + -
216B HIS 3.8 5.4 - - - +
217B MET* 4.2 17.7 - - + -
257B ILE* 6.3 0.7 - - + -
283B ILE* 4.3 6.5 - - + -
284B ILE* 1.3 76.1 - - - +
286B ILE* 1.3 68.7 + - - +
300B ALA 3.5 6.1 - - - +
302B THR* 3.1 37.5 + - + +
304B TYR* 3.8 17.0 - - + -
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Residues in contact with ILE 286 (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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214B THR 3.7 0.7 - - - +
215B ILE* 3.4 6.2 - - - +
216B HIS* 2.8 56.5 + - + +
218B GLN* 5.8 2.9 - - + +
284B ILE* 3.7 20.2 - - + +
285B VAL* 1.3 84.5 - - - +
287B LEU* 1.3 62.8 + - - +
288B GLU* 3.8 14.4 - - + +
299B GLN* 3.3 32.5 - - + +
300B ALA 3.7 1.3 - - - +
301B ARG* 3.7 16.6 - - + -
250C PHE* 3.6 41.1 - - + -
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Residues in contact with LEU 287 (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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181B LEU* 3.7 34.9 - - + +
183B PHE* 3.7 17.0 - - + -
202B VAL* 4.0 24.5 - - + -
210B ILE* 5.3 4.0 - - + -
213B ALA* 4.5 11.0 - - + -
214B THR 3.5 9.9 - - - +
215B ILE* 3.5 29.2 - - + -
249B ILE* 4.9 2.0 - - + -
251B LEU* 4.9 8.1 - - + -
285B VAL* 5.8 0.2 - - + -
286B ILE* 1.3 72.9 - - - +
288B GLU* 1.3 68.6 + - - +
298B THR 3.8 0.5 - - - +
299B GLN* 3.4 3.5 - - - -
300B ALA* 2.9 37.3 + - + +
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Residues in contact with GLU 288 (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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210B ILE* 4.4 2.5 - - - +
212B SER 4.6 0.2 - - - -
213B ALA* 3.4 5.9 - - - +
214B THR* 2.8 39.7 + - - +
216B HIS* 3.5 28.4 + - + -
286B ILE* 3.8 7.8 - - + +
287B LEU* 1.3 82.6 - - - +
289B GLY* 1.3 59.9 + - - +
298B THR 3.4 9.0 - - - +
299B GLN* 2.8 29.5 + - + +
211C ILE* 3.1 6.9 - - + +
212C SER* 2.6 52.2 + - - +
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Residues in contact with GLY 289 (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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210B ILE* 3.7 13.0 - - - -
211B ILE 3.6 11.2 - - - -
212B SER* 3.9 8.5 - - - -
288B GLU* 1.3 79.1 - - - +
290B VAL* 1.3 59.5 + - - -
297B THR* 3.4 9.8 - - - +
298B THR* 2.8 32.2 + - - +
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Residues in contact with VAL 290 (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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297A THR* 3.9 26.5 - - + +
210B ILE* 3.3 6.8 - - - +
211B ILE* 2.8 59.0 + - + +
212B SER* 5.0 3.1 - - - -
289B GLY* 1.3 73.7 - - - -
291B VAL* 1.3 67.8 + - - +
292B GLU 3.4 0.2 + - - -
295B GLY* 3.1 43.7 - - - +
296B ILE 3.5 6.5 - - - +
297B THR* 4.2 7.9 - - - +
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Residues in contact with VAL 291 (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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61A THR* 4.6 2.0 - - + +
297A THR 5.3 0.3 - - - +
174B ALA* 3.8 26.9 - - + -
177B ARG* 3.7 46.2 - - + +
209B MET 4.2 2.9 - - - -
210B ILE* 4.8 6.1 - - + +
290B VAL* 1.3 79.8 - - - +
292B GLU* 1.3 63.0 + - - +
293B THR* 3.2 27.8 - - + +
294B THR* 3.6 12.8 - - + +
295B GLY* 2.9 26.9 + - - -
296B ILE 3.2 5.1 + - - +
298B THR* 4.3 8.5 - - + +
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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