Contacts of the strand formed by residues 279 - 288 (chain B) in PDB entry 1S9C
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 ILE 279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247B ALA* 3.1 21.0 - - + +
248B LYS* 3.2 18.5 + - - +
270B GLN* 3.3 28.5 - - + +
271B THR 3.5 5.2 - - - +
272B LYS* 3.9 23.8 - - + -
277B GLY 4.5 2.5 - - - +
278B ASP* 1.3 72.7 - - - +
280B VAL* 1.3 60.8 + - - +
281B ILE 3.6 21.5 - - - +
282B SER* 4.0 17.9 - - - -
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B THR* 3.9 10.1 - - + -
246B PHE* 3.7 3.8 - - - +
247B ALA* 2.8 23.3 + - - -
248B LYS* 3.3 23.4 - - + +
249B PRO 3.6 5.6 - - - +
250B VAL* 3.3 33.4 - - + -
256B LEU* 4.7 0.4 - - + -
271B THR* 2.8 38.9 + - + +
272B LYS* 4.2 3.4 - - - +
273B VAL* 3.5 18.6 - - + -
278B ASP* 4.1 6.1 - - + +
279B ILE* 1.3 75.3 - - - +
281B ILE* 1.3 66.5 + - + +
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Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B THR* 3.7 17.7 - - + +
220B PHE* 3.6 39.7 - - + +
223B SER* 4.6 1.1 - - - +
244B ALA* 3.8 22.4 - - + -
245B ARG 3.3 10.8 - - - +
246B PHE* 4.2 13.9 - - + -
269B PHE* 4.0 17.0 - - + -
270B GLN* 3.5 8.4 - - - +
271B THR* 2.9 38.6 + - - +
279B ILE* 3.6 3.2 - - - +
280B VAL* 1.3 93.8 - - + +
282B SER* 1.3 62.4 + - - +
284B ALA* 4.1 4.5 - - + -
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ARG* 2.8 44.9 + - - +
247B ALA* 4.9 7.6 - - - +
270B GLN* 4.4 9.9 - - - +
279B ILE* 4.0 16.2 - - - -
281B ILE* 1.3 76.1 - - - +
283B ASN* 1.3 87.0 + - - +
284B ALA* 3.0 5.3 + - - -
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Residues in contact with ASN 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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164B ALA* 3.6 16.9 - - + +
165B VAL 2.7 44.8 + - - +
166B ALA* 3.2 23.1 - - - +
167B ILE* 4.2 16.9 + - - +
243B LYS* 4.3 1.9 - - - +
244B ALA* 4.8 0.5 - - - -
245B ARG* 3.6 21.9 - - + +
269B PHE 4.4 0.6 + - - -
282B SER* 1.3 96.8 + - - +
284B ALA* 1.3 57.8 + - - +
285B TYR* 4.7 1.0 - - - -
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Residues in contact with ALA 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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165B VAL 4.6 1.8 - - - +
167B ILE* 5.2 1.4 - - - +
243B LYS 3.0 16.4 - - - +
244B ALA* 3.6 12.6 - - + -
268B HIS* 3.5 6.8 + - - +
269B PHE* 2.9 58.9 + - + +
281B ILE* 4.1 3.8 - - + -
282B SER 3.1 4.2 - - - +
283B ASN* 1.3 79.7 - - - +
285B TYR* 1.3 67.1 + - - +
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Residues in contact with TYR 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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93B TYR* 4.1 14.2 - - - -
162B LYS* 5.7 1.4 - - - +
163B VAL 4.1 5.7 + - - -
165B VAL* 3.5 36.8 - - + -
241B ALA* 4.8 4.7 - - + +
242B VAL* 3.2 6.4 - - - +
243B LYS* 2.9 60.8 + - + +
266B ARG* 3.2 50.6 + - + -
267B ILE 3.2 14.8 - - - +
268B HIS* 4.1 5.8 - - - +
269B PHE* 3.5 5.2 - - - -
284B ALA* 1.3 78.7 - - - +
286B VAL* 1.3 69.3 + - - +
287B ASP* 3.2 17.9 + - - -
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Residues in contact with VAL 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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224B ALA* 6.0 1.3 - - - -
227B VAL* 3.1 38.1 - - + -
239B PHE* 3.8 28.7 - - + -
241B ALA 3.0 13.2 - - - +
242B VAL* 4.1 8.3 - - + -
265B ASN 3.8 0.2 - - - +
266B ARG* 3.7 0.5 - - - -
267B ILE* 3.0 36.8 + - + +
269B PHE* 4.3 4.0 - - + -
285B TYR* 1.3 80.0 - - - +
287B ASP* 1.3 66.4 + - - +
288B LEU* 3.8 20.6 + - + -
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Residues in contact with ASP 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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240B LYS* 3.0 35.3 + - + +
241B ALA* 2.7 25.4 + - + +
265B ASN* 3.5 4.1 - - + +
266B ARG* 2.8 54.2 + - - +
285B TYR* 3.2 11.2 + - - -
286B VAL* 1.3 72.4 - - - +
288B LEU* 1.3 64.7 + - - +
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Residues in contact with LEU 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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227B VAL* 5.2 4.7 - - + -
228B LEU* 5.6 0.4 - - - -
231B PHE* 3.1 33.4 - - + +
232B ALA* 3.9 15.9 - - + -
238B ARG* 3.1 19.5 - - + +
239B PHE* 4.2 11.4 - - + -
240B LYS* 4.4 11.3 + - - +
265B ASN* 2.7 36.3 + - - +
267B ILE* 3.8 28.5 - - + -
286B VAL* 3.9 18.2 - - + +
287B ASP* 1.3 81.0 - - - +
289B ALA* 1.3 67.7 + - - +
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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