Contacts of the helix formed by residues 279 - 293 (chain B) in PDB entry 3CS9
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 279 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B LEU* 4.0 23.4 - - + +
277B THR* 3.3 11.9 - - + +
278B MET* 1.3 77.3 - - + +
280B VAL* 1.3 63.2 + - - +
281B GLU 3.2 2.9 - - - -
282B GLU* 3.3 15.7 + - + +
283B PHE* 3.1 23.0 + - - +
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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
----------------------------------------------------------
273B LEU* 3.6 16.6 - - + -
277B THR* 3.6 32.1 - - - +
278B MET 3.2 1.0 - - - -
279B GLU* 1.3 78.0 - - - +
281B GLU* 1.3 56.8 + - - +
283B PHE* 3.6 2.4 + - + +
284B LEU* 3.0 37.8 + - + +
311B PHE* 3.5 43.1 - - + -
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B MET 3.6 12.1 + - - +
279B GLU 3.2 0.2 - - - -
280B VAL* 1.3 79.1 - - - +
282B GLU* 1.3 57.2 + - + +
284B LEU* 3.2 16.5 - - - +
285B LYS* 2.8 58.8 + - + +
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Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B MET 5.3 1.1 - - - +
279B GLU* 3.3 19.6 + - + +
281B GLU* 1.3 80.6 - - + +
283B PHE* 1.3 60.2 + - - +
285B LYS* 2.6 46.0 + - - +
286B GLU* 2.8 30.3 + - - +
600B NIL 5.4 0.3 - - - +
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Residues in contact with PHE 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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271B LYS* 3.4 44.0 - - + -
272B THR 3.9 5.2 - - - -
273B LEU* 3.9 28.3 - - + -
279B GLU 3.1 13.8 + - - +
280B VAL* 3.7 5.2 - - + +
282B GLU* 1.3 78.1 - - - +
284B LEU* 1.3 63.6 + - + +
286B GLU* 3.4 8.6 + - - +
287B ALA* 3.3 17.0 + - - +
306B THR* 5.4 6.5 - - + -
311B PHE* 3.4 47.3 - + + -
312B TYR 3.9 3.1 - - - -
313B ILE* 3.4 38.5 - - + +
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B VAL* 3.0 26.8 + - + +
281B GLU* 3.2 14.6 - - - +
283B PHE* 1.3 79.2 - - + +
285B LYS* 1.3 63.8 + - - +
287B ALA* 3.4 6.8 + - + +
288B ALA* 3.1 22.2 + - - +
306B THR* 4.3 30.7 - - + +
311B PHE* 6.5 0.4 - - + -
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Residues in contact with LYS 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLU* 2.8 41.9 + - + +
282B GLU* 2.6 47.8 + - - +
284B LEU* 1.3 72.6 - - - +
286B GLU* 1.3 65.6 - - - +
288B ALA* 3.3 15.2 + - - +
289B VAL* 3.3 17.5 + - + +
600B NIL 4.0 11.0 - - + -
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Residues in contact with GLU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LYS* 3.5 27.6 + - - +
282B GLU 2.8 15.0 + - - +
283B PHE* 3.7 10.0 - - - +
284B LEU 3.2 0.2 - - - -
285B LYS* 1.3 76.5 - - - +
287B ALA* 1.3 61.3 + - - +
289B VAL* 3.3 5.5 + - - +
290B MET* 3.2 32.3 + - - +
313B ILE* 4.2 13.4 - - + +
381B ASP 4.3 3.0 - - - +
600B NIL 3.0 69.1 + - + +
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Residues in contact with ALA 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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283B PHE* 3.3 10.4 + - + +
284B LEU* 3.8 10.5 - - + +
285B LYS 3.2 0.4 - - - -
286B GLU* 1.3 76.1 - - - +
288B ALA* 1.3 65.4 - - - +
290B MET* 3.3 9.5 + - - +
291B LYS* 3.0 35.0 + - - +
301B LEU* 4.3 1.2 - - + +
304B VAL* 4.0 27.1 - - + -
306B THR* 5.6 5.2 - - + -
313B ILE* 4.0 13.7 - - + -
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Residues in contact with ALA 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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284B LEU 3.1 13.9 + - - +
285B LYS* 3.3 11.9 + - - +
287B ALA* 1.3 78.5 - - - +
289B VAL* 1.3 67.0 + - + +
291B LYS* 3.2 21.3 + - - +
292B GLU* 3.5 13.0 + - - +
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Residues in contact with VAL 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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285B LYS 3.3 5.2 + - - +
286B GLU 3.6 7.0 - - - +
287B ALA 3.3 0.6 - - - -
288B ALA* 1.3 76.9 - - + +
290B MET* 1.3 55.8 + - - +
292B GLU* 2.7 36.8 + - - +
293B ILE* 3.3 27.1 + - + +
359B PHE* 4.7 14.1 - - + -
600B NIL 3.6 48.7 - - + +
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Residues in contact with MET 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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286B GLU* 3.2 21.9 + - - +
287B ALA* 3.6 8.1 - - - +
289B VAL* 1.3 77.0 - - + +
291B LYS* 1.3 59.8 + - - +
293B ILE* 3.1 32.0 - - + +
299B VAL* 4.3 12.8 - - + +
300B GLN* 4.9 1.7 + - - -
301B LEU* 4.2 32.7 - - + +
313B ILE* 4.1 11.0 - - - -
315B THR* 3.8 28.3 - - + -
600B NIL 3.5 54.5 - - + +
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Residues in contact with LYS 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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233B ASP* 3.0 35.2 + - - +
235B TRP* 3.4 49.6 + - + +
287B ALA* 3.0 33.5 + - - +
288B ALA* 3.2 12.9 + - - +
290B MET* 1.3 75.0 - - - +
292B GLU* 1.3 65.1 + - + +
293B ILE 4.7 0.8 - - - -
301B LEU* 3.4 15.0 - - + -
304B VAL* 4.5 12.1 - - - +
306B THR* 5.8 0.6 + - - -
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Residues in contact with GLU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ALA 3.8 13.0 - - - +
289B VAL* 2.7 20.1 + - - +
291B LYS* 1.3 78.9 - - - +
293B ILE* 1.3 62.9 + - + +
294B LYS* 3.9 1.6 + - - +
353B TYR* 3.6 8.7 + - - -
357B LYS* 5.7 2.3 - - - +
359B PHE* 4.5 16.3 - - + -
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Residues in contact with ILE 293 (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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289B VAL* 3.6 17.9 - - + +
290B MET* 3.1 29.0 - - + +
291B LYS 4.7 1.1 - - - -
292B GLU* 1.3 79.3 - - - +
294B LYS* 1.3 62.2 + - - +
295B HIS 4.3 0.2 - - - -
298B LEU* 4.5 12.3 - - + -
299B VAL 5.6 5.6 - - - +
300B GLN* 4.1 9.4 + - - +
353B TYR* 3.5 15.9 - - + +
354B LEU* 4.5 6.5 - - + -
357B LYS* 5.8 0.7 - - + -
359B PHE* 3.6 37.0 - - + -
600B NIL 3.3 43.3 - - + -
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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