Contacts of the helix formed by residues 275 - 286 (chain B) in PDB entry 3C6G
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 HIS 275 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B PHE* 3.5 18.4 - - - -
193B LEU 4.5 0.7 - - - +
194B ILE 3.3 15.0 - - - +
195B ILE 3.4 8.4 + - - +
196B PHE 3.1 25.1 + - - -
197B GLY* 3.5 15.3 - - - +
264B ALA* 3.0 25.0 + - + -
274B GLN* 1.3 88.3 - - + +
276B PHE* 1.3 68.1 + - - +
277B VAL* 3.4 13.3 + - + -
278B ASP* 3.1 44.7 + - - +
279B ALA 2.9 18.4 + - - -
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Residues in contact with PHE 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 6.0 0.4 - - + -
136B HIS* 5.4 3.1 - + - -
139B LEU* 3.9 21.3 - - + -
140B ALA* 3.9 19.5 - - + -
143B SER* 3.5 24.0 - - - -
144B PHE* 5.1 2.2 - + - -
147B PHE* 3.9 4.7 - - - -
194B ILE* 3.0 12.7 + - + +
195B ILE* 3.5 25.5 + - + -
275B HIS* 1.3 71.7 - - - +
277B VAL* 1.3 66.9 + - - +
279B ALA* 3.1 7.1 + - - +
280B TYR* 2.9 41.4 + + - +
300B LEU* 4.2 0.7 - - + -
303B SER* 4.0 20.2 - - - -
304B VAL* 3.8 29.4 - - + -
307B LEU* 4.0 20.4 - - + -
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ILE* 3.3 23.0 + - + +
196B PHE* 4.2 20.9 - - + -
261B ILE* 3.6 44.2 - - + +
264B ALA* 4.5 4.0 - - + +
265B SER* 4.3 5.4 - - - -
275B HIS* 3.3 12.2 - - + +
276B PHE* 1.3 75.3 - - - +
278B ASP* 1.3 61.9 + - - +
280B TYR* 3.2 3.6 + - - +
281B LEU* 3.1 36.3 + - + +
300B LEU* 4.3 11.4 - - + -
304B VAL* 4.5 6.3 - - + -
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Residues in contact with ASP 278 (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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264B ALA 3.9 4.9 - - - +
265B SER* 4.3 3.6 - - - -
267B ASN 5.2 0.7 - - - +
268B ARG* 3.5 39.3 + - + +
269B LYS 5.0 0.3 + - - -
272B LEU 4.7 0.9 - - - +
273B PRO* 3.7 10.1 - - + +
274B GLN* 3.1 40.4 + - - +
275B HIS* 3.1 31.5 + - - +
277B VAL* 1.3 72.3 - - - +
279B ALA* 1.3 66.3 + - - +
280B TYR 3.0 0.5 + - - -
281B LEU* 3.2 7.9 + - - +
282B ASP* 3.0 25.4 + - - +
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 3.7 22.8 - - + +
143B SER* 3.9 3.1 - - - +
147B PHE* 3.9 20.6 - - + -
273B PRO* 3.8 11.3 - - + +
275B HIS 2.9 12.8 + - - +
276B PHE 3.1 8.5 + - - +
278B ASP* 1.3 75.7 - - - +
280B TYR* 1.3 62.7 + - - +
282B ASP* 3.4 7.1 - - - +
283B GLU* 3.3 23.6 + - - +
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Residues in contact with TYR 280 (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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136B HIS* 2.7 41.1 + + - -
139B LEU* 3.7 22.2 - - + +
276B PHE* 2.9 21.0 + + - +
277B VAL 3.5 8.3 - - - +
278B ASP 3.1 0.2 - - - -
279B ALA* 1.3 73.6 - - - +
281B LEU* 1.3 58.4 + - - +
283B GLU* 2.7 27.2 + - - +
284B MET* 3.0 18.4 + - + -
295B PHE* 3.3 16.1 - + + -
296B SER 3.0 44.7 + - - -
299B ASN* 3.1 8.8 - - - +
300B LEU* 3.5 41.5 - - + -
303B SER* 3.9 3.1 - - - -
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Residues in contact with LEU 281 (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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261B ILE* 5.4 1.1 - - + +
265B SER* 3.5 33.7 - - - +
268B ARG* 3.2 38.1 + - - +
277B VAL* 3.1 25.8 + - + +
278B ASP* 3.9 1.6 - - - +
280B TYR* 1.3 76.8 - - - +
282B ASP* 1.3 61.4 + - - +
284B MET* 3.4 22.2 + - + +
285B ASP* 3.1 21.3 + - - -
297B LYS* 6.4 2.7 - - + -
300B LEU* 4.2 17.3 - - + -
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Residues in contact with ASP 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ARG* 2.8 25.0 + - - +
271B GLN* 3.0 40.8 + - + +
273B PRO* 3.8 23.6 - - - +
278B ASP* 3.0 15.0 + - - +
279B ALA* 3.4 12.4 - - - +
281B LEU* 1.3 75.0 - - - +
283B GLU* 1.3 58.1 + - + +
285B ASP* 3.0 7.6 + - - +
286B GLN* 2.9 40.2 + - - +
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Residues in contact with GLU 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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139B LEU* 4.1 18.8 - - + +
279B ALA 3.3 14.5 - - - +
280B TYR 2.7 13.4 + - - +
282B ASP* 1.3 77.6 - - + +
284B MET* 1.3 59.9 + - - +
286B GLN* 3.3 25.7 + - - +
287B GLY* 3.2 17.7 + - - -
293B SER* 4.7 0.9 + - - -
295B PHE* 3.8 51.4 - - + -
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Residues in contact with MET 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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280B TYR* 3.0 22.4 + - + +
281B LEU* 3.5 26.5 - - - +
283B GLU* 1.3 77.6 - - - +
285B ASP* 1.3 59.6 + - - +
287B GLY* 3.2 6.0 + - - -
288B LYS* 3.1 27.1 + - - +
293B SER* 5.3 1.8 - - - -
295B PHE* 3.9 27.1 - - + +
296B SER* 3.8 22.7 - - - -
297B LYS* 3.9 20.4 - - + +
300B LEU* 5.7 0.9 - - - -
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Residues in contact with ASP 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ARG* 3.1 30.6 + - - +
270B PRO* 4.9 5.0 - - - +
271B GLN* 5.9 5.6 - - + +
281B LEU 3.1 9.9 + - - +
282B ASP* 3.0 10.1 + - - +
284B MET* 1.3 73.9 - - - +
286B GLN* 1.3 57.0 + - + +
287B GLY 3.0 9.2 + - - -
288B LYS* 3.4 41.1 + - + +
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Residues in contact with GLN 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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271B GLN* 5.2 16.4 - - + +
282B ASP* 2.9 28.9 + - - +
283B GLU* 3.3 33.3 + - - +
285B ASP* 1.3 70.7 - - + +
287B GLY* 1.3 55.1 + - - +
288B LYS 3.9 0.4 - - - -
289B ASN* 6.0 0.7 - - - +
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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