Contacts of the helix formed by residues 278 - 287 (chain A) in PDB entry 1C5G
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 SER 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ASP* 4.8 8.3 - - - -
40A VAL* 3.9 13.7 - - - -
41A ARG* 6.6 0.7 - - - -
276A ILE 3.6 7.1 + - - -
277A LEU* 1.3 76.6 - - - +
279A ALA* 1.3 63.8 + - - +
280A GLN* 3.9 10.6 + - - +
281A LEU* 3.3 32.9 + - - +
282A ILE* 3.3 19.2 + - - +
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A HIS* 3.9 21.9 - - + +
36A SER* 4.0 13.9 - - - +
37A ASP* 3.6 36.7 + - + +
40A VAL* 4.3 6.6 - - + +
278A SER* 1.3 74.5 - - - +
280A GLN* 1.3 61.2 + - - +
282A ILE* 3.8 12.8 + - - +
283A SER* 3.3 18.0 + - - -
386A ARG* 5.3 2.8 + - - -
393A VAL* 5.0 1.8 - - + -
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Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A HIS* 4.0 21.8 + - + +
278A SER* 3.2 10.9 - - - +
279A ALA* 1.3 77.6 - - - +
281A LEU* 1.3 63.0 + - - +
282A ILE 3.3 0.4 - - - -
283A SER* 3.0 10.1 - - - -
284A HIS* 2.8 59.2 + - + +
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A PHE* 3.8 27.6 - - + -
273A LEU* 4.4 9.9 - - + -
276A ILE* 4.3 10.1 - - + +
277A LEU* 3.6 39.7 - - + +
278A SER* 3.3 24.9 + - - +
280A GLN* 1.3 78.9 - - - +
282A ILE* 1.3 55.1 + - - +
284A HIS* 3.1 13.0 + - + +
285A TRP* 2.8 50.3 + - + +
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Residues in contact with ILE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 4.6 12.6 - - + -
259A PHE* 4.6 10.2 - - + -
277A LEU* 4.4 13.2 - - + -
278A SER 3.3 17.0 + - - +
279A ALA* 3.9 12.6 - - - +
280A GLN 3.3 0.2 - - - -
281A LEU* 1.3 76.0 - - - +
283A SER* 1.3 64.9 + - - +
285A TRP* 3.2 33.7 + - + +
286A LYS* 3.2 18.9 + - - +
384A VAL* 4.2 28.9 - - + -
386A ARG* 3.9 28.6 - - - +
393A VAL* 4.7 8.1 - - + -
396A MET* 5.5 2.5 - - - -
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Residues in contact with SER 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A HIS* 6.0 1.6 - - - -
279A ALA 3.3 13.1 + - - -
280A GLN* 3.0 19.5 + - - -
282A ILE* 1.3 78.6 - - - +
284A HIS* 1.3 67.4 + - - +
286A LYS* 3.1 16.8 + - - +
287A GLY* 3.2 9.4 + - - -
386A ARG* 4.0 21.3 + - - +
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Residues in contact with HIS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A GLN* 2.8 50.0 + - + -
281A LEU* 3.5 13.9 - - + +
283A SER* 1.3 79.6 + - - +
285A TRP* 1.3 67.4 + - + +
287A GLY* 3.1 13.0 + - - +
288A ASN* 3.3 24.7 + - - +
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Residues in contact with TRP 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A THR* 4.1 6.5 - - + +
236A PHE* 3.8 26.3 - + - -
246A ILE* 3.5 45.1 - - + +
259A PHE* 4.3 14.1 - + + -
261A ALA* 4.3 8.1 - - + -
273A LEU* 4.1 22.4 - - + -
277A LEU* 3.8 17.0 - - + -
281A LEU* 2.8 47.9 + - + +
282A ILE* 3.3 36.3 - - + +
284A HIS* 1.3 75.9 - - + +
286A LYS* 1.3 64.3 + - - +
288A ASN* 3.1 15.6 + - - +
289A MET* 3.2 27.1 - - + +
382A LEU* 4.5 3.6 - - + -
384A VAL* 4.9 8.3 - - + -
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Residues in contact with LYS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ASN* 4.2 9.1 - - - +
248A GLU* 3.0 36.8 + - - +
259A PHE* 3.3 26.2 - - + -
282A ILE 3.2 6.4 + - - +
283A SER 3.1 10.9 + - - +
285A TRP* 1.3 80.3 - - - +
287A GLY* 1.3 57.2 + - - +
288A ASN 3.0 5.5 + - - -
289A MET* 3.5 18.5 + - - +
386A ARG* 4.2 12.3 - - - +
388A ASN* 3.7 22.4 - - - +
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Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A SER 3.2 6.2 + - - -
284A HIS* 3.1 9.0 + - - -
286A LYS* 1.3 77.5 - - - +
288A ASN* 1.3 68.6 + - - +
289A MET 3.8 0.4 - - - -
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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