Contacts of the helix formed by residues 259 - 277 (chain G) in PDB entry 6C3P
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 ALA 259 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257G MET 2.9 8.3 + - - +
258G ARG* 1.3 78.2 - - - +
260G LEU* 1.3 60.5 + - - +
261G THR 3.1 0.7 - - - -
262G ASN* 3.2 4.7 + - - +
263G TYR* 2.9 27.7 + - - +
1227G LEU* 5.1 13.5 - - + -
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Residues in contact with LEU 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255G ILE 5.0 2.5 - - - +
256G ALA* 4.2 27.6 + - + +
259G ALA* 1.3 77.5 - - - +
261G THR* 1.3 57.9 + - - +
263G TYR* 3.8 7.4 - - - +
264G GLN* 2.8 31.0 + - - +
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Residues in contact with THR 261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256G ALA 4.2 7.2 + - - -
258G ARG* 3.7 24.0 - - - -
259G ALA 3.1 1.2 - - - +
260G LEU* 1.3 78.7 - - - +
262G ASN* 1.3 56.7 + - - +
264G GLN* 3.3 6.2 + - - +
265G ARG* 2.9 29.5 + - - +
386G ASN* 4.9 19.5 - - - -
390G ALA* 4.7 13.8 - - - +
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Residues in contact with ASN 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258G ARG 3.6 17.3 + - - +
259G ALA* 3.2 7.7 + - - +
261G THR* 1.3 78.7 - - - +
263G TYR* 1.3 57.6 + - - +
265G ARG* 3.3 7.1 + - - +
266G LEU* 2.9 30.4 + - - +
390G ALA* 4.9 6.9 - - - +
393G THR* 4.0 26.9 - - + +
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Residues in contact with TYR 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259G ALA 2.9 16.9 + - - +
260G LEU* 3.8 8.3 - - - +
261G THR 3.3 0.2 - - - -
262G ASN* 1.3 77.4 - - - +
264G GLN* 1.3 57.4 + - - +
266G LEU* 3.3 6.5 + - - +
267G CYS* 2.9 30.0 + - - +
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Residues in contact with GLN 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260G LEU 2.8 21.7 + - - +
261G THR* 3.6 7.0 - - - +
263G TYR* 1.3 74.7 - - - +
265G ARG* 1.3 56.2 + - - +
267G CYS* 3.3 5.5 + - - +
268G GLU* 2.8 31.6 + - - +
294G ALA* 4.8 6.5 - - + +
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Residues in contact with ARG 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261G THR 2.9 16.9 + - - +
262G ASN* 3.6 8.1 - - - +
264G GLN* 1.3 76.0 - - - +
266G LEU* 1.3 58.4 + - - +
268G GLU* 3.8 4.9 - - - +
269G ALA* 2.9 30.5 + - - +
294G ALA* 4.8 8.3 - - + -
390G ALA* 4.7 14.6 - - + +
394G LYS* 4.9 19.3 + - - +
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Residues in contact with LEU 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262G ASN 2.9 15.8 + - - +
263G TYR* 3.7 7.2 - - - +
265G ARG* 1.3 74.7 - - - +
267G CYS* 1.3 59.5 + - - +
269G ALA* 3.3 7.2 + - - +
270G PHE* 2.9 27.7 + - - +
394G LYS* 5.9 2.2 - - - +
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Residues in contact with CYS 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263G TYR 2.9 17.2 + - - +
264G GLN* 3.8 7.0 - - - +
266G LEU* 1.3 77.5 - - - +
268G GLU* 1.3 58.6 + - - +
270G PHE* 3.2 9.2 + - - +
271G ASP* 2.9 26.2 + - - +
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Residues in contact with GLU 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264G GLN 2.8 18.1 + - - +
265G ARG 3.9 2.0 - - - +
267G CYS* 1.3 75.0 - - - +
269G ALA* 1.3 60.6 + - - +
271G ASP* 3.3 8.8 + - - +
272G ALA* 2.9 29.2 + - - +
290G ALA* 4.5 5.4 - - - +
293G HIS* 4.1 8.9 + - + +
294G ALA* 3.4 37.5 - - + +
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Residues in contact with ALA 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G ARG 2.9 18.2 + - - +
266G LEU* 3.6 7.0 - - - +
268G GLU* 1.3 76.1 - - - +
270G PHE* 1.3 57.2 + - - +
272G ALA* 3.4 6.9 + - - +
273G GLN* 2.9 29.5 + - - +
290G ALA* 4.5 13.6 - - + +
394G LYS* 5.0 12.1 - - - +
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Residues in contact with PHE 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266G LEU 2.9 14.5 + - - +
267G CYS* 3.3 12.8 - - - +
268G GLU 3.2 0.2 - - - -
269G ALA* 1.3 76.9 - - - +
271G ASP* 1.3 57.5 + - - +
273G GLN* 3.2 6.7 + - - +
274G VAL* 2.9 28.6 + - - +
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Residues in contact with ASP 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267G CYS 2.9 14.6 + - - +
268G GLU* 3.3 8.9 + - - +
270G PHE* 1.3 75.0 - - - +
272G ALA* 1.3 59.1 + - - +
274G VAL* 3.3 7.8 + - - +
275G ARG* 2.9 27.0 + - - +
293G HIS* 3.7 23.4 - - + -
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Residues in contact with ALA 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268G GLU 2.9 17.6 + - - +
269G ALA* 3.8 3.8 - - - +
271G ASP* 1.3 77.5 - - - +
273G GLN* 1.3 57.4 + - - +
275G ARG* 3.4 10.1 - - - +
276G LYS* 2.9 25.5 + - - +
289G GLN* 5.4 3.6 - - + -
290G ALA* 4.3 25.8 - - + +
293G HIS* 4.3 10.2 + - + +
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Residues in contact with GLN 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269G ALA 2.9 17.7 + - - +
270G PHE* 3.2 7.6 + - - +
272G ALA* 1.3 75.4 - - - +
274G VAL* 1.3 54.2 + - - +
276G LYS* 2.9 8.7 + - - +
277G ASP* 2.4 39.5 + - - +
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Residues in contact with VAL 274 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G PHE 2.9 13.3 + - - +
271G ASP* 3.6 11.4 - - - +
273G GLN* 1.3 77.5 - - - +
275G ARG* 1.3 60.9 + - - +
277G ASP* 3.2 25.6 + - - +
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Residues in contact with ARG 275 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271G ASP 2.9 14.6 + - - +
272G ALA* 3.4 12.8 - - - +
274G VAL* 1.3 77.0 - - - +
276G LYS* 1.3 60.4 + - - +
277G ASP 4.2 3.1 - - - +
293G HIS* 6.4 1.1 - - + -
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Residues in contact with LYS 276 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272G ALA 2.9 14.9 + - - +
273G GLN* 2.9 12.5 + - - +
275G ARG* 1.3 75.7 - - - +
277G ASP* 1.3 65.8 + - - +
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Residues in contact with ASP 277 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273G GLN 2.4 29.4 + - - +
274G VAL* 3.2 22.6 + - - +
275G ARG 4.2 2.5 - - - +
276G LYS* 1.3 73.7 - - - +
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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