Contacts of the helix formed by residues 266 - 279 (chain G) in PDB entry 2QC8
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 GLY 266 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260G ALA 3.4 25.6 - - - -
261G MET* 3.5 18.3 - - - -
263G GLU 3.0 9.4 + - - -
264G GLU 3.1 1.2 + - - -
265G ASN* 1.3 74.6 - - - +
267G LEU* 1.3 63.7 + - - +
268G LYS 3.1 0.9 - - - -
269G TYR* 3.0 21.5 + - - +
270G ILE* 3.0 13.9 + - - +
333G LYS 3.2 2.8 + - - -
334G LYS* 4.1 0.2 - - - +
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Residues in contact with LEU 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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265G ASN* 2.9 1.9 + - - +
266G GLY* 1.3 75.4 - - - +
268G LYS* 1.3 62.7 + - - +
270G ILE* 3.2 27.1 + - + -
271G GLU* 3.0 50.1 + - + +
325G ILE* 4.5 11.9 - - + -
329G VAL* 4.2 12.1 - - + +
330G GLY* 4.1 15.7 - - - +
333G LYS* 3.2 43.8 + - + +
334G LYS* 4.1 0.6 - - - +
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Residues in contact with LYS 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G ASN* 3.1 17.2 + - + +
267G LEU* 1.3 77.4 - - - +
269G TYR* 1.3 82.0 + - + +
271G GLU* 3.5 9.9 + - - +
272G GLU* 3.2 48.9 + - + +
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Residues in contact with TYR 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258G THR* 5.2 0.2 - - - +
260G ALA* 3.8 39.0 - - + -
261G MET* 3.7 19.2 - - + +
264G GLU 6.0 0.7 - - - -
265G ASN 5.1 2.0 - - - -
266G GLY* 3.0 15.5 + - - +
268G LYS* 1.3 94.1 - - + +
270G ILE* 1.3 59.8 + - - +
272G GLU* 3.3 25.6 + - - +
273G ALA* 2.8 30.3 + - - +
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Residues in contact with ILE 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261G MET* 3.7 24.0 - - + -
266G GLY 3.0 14.2 + - - +
267G LEU* 3.2 26.9 + - + +
269G TYR* 1.3 76.7 - - - +
271G GLU* 1.3 57.9 + - - +
273G ALA* 3.0 5.1 + - - +
274G ILE* 2.9 38.0 + - + +
325G ILE* 4.7 4.3 - - + -
329G VAL* 3.5 30.1 - - + -
335G GLY 3.9 8.3 - - - +
336G TYR* 3.7 20.6 - - - +
337G PHE* 3.8 28.5 - - + -
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Residues in contact with GLU 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267G LEU* 3.0 45.7 + - + +
268G LYS* 3.8 7.7 - - - +
270G ILE* 1.3 75.7 - - - +
272G GLU* 1.3 57.4 + - - +
274G ILE* 3.5 10.8 + - + +
275G GLU* 3.0 27.3 + - - +
325G ILE* 4.7 14.9 - - + +
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Residues in contact with GLU 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268G LYS* 3.2 39.9 + - + +
269G TYR* 3.5 32.0 - - - +
270G ILE 3.2 0.6 - - - -
271G GLU* 1.3 72.6 - - - +
273G ALA* 1.3 64.4 + - - +
275G GLU* 3.4 9.0 + - - +
276G LYS* 3.3 35.3 + - - +
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Residues in contact with ALA 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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261G MET* 3.3 33.9 - - + -
269G TYR 2.8 6.8 + - - +
270G ILE 3.0 6.3 + - - +
272G GLU* 1.3 72.3 - - - +
274G ILE* 1.3 66.4 + - - +
276G LYS* 3.3 11.9 + - - +
277G LEU* 3.2 25.8 + - - +
337G PHE* 3.9 11.9 - - + -
359G CYS* 3.8 21.1 - - + +
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Residues in contact with ILE 274 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G ILE* 2.9 29.5 + - + +
271G GLU* 3.7 11.4 - - + +
273G ALA* 1.3 73.9 - - - +
275G GLU* 1.3 65.8 + - - +
277G LEU* 2.9 11.1 + - - +
278G SER* 2.9 21.6 + - - -
312G PHE* 4.2 15.5 - - + -
314G ALA* 4.0 24.9 - - + -
323G ILE* 4.0 26.9 - - + -
325G ILE* 3.9 29.4 - - + -
337G PHE* 4.5 8.5 - - + -
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Residues in contact with GLU 275 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271G GLU 3.0 14.5 + - - +
272G GLU* 3.4 13.9 - - - +
274G ILE* 1.3 76.3 - - - +
276G LYS* 1.3 64.0 + - + +
278G SER* 2.7 32.7 + - - -
279G LYS* 3.4 31.7 + - - +
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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 GLU* 3.3 23.8 + - - +
273G ALA* 3.6 9.9 - - - +
274G ILE 3.2 0.2 - - - -
275G GLU* 1.3 78.8 - - + +
277G LEU* 1.3 61.3 + - - +
279G LYS* 3.3 20.3 + - - +
280G ARG* 3.7 6.2 + - - +
358G THR* 3.5 35.3 - - + +
359G CYS* 3.5 18.7 + - - +
362G ASN* 2.3 37.5 + - - +
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Residues in contact with LEU 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 ALA 3.2 14.5 + - - +
274G ILE* 2.9 10.8 + - - +
276G LYS* 1.3 72.7 - - - +
278G SER* 1.3 64.8 + - - +
279G LYS 3.1 0.9 - - - -
280G ARG* 3.2 12.3 + - - +
281G HIS* 3.4 10.6 + - - -
284G HIS* 3.2 41.3 - - + +
312G PHE* 3.5 18.9 - - + -
323G ILE* 4.2 8.7 - - + -
337G PHE* 3.7 35.7 - - + -
341G ARG* 4.1 12.8 + - - +
355G LEU* 4.1 12.3 - - + -
358G THR* 3.8 11.2 - - + -
359G CYS* 3.8 12.1 - - - -
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Residues in contact with SER 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G ILE* 2.9 8.5 + - - -
275G GLU* 2.7 30.9 + - - -
277G LEU* 1.3 78.0 - - - +
279G LYS* 1.3 64.0 + - - +
280G ARG 3.3 1.3 + - - -
281G HIS* 4.2 8.1 + - - +
312G PHE* 3.6 38.0 - - - +
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Residues in contact with LYS 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G GLU* 3.4 33.0 - - + +
276G LYS* 3.3 11.5 + - - +
277G LEU 3.1 0.8 - - - -
278G SER* 1.3 88.9 + - - +
280G ARG* 1.3 67.4 + - - +
281G HIS 3.9 0.4 - - - -
364G THR* 5.6 10.9 - - + +
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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