Contacts of the helix formed by residues 262 - 279 (chain Z) in PDB entry 6QXT
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 LEU 262 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248Z ILE* 4.5 16.2 - - + +
249Z PHE* 5.3 7.6 + - - +
251Z GLU 4.5 6.9 + - - +
253Z TYR* 5.3 7.2 - - + +
260Z MET 4.1 0.2 + - - -
261Z TYR* 1.3 74.1 - - - +
263Z SER* 1.3 58.2 + - - +
265Z ILE* 3.3 6.6 + - - +
266Z VAL* 2.9 31.1 + - - +
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Residues in contact with SER 263 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Z ASP* 6.0 6.5 - - - -
261Z TYR* 3.3 4.6 - - - +
262Z LEU* 1.3 79.0 - - - +
264Z ASN* 1.3 58.2 + - - +
266Z VAL* 3.4 5.7 + - - +
267Z SER* 2.9 30.1 + - - -
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Residues in contact with ASN 264 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260Z MET* 4.5 13.2 - - + -
261Z TYR* 3.4 15.6 + - + +
262Z LEU 3.3 0.6 - - - -
263Z SER* 1.3 76.2 - - - +
265Z ILE* 1.3 60.3 + - - +
267Z SER* 3.9 5.4 - - - -
268Z ASP* 2.9 33.1 + - - +
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Residues in contact with ILE 265 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253Z TYR* 6.1 5.6 - - + +
255Z TYR* 5.3 11.9 - - + -
260Z MET* 4.9 9.1 - - + +
261Z TYR 3.0 17.0 + - - +
262Z LEU* 3.3 7.6 + - - +
264Z ASN* 1.3 76.4 - - - +
266Z VAL* 1.3 58.4 + - - +
268Z ASP* 4.9 2.7 - - - -
269Z TYR* 2.9 32.4 + - - +
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Residues in contact with VAL 266 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187Z MET* 5.8 8.1 - - + +
188Z PHE* 5.8 8.1 - - + -
191Z GLU* 4.7 7.5 - - + +
262Z LEU 2.9 18.0 + - - +
263Z SER* 3.8 5.8 - - - +
265Z ILE* 1.3 75.3 - - - +
267Z SER* 1.3 58.8 + - - +
269Z TYR* 3.9 4.1 - - - +
270Z THR* 2.9 31.7 + - - -
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Residues in contact with SER 267 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191Z GLU* 5.0 8.3 - - - -
263Z SER 2.9 18.5 + - - -
264Z ASN* 3.9 6.1 - - - -
266Z VAL* 1.3 77.9 - - - +
268Z ASP* 1.3 58.1 + - - +
270Z THR* 3.8 4.6 - - - -
271Z LYS* 2.9 28.8 + - - +
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Residues in contact with ASP 268 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264Z ASN 2.9 17.9 + - - +
265Z ILE* 4.4 2.9 - - - +
267Z SER* 1.3 77.8 - - - +
269Z TYR* 1.3 57.4 + - - +
271Z LYS* 3.3 7.6 + - - +
272Z LYS* 2.9 30.1 + - - +
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Residues in contact with TYR 269 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265Z ILE 2.9 22.2 + - - +
266Z VAL* 3.9 4.9 - - - +
268Z ASP* 1.3 77.6 - - - +
270Z THR* 1.3 58.2 + - - +
272Z LYS* 3.3 6.3 + - - +
273Z VAL* 2.9 27.9 + - - +
285Z PRO* 4.7 14.2 - - + +
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Residues in contact with THR 270 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188Z PHE 5.9 0.4 - - - -
191Z GLU* 4.2 25.4 - - - -
192Z VAL* 5.4 1.6 - - - -
195Z CYS* 5.6 4.9 - - - +
218Z ILE* 5.9 8.1 - - - -
266Z VAL 2.9 19.5 + - - -
267Z SER 3.8 2.9 - - - -
269Z TYR* 1.3 76.7 - - - +
271Z LYS* 1.3 57.4 + - - +
273Z VAL* 3.3 7.1 + - - +
274Z ILE* 2.9 31.2 + - - +
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Residues in contact with LYS 271 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195Z CYS* 6.4 1.1 - - - -
267Z SER 2.9 18.1 + - - +
268Z ASP* 3.6 8.7 - - - +
270Z THR* 1.3 77.9 - - - +
272Z LYS* 1.3 56.6 + - - +
274Z ILE* 3.4 4.9 + - - +
275Z LYS* 2.9 31.1 + - - +
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Residues in contact with LYS 272 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268Z ASP 2.9 17.1 + - - +
269Z TYR 3.8 3.8 - - - +
271Z LYS* 1.3 77.1 - - - +
273Z VAL* 1.3 57.1 + - - +
275Z LYS* 4.0 5.7 - - - +
276Z ALA* 2.9 30.5 + - - +
283Z GLU 4.3 4.1 - - - +
285Z PRO* 4.0 25.1 - - + -
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Residues in contact with VAL 273 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218Z ILE* 6.0 5.6 - - + -
269Z TYR 2.9 17.7 + - - +
270Z THR* 3.6 8.5 - - - +
271Z LYS 3.2 0.2 - - - -
272Z LYS* 1.3 75.0 - - - +
274Z ILE* 1.3 60.4 + - - +
276Z ALA* 3.3 6.0 + - - +
277Z LEU* 2.9 28.9 + - - +
285Z PRO* 5.5 1.5 - - + +
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Residues in contact with ILE 274 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195Z CYS* 4.6 19.1 - - + -
270Z THR 2.9 17.1 + - - +
271Z LYS* 4.0 4.5 - - - +
273Z VAL* 1.3 75.5 - - - +
275Z LYS* 1.3 58.8 + - - +
277Z LEU* 3.2 7.4 + - - +
278Z ASN* 2.9 30.4 + - - +
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Residues in contact with LYS 275 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271Z LYS 2.9 19.0 + - - +
272Z LYS* 4.0 6.5 - - - +
274Z ILE* 1.3 76.9 - - - +
276Z ALA* 1.3 57.4 + - - +
278Z ASN* 3.9 4.9 - - - +
279Z GLN* 2.9 32.7 + - - +
282Z GLU* 6.1 0.2 - - - -
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Residues in contact with ALA 276 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105Z VAL* 6.3 3.4 - - + -
272Z LYS 2.9 20.7 + - - +
273Z VAL* 3.7 6.1 - - - +
274Z ILE 3.2 0.2 - - - -
275Z LYS* 1.3 76.2 - - - +
277Z LEU* 1.3 57.6 + - - +
279Z GLN* 4.7 0.2 - - - -
280Z LEU 2.9 7.1 + - - -
281Z GLY* 2.6 38.5 + - - +
282Z GLU* 4.4 7.6 - - - +
283Z GLU 3.3 24.9 - - - +
284Z ILE* 5.3 2.0 - - - -
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Residues in contact with LEU 277 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97Z TRP* 5.7 5.4 - - - +
101Z VAL* 5.1 11.2 - - + +
105Z VAL* 6.1 6.7 - - + -
273Z VAL 2.9 16.5 + - - +
274Z ILE* 3.6 7.2 - - - +
276Z ALA* 1.3 77.4 - - - +
278Z ASN* 1.3 61.0 + - - +
280Z LEU* 3.5 10.0 + - - +
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Residues in contact with ASN 278 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93Z ARG* 5.2 14.6 - - + -
274Z ILE 2.9 16.1 + - - +
275Z LYS* 4.1 5.2 - - - +
277Z LEU* 1.3 78.5 - - - +
279Z GLN* 1.3 58.1 + - - +
280Z LEU* 3.3 2.1 + - - +
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Residues in contact with GLN 279 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275Z LYS 2.9 19.6 + - - +
276Z ALA 4.5 0.4 - - - +
278Z ASN* 1.3 74.6 - - - +
280Z LEU* 1.3 72.0 + - - +
281Z GLY 3.6 0.2 - - - -
282Z GLU* 4.3 21.5 + - + +
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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