Contacts of the helix formed by residues 262 - 279 (chain y) 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 y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248y ILE 4.6 15.0 - - - +
249y PHE* 5.3 7.0 + - - +
251y GLU 4.6 6.9 + - - +
253y TYR* 5.3 9.0 - - + +
260y MET 4.1 0.2 + - - -
261y TYR* 1.3 74.7 - - - +
263y SER* 1.3 57.8 + - - +
265y ILE* 3.8 5.9 - - - +
266y VAL* 2.9 32.6 + - - +
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Residues in contact with SER 263 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187y MET* 6.4 1.8 - - - -
261y TYR* 3.2 6.7 - - - +
262y LEU* 1.3 79.5 - - - +
264y ASN* 1.3 57.3 + - - +
266y VAL* 3.8 3.8 - - - +
267y SER* 2.9 29.5 + - - -
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Residues in contact with ASN 264 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260y MET* 4.7 11.9 - - + -
261y TYR* 3.4 13.8 + - + +
262y LEU 3.4 0.2 - - - -
263y SER* 1.3 79.5 - - - +
265y ILE* 1.3 57.8 + - - +
267y SER* 3.5 6.6 - - - -
268y ASP* 2.9 30.7 + - - +
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Residues in contact with ILE 265 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253y TYR* 6.3 2.2 - - + -
255y TYR* 4.8 18.6 - - + -
260y MET* 4.9 5.9 - - + +
261y TYR 3.1 16.8 + - - +
262y LEU* 3.8 7.4 - - - +
264y ASN* 1.3 77.4 - - - +
266y VAL* 1.3 57.7 + - - +
268y ASP* 3.4 4.8 + - - +
269y TYR* 2.9 31.1 + - - +
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Residues in contact with VAL 266 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187y MET* 5.4 12.6 - - + -
188y PHE* 5.5 8.3 - - + +
191y GLU* 4.4 8.7 - - + +
262y LEU 2.9 17.5 + - - +
263y SER* 4.0 4.5 - - - +
265y ILE* 1.3 76.1 - - - +
267y SER* 1.3 57.2 - - - +
269y TYR* 3.9 5.3 - - - +
270y THR* 2.9 31.7 + - - -
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Residues in contact with SER 267 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191y GLU* 4.8 8.9 - - - +
263y SER 2.9 19.2 + - - -
264y ASN* 3.5 8.1 - - - -
265y ILE 3.2 0.2 - - - -
266y VAL* 1.3 77.2 - - - +
268y ASP* 1.3 57.2 + - - +
270y THR* 3.4 4.1 + - - -
271y LYS* 2.9 30.9 + - - +
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Residues in contact with ASP 268 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264y ASN 2.9 16.3 + - - +
265y ILE* 3.9 4.7 - - - +
267y SER* 1.3 76.9 - - - +
269y TYR* 1.3 57.6 + - - +
271y LYS* 3.8 5.5 - - - +
272y LYS* 2.9 31.2 + - - +
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Residues in contact with TYR 269 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265y ILE 2.9 18.1 + - - +
266y VAL* 3.9 7.2 - - - +
268y ASP* 1.3 76.6 - - - +
270y THR* 1.3 57.5 + - - +
272y LYS* 3.4 2.6 + - - +
273y VAL* 2.9 29.2 + - - +
285y PRO* 4.3 20.6 - - + +
287y PHE* 6.2 4.3 - - + -
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Residues in contact with THR 270 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188y PHE* 5.6 0.7 - - - -
191y GLU* 3.9 28.3 - - - -
192y VAL* 5.0 3.1 - - - -
195y CYS* 5.5 4.2 - - - +
218y ILE* 6.2 5.4 - - - -
266y VAL 2.9 19.0 + - - -
267y SER 3.8 3.1 - - - -
269y TYR* 1.3 76.9 - - - +
271y LYS* 1.3 58.2 + - - +
273y VAL* 3.2 7.4 + - - +
274y ILE* 2.9 30.8 + - - +
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Residues in contact with LYS 271 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195y CYS* 6.1 2.2 - - - -
267y SER 2.9 18.5 + - - +
268y ASP* 3.8 6.1 - - - +
270y THR* 1.3 76.8 - - - +
272y LYS* 1.3 56.6 + - - +
274y ILE* 3.4 4.2 + - - +
275y LYS* 2.9 32.6 + - - +
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Residues in contact with LYS 272 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268y ASP 2.9 17.4 + - - +
269y TYR 3.8 3.8 - - - +
270y THR 3.3 0.2 - - - -
271y LYS* 1.3 75.7 - - - +
273y VAL* 1.3 57.4 + - - +
275y LYS* 4.2 5.1 - - - +
276y ALA* 2.9 32.7 + - - +
283y GLU 4.2 4.0 - - - +
285y PRO* 3.8 24.2 - - + -
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Residues in contact with VAL 273 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218y ILE* 5.9 7.4 - - + -
269y TYR 2.9 17.4 + - - +
270y THR* 3.6 8.5 - - - +
272y LYS* 1.3 74.6 - - - +
274y ILE* 1.3 60.4 + - - +
276y ALA* 3.4 4.8 + - - +
277y LEU* 2.9 29.9 + - - +
285y PRO* 5.1 3.5 - - + +
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Residues in contact with ILE 274 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195y CYS* 4.5 21.3 - - + -
270y THR 2.9 16.1 + - - +
271y LYS* 4.0 4.0 - - - +
273y VAL* 1.3 77.8 - - - +
275y LYS* 1.3 57.5 + - - +
277y LEU* 3.1 7.1 + - - +
278y ASN* 2.9 30.6 + - - +
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Residues in contact with LYS 275 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271y LYS 2.9 18.8 + - - +
272y LYS* 4.2 4.9 - - - +
274y ILE* 1.3 76.6 - - - +
276y ALA* 1.3 57.6 + - - +
278y ASN* 3.5 5.1 + - - +
279y GLN* 3.0 32.9 + - - +
282y GLU* 6.2 0.4 - - - -
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Residues in contact with ALA 276 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101y VAL* 5.6 0.2 - - - +
272y LYS 2.9 21.7 + - - +
273y VAL* 3.7 5.4 - - - +
275y LYS* 1.3 77.9 - - - +
277y LEU* 1.3 56.5 + - - +
279y GLN* 4.6 1.6 - - - +
280y LEU 2.9 7.6 + - - -
281y GLY* 2.6 33.7 + - - +
282y GLU* 4.4 12.1 - - - +
283y GLU 3.2 25.6 - - - +
284y ILE* 5.3 1.6 - - - -
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Residues in contact with LEU 277 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93y ARG 5.6 1.1 - - - +
97y TRP* 5.3 18.9 - - + +
98y LYS 5.9 0.2 + - - -
101y VAL* 5.1 12.7 - - + +
273y VAL 2.9 16.8 + - - +
274y ILE* 3.1 7.8 + - - +
276y ALA* 1.3 77.7 - - - +
278y ASN* 1.3 60.7 - - - +
280y LEU* 3.5 9.8 + - - +
281y GLY 5.0 0.2 - - - +
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Residues in contact with ASN 278 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93y ARG* 4.6 24.0 - - + +
274y ILE 2.9 14.5 + - - +
275y LYS* 4.1 6.1 - - - +
277y LEU* 1.3 78.0 - - - +
279y GLN* 1.3 58.2 + - - +
280y LEU* 3.3 1.8 + - - +
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Residues in contact with GLN 279 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275y LYS 3.0 19.3 + - - +
276y ALA 3.7 1.1 - - - +
278y ASN* 1.3 74.7 - - - +
280y LEU* 1.3 69.4 + - - +
281y GLY 3.6 0.2 - - - -
282y GLU* 4.5 18.5 + - + +
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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