Contacts of the helix formed by residues 262 - 279 (chain J) in PDB entry 6QY3
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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248J ILE* 4.5 16.2 - - + +
249J PHE* 5.3 7.0 + - - -
251J GLU 4.5 6.3 + - - +
253J TYR* 5.2 7.0 - - + +
260J MET 4.0 0.2 + - - -
261J TYR* 1.3 74.5 - - - +
263J SER* 1.3 57.6 + - - +
265J ILE* 3.3 6.0 + - - +
266J VAL* 2.9 30.9 + - - +
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Residues in contact with SER 263 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J GLY 5.9 2.5 - - - -
39J ASP* 6.1 4.9 - - - -
261J TYR* 3.3 5.6 - - - +
262J LEU* 1.3 79.4 - - - +
264J ASN* 1.3 57.8 + - - +
266J VAL* 3.4 6.5 + - - +
267J SER* 2.9 29.9 + - - -
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Residues in contact with ASN 264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260J MET* 4.5 14.1 - - + -
261J TYR* 3.4 15.8 + - + +
262J LEU 3.3 0.4 - - - -
263J SER* 1.3 76.1 - - - +
265J ILE* 1.3 60.0 + - - +
267J SER* 3.9 5.4 - - - -
268J ASP* 2.9 32.4 + - - +
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Residues in contact with ILE 265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253J TYR* 6.1 5.2 - - + +
255J TYR* 5.3 11.7 - - + -
260J MET* 4.9 8.0 - - + +
261J TYR 3.0 17.7 + - - +
262J LEU* 3.7 7.0 - - - +
264J ASN* 1.3 75.8 - - - +
266J VAL* 1.3 58.0 + - - +
268J ASP* 4.4 3.1 - - - +
269J TYR* 2.9 32.6 + - - +
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Residues in contact with VAL 266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187J MET* 5.8 8.1 - - + +
188J PHE* 5.8 8.1 - - + -
191J GLU* 4.7 7.5 - - + +
262J LEU 2.9 17.6 + - - +
263J SER* 3.8 5.8 - - - +
265J ILE* 1.3 76.1 - - - +
267J SER* 1.3 59.7 + - - +
269J TYR* 3.9 3.8 - - - +
270J THR* 2.9 31.5 + - - -
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Residues in contact with SER 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191J GLU* 5.0 8.5 - - - -
263J SER 2.9 18.3 + - - -
264J ASN* 3.9 5.8 - - - -
266J VAL* 1.3 76.7 - - - +
268J ASP* 1.3 58.9 + - - +
270J THR* 3.8 4.0 - - - -
271J LYS* 2.9 29.6 + - - +
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Residues in contact with ASP 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264J ASN 2.9 18.1 + - - +
265J ILE* 4.4 3.1 - - - +
267J SER* 1.3 76.0 - - - +
269J TYR* 1.3 58.3 + - - +
271J LYS* 3.6 7.0 - - - +
272J LYS* 2.9 30.7 + - - +
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Residues in contact with TYR 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265J ILE 2.9 22.2 + - - +
266J VAL* 3.9 4.9 - - - +
268J ASP* 1.3 79.7 - - - +
270J THR* 1.3 57.9 + - - +
272J LYS* 3.4 6.0 + - - +
273J VAL* 2.9 29.0 + - - +
285J PRO* 4.7 13.6 - - + +
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Residues in contact with THR 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191J GLU* 4.2 25.1 - - - -
192J VAL* 5.4 1.6 - - - -
195J CYS* 5.6 3.8 - - - +
218J ILE* 5.9 8.1 - - - -
266J VAL 2.9 19.0 + - - -
267J SER 3.8 3.4 - - - -
269J TYR* 1.3 76.3 - - - +
271J LYS* 1.3 58.7 + - - +
273J VAL* 3.6 6.9 - - - +
274J ILE* 2.9 30.7 + - - +
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Residues in contact with LYS 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267J SER 2.9 17.2 + - - +
268J ASP* 3.6 8.5 - - - +
269J TYR 3.2 0.2 - - - -
270J THR* 1.3 77.0 - - - +
272J LYS* 1.3 57.9 + - - +
274J ILE* 3.4 4.9 + - - +
275J LYS* 2.9 31.1 + - - +
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Residues in contact with LYS 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268J ASP 2.9 17.9 + - - +
269J TYR 3.8 3.8 - - - +
271J LYS* 1.3 76.4 - - - +
273J VAL* 1.3 56.9 + - - +
275J LYS* 4.0 5.2 - - - +
276J ALA* 2.9 30.3 + - - +
283J GLU 4.3 4.8 - - - +
285J PRO* 4.0 24.0 - - + -
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Residues in contact with VAL 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218J ILE* 6.0 5.8 - - + -
269J TYR 2.9 17.9 + - - +
270J THR* 3.6 8.5 - - - +
271J LYS 3.2 0.2 - - - -
272J LYS* 1.3 75.4 - - - +
274J ILE* 1.3 59.7 + - - +
276J ALA* 3.3 5.8 + - - +
277J LEU* 2.9 28.8 + - - +
285J PRO* 5.5 2.0 - - + +
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Residues in contact with ILE 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195J CYS* 4.7 18.8 - - + -
270J THR 2.9 16.5 + - - +
271J LYS* 4.0 5.4 - - - +
273J VAL* 1.3 76.0 - - - +
275J LYS* 1.3 58.2 + - - +
277J LEU* 3.2 7.4 + - - +
278J ASN* 2.9 30.3 + - - +
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Residues in contact with LYS 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271J LYS 2.9 18.6 + - - +
272J LYS* 4.0 6.3 - - - +
274J ILE* 1.3 76.6 - - - +
276J ALA* 1.3 57.4 + - - +
278J ASN* 4.0 4.5 - - - +
279J GLN* 2.9 33.3 + - - +
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Residues in contact with ALA 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272J LYS 2.9 21.3 + - - +
273J VAL* 3.7 6.1 - - - +
275J LYS* 1.3 75.8 - - - +
277J LEU* 1.3 58.1 + - - +
279J GLN* 4.5 0.9 - - - +
280J LEU 3.0 7.1 + - - -
281J GLY* 2.6 38.5 + - - +
282J GLU* 4.4 7.0 - - - +
283J GLU 3.3 24.7 - - - +
284J ILE* 5.3 1.6 - - - -
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Residues in contact with LEU 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97J TRP* 5.7 8.3 - - + +
101J VAL* 5.1 10.9 - - + +
273J VAL 2.9 16.8 + - - +
274J ILE* 3.2 8.3 + - - +
276J ALA* 1.3 77.9 - - - +
278J ASN* 1.3 61.6 + - - +
280J LEU* 3.5 9.8 + - - +
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Residues in contact with ASN 278 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93J ARG* 5.2 15.0 - - + -
274J ILE 2.9 16.3 + - - +
275J LYS* 4.1 5.4 - - - +
277J LEU* 1.3 77.5 - - - +
279J GLN* 1.3 60.3 + - - +
280J LEU* 3.3 2.1 + - - +
282z GLU* 5.4 5.7 - - - +
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Residues in contact with GLN 279 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275J LYS 2.9 19.4 + - - +
276J ALA 4.5 0.4 - - - +
278J ASN* 1.3 76.2 - - - +
280J LEU* 1.3 71.4 + - - +
281J GLY 3.6 0.2 - - - -
282J GLU* 4.2 15.5 + - + +
279z GLN* 3.0 48.2 - - + +
280z LEU* 4.8 1.9 - - - +
282z GLU* 5.6 3.8 - - - -
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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