Contacts of the helix formed by residues 269 - 283 (chain J) in PDB entry 6QX2
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 ASN 269 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113J MET 3.7 5.2 - - - -
114J ASP 3.1 24.8 + - - +
115J GLY* 3.3 17.0 - - - -
267J GLN 3.9 3.0 + - - +
268J VAL* 1.3 71.8 - - - +
270J LYS* 1.3 57.3 + - - +
271J ALA* 3.0 7.1 + - - +
272J ARG* 3.0 65.0 + - + +
273J MET* 2.9 30.5 + - - +
4N C 4.9 3.1 + - - +
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Residues in contact with LYS 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J MET* 3.1 23.1 + - + +
114J ASP* 3.4 16.4 - - - +
264J ILE* 3.9 22.4 - - + -
268J VAL 3.5 3.6 + - - -
269J ASN* 1.3 69.5 - - - +
271J ALA* 1.3 64.0 - - - +
273J MET* 3.2 10.8 + - + +
274J ILE* 3.0 38.2 + - + +
294J ASP* 3.9 15.9 - - - +
296J THR* 3.9 20.9 - - + +
302J VAL* 4.4 16.8 - - + -
304J VAL* 4.3 12.1 - - + -
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Residues in contact with ALA 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114J ASP* 3.0 37.3 + - + +
269J ASN* 3.0 7.7 + - - +
270J LYS* 1.3 75.8 - - - +
272J ARG* 1.3 61.9 - - - +
274J ILE* 3.5 9.8 + - - +
275J GLU* 3.2 21.8 + - - +
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Residues in contact with ARG 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269J ASN* 3.0 49.9 + - + +
271J ALA* 1.3 75.1 - - - +
273J MET* 1.3 59.1 + - - +
275J GLU* 3.1 11.5 + - + +
276J LYS* 2.9 41.5 + - + +
4N C 3.1 31.7 + - - -
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Residues in contact with MET 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245J SER* 4.5 0.9 - - - -
261J VAL* 5.1 1.1 - - + -
264J ILE* 4.2 27.6 - - + -
265J PRO* 4.9 0.2 - - - -
268J VAL* 4.1 13.5 - - + -
269J ASN 2.9 18.5 + - - +
270J LYS* 3.5 8.5 - - - +
272J ARG* 1.3 76.1 - - - +
274J ILE* 1.3 70.5 + - + +
276J LYS* 3.4 5.2 + - - +
277J ILE* 3.3 31.3 + - + +
304J VAL* 4.9 12.8 - - + -
326J PRO* 4.1 32.9 - - + +
327J LEU* 3.5 45.1 - - + +
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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
----------------------------------------------------------
270J LYS* 3.0 28.0 + - + +
271J ALA* 3.7 10.5 - - - +
273J MET* 1.3 76.2 - - + +
275J GLU* 1.3 62.1 + - - +
277J ILE* 3.0 11.4 + - + +
278J ALA* 2.9 27.2 + - + +
292J LEU* 3.5 22.6 - - + +
293J ARG 5.5 0.4 - - - -
294J ASP* 3.6 41.7 - - + +
304J VAL* 3.9 26.2 - - + -
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Residues in contact with GLU 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 ALA 3.2 13.0 + - - +
272J ARG* 3.1 14.2 + - + +
274J ILE* 1.3 76.5 - - - +
276J LYS* 1.3 54.5 + - - +
278J ALA* 3.3 11.7 + - - +
279J GLU* 2.8 44.9 + - + +
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Residues in contact with LYS 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272J ARG* 2.9 28.7 + - + +
273J MET 3.6 8.5 - - - +
275J GLU* 1.3 75.3 - - - +
277J ILE* 1.3 57.1 + - - +
279J GLU* 3.4 19.1 + - - +
280J LEU* 3.0 32.2 + - - +
324J GLN 5.8 1.3 - - - +
325J THR* 4.5 6.7 - - + -
326J PRO* 3.7 35.7 - - + -
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Residues in contact with ILE 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273J MET* 3.5 21.8 - - + +
274J ILE* 3.0 14.4 + - + +
276J LYS* 1.3 72.9 - - - +
278J ALA* 1.3 65.2 + - - +
280J LEU* 3.2 6.6 + - + +
281J VAL* 3.1 24.1 + - + +
289J ILE* 4.4 14.1 - - + -
292J LEU* 3.7 24.9 - - + -
304J VAL* 5.5 1.8 - - + -
306J ILE* 4.6 12.6 - - + -
321J LEU* 3.9 23.3 - - + -
325J THR* 3.7 24.5 - - + +
327J LEU* 4.4 23.3 - - + -
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Residues in contact with ALA 278 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274J ILE* 2.9 13.9 + - + +
275J GLU* 3.7 19.7 - - - +
277J ILE* 1.3 76.2 - - - +
279J GLU* 1.3 52.2 + - - +
281J VAL* 3.3 7.8 + - - +
282J ARG* 2.8 35.8 + - - +
292J LEU* 3.6 15.8 - - + +
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Residues in contact with GLU 279 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275J GLU* 2.8 27.3 + - - +
276J LYS* 3.5 23.5 - - - +
278J ALA* 1.3 73.2 - - - +
280J LEU* 1.3 62.2 + - + +
282J ARG* 4.2 6.3 - - - -
283J ASP* 3.0 51.9 + - - +
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Residues in contact with LEU 280 (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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276J LYS* 3.0 18.0 + - + +
277J ILE* 3.2 8.9 + - - +
279J GLU* 1.3 78.2 - - + +
281J VAL* 1.3 60.8 + - - +
283J ASP* 3.6 1.7 + - + -
284J LYS 3.3 2.6 + - - -
285J LYS* 2.8 50.2 + - + -
286J ILE* 3.6 24.2 + - + -
321J LEU* 5.1 1.1 - - + -
324J GLN* 3.4 46.9 - - + +
325J THR* 3.8 17.9 - - + -
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Residues in contact with VAL 281 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277J ILE* 3.1 16.3 + - + +
278J ALA* 3.6 10.1 - - - +
280J LEU* 1.3 74.1 - - - +
282J ARG* 1.3 65.9 + - - +
284J LYS* 2.9 16.1 + - - +
286J ILE* 3.9 21.3 - - + +
289J ILE* 3.8 48.7 - - + +
292J LEU* 6.0 1.1 - - + -
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Residues in contact with ARG 282 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278J ALA 2.8 22.2 + - - +
279J GLU* 3.8 9.6 - - - +
281J VAL* 1.3 73.2 - - - +
283J ASP* 1.3 64.0 - - - +
284J LYS* 3.2 4.2 + - - +
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Residues in contact with ASP 283 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279J GLU* 3.0 38.9 + - - +
280J LEU* 4.2 2.9 - - + +
281J VAL 3.2 0.2 - - - -
282J ARG* 1.3 80.9 - - - +
284J LYS* 1.3 67.3 + - - +
285J LYS* 2.9 13.0 + - + +
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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