Contacts of the helix formed by residues 263 - 278 (chain J) in PDB entry 6NRB
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 LYS 263 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257J ARG* 3.0 44.6 - - + +
258J VAL* 3.5 25.4 - - + -
259J ASP* 4.8 11.3 + - - +
260J SER 4.0 2.4 + - - +
261J THR 3.5 0.2 - - - -
262J ALA* 1.3 81.0 - - + +
264J VAL* 1.3 55.6 + - - +
265J ALA 3.2 3.1 - - - -
266J GLU* 2.9 33.4 + - + +
267J ILE* 2.5 36.2 + - - +
265L VAL* 3.7 23.7 - - - +
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Residues in contact with VAL 264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258J VAL* 4.4 7.4 - - + +
260J SER 4.2 7.9 - - - +
261J THR* 3.9 26.2 - - - +
262J ALA 3.2 1.2 - - - -
263J LYS* 1.3 77.8 - - - +
265J ALA* 1.3 63.9 + - - +
267J ILE* 3.3 11.8 - - + +
268J GLU* 3.2 39.3 - - - +
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Residues in contact with ALA 265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261J THR 5.3 0.2 + - - -
262J ALA 4.0 6.7 + - - +
263J LYS 3.2 0.8 - - - -
264J VAL* 1.3 79.9 - - - +
266J GLU* 1.3 53.7 + - - +
268J GLU* 3.9 12.3 + - - +
269J HIS* 2.7 32.4 + - - -
257L LYS* 3.2 26.7 - - - +
266L VAL* 4.8 10.1 - - + -
272L MET* 6.0 4.9 - - + -
275L VAL* 5.9 0.7 - - + -
306L ARG* 4.2 6.7 + - - +
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Residues in contact with GLU 266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257J ARG* 2.7 38.4 + - - +
262J ALA 4.4 7.6 + - - +
263J LYS* 2.9 26.7 + - - +
265J ALA* 1.3 77.0 - - - +
267J ILE* 1.3 59.8 + - - +
268J GLU 3.0 2.2 - - - -
269J HIS* 2.8 34.2 + - - +
270J ALA* 3.7 4.2 + - - +
257L LYS* 4.2 4.9 - - - +
262L ASN 3.3 20.0 - - - +
263L GLN* 3.0 10.1 - - - +
264L ILE 2.7 35.2 - - - +
265L VAL* 3.3 8.8 - - - +
266L VAL* 5.8 1.1 - - + +
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Residues in contact with ILE 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255J ARG* 4.8 8.1 - - + +
256J VAL* 4.7 6.3 - - + -
257J ARG* 3.7 43.3 - - + +
258J VAL* 3.6 22.0 - - + -
263J LYS 2.5 28.0 + - - +
264J VAL* 3.3 15.3 - - + +
266J GLU* 1.3 73.3 - - - +
268J GLU* 1.3 67.8 + - + +
269J HIS 3.1 0.8 + - - -
270J ALA* 3.7 11.4 + - + +
271J GLU* 3.5 24.3 + - + +
274J LYS* 6.1 1.1 - - - +
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Residues in contact with GLU 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264J VAL* 3.2 31.7 + - - +
265J ALA* 4.1 3.0 - - - +
266J GLU 3.0 1.0 - - - -
267J ILE* 1.3 80.8 - - + +
269J HIS* 1.3 65.1 + - - +
271J GLU* 4.2 24.7 + - - +
272J LYS* 4.2 7.1 - - - +
306L ARG* 2.3 69.3 + - + +
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Residues in contact with HIS 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265J ALA 2.7 21.3 + - - -
266J GLU* 2.8 16.7 + - - +
268J GLU* 1.3 79.3 - - + +
270J ALA* 1.3 58.6 + - - +
271J GLU 3.1 2.5 - - - -
272J LYS* 3.0 32.8 + - - +
273J GLU 4.2 0.5 + - - -
257L LYS* 3.1 61.5 + - + +
258L THR 4.6 5.6 - - - -
259L ASP 4.2 1.0 - - - +
260L MET 3.3 17.3 - - - +
261L ASP* 3.1 22.0 - - + +
262L ASN* 3.0 31.1 + - + -
306L ARG* 4.9 2.8 + - - -
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Residues in contact with ALA 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255J ARG* 4.7 20.5 + - + +
257J ARG* 5.0 13.5 - - - -
266J GLU 3.7 4.9 + - - +
267J ILE* 3.7 9.5 + - + +
268J GLU 3.6 0.4 - - - -
269J HIS* 1.3 73.9 - - - +
271J GLU* 1.3 64.5 + - - +
272J LYS 3.0 2.2 - - - -
273J GLU* 3.1 18.7 + - + +
274J LYS* 3.3 17.4 + - - +
261L ASP* 3.5 16.2 - - - +
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Residues in contact with GLU 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246J THR* 5.4 4.4 + - - +
247J ASP* 2.8 43.7 - - - +
267J ILE* 3.5 25.5 + - + +
268J GLU* 4.2 21.9 - - - +
269J HIS 3.1 0.8 - - - -
270J ALA* 1.3 78.2 - - - +
272J LYS* 1.3 61.8 + - + +
274J LYS* 3.5 6.6 + - + +
275J MET* 3.3 17.2 + - + +
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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
----------------------------------------------------------
268J GLU 4.2 9.6 - - - +
269J HIS 3.0 16.3 + - - +
271J GLU* 1.3 80.4 - - + +
273J GLU* 1.3 59.7 + - - +
275J MET* 3.2 36.1 - - + +
276J LYS* 3.3 21.4 - - - +
297J TYR* 5.9 0.2 - - - -
299J TYR* 3.4 45.9 - - + +
303J LEU* 4.7 0.5 - - - +
258L THR 4.9 1.3 - - - +
259L ASP* 3.2 54.7 + - + +
305L LEU* 3.9 22.7 + - - +
306L ARG* 4.6 4.2 - - + +
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Residues in contact with GLU 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255J ARG* 5.0 3.6 - - - +
269J HIS 4.2 1.0 + - - -
270J ALA* 3.1 16.3 + - + +
272J LYS* 1.3 75.2 - - - +
274J LYS* 1.3 54.6 + - - +
275J MET 3.0 5.4 - - - -
276J LYS* 2.6 44.0 + - - +
277J GLU* 2.8 48.9 + - - +
280J GLU* 4.9 5.4 - - - +
261L ASP* 5.0 9.9 - - - +
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Residues in contact with LYS 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244J MET* 4.2 1.6 - - - +
247J ASP* 3.6 36.8 - - + +
248J LYS* 3.4 32.9 + - - +
249J ILE* 5.6 1.5 - - + +
253J GLY 3.2 25.5 + - - +
254J SER* 4.8 0.2 - - - +
255J ARG* 3.3 59.9 + - - +
267J ILE* 6.1 1.6 - - - +
270J ALA* 3.3 11.5 + - - +
271J GLU* 3.8 4.7 - - + +
272J LYS 3.4 0.2 - - - -
273J GLU* 1.3 75.5 - - - +
275J MET* 1.3 60.4 + - - +
276J LYS 3.3 0.2 - - - -
277J GLU* 3.8 17.9 + - - +
278J LYS 4.2 1.9 + - - -
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Residues in contact with MET 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244J MET* 3.9 17.4 - - - +
246J THR* 3.3 15.7 - - - +
247J ASP* 3.2 16.8 - - - +
271J GLU* 3.3 15.7 + - + +
272J LYS* 3.2 42.8 - - + +
273J GLU 3.0 0.4 - - - -
274J LYS* 1.3 79.5 - - - +
276J LYS* 1.3 58.3 + - - +
277J GLU 3.4 0.2 - - - -
278J LYS 4.5 0.2 + - - -
279J VAL* 3.5 17.8 - - - +
297J TYR* 3.6 32.8 - - + -
299J TYR* 4.5 1.8 - - - -
300J PRO* 3.8 36.6 - - + +
303J LEU* 4.3 8.2 - - + +
305L LEU 4.8 2.7 - - - +
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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 LYS* 3.3 19.9 - - - +
273J GLU* 2.6 35.4 + - - +
275J MET* 1.3 71.5 - - - +
277J GLU* 1.3 61.3 + - - +
278J LYS 3.6 0.2 - - - -
279J VAL* 3.7 19.2 + - - +
280J GLU* 4.0 10.8 - - - +
299J TYR* 3.7 26.8 + - - -
303J LEU* 3.4 32.5 - - + -
259L ASP 4.9 8.5 + - - -
260L MET* 6.3 0.8 - - - +
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Residues in contact with GLU 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248J LYS 4.5 0.8 - - - +
250J LYS* 2.3 46.4 + - - +
252J PHE* 5.3 1.3 - - - +
253J GLY* 4.1 3.6 - - - -
255J ARG* 3.3 32.6 + - - -
273J GLU* 2.8 47.8 + - - +
274J LYS* 3.8 11.4 + - - +
275J MET 3.4 0.6 - - - -
276J LYS* 1.3 75.8 - - - +
278J LYS* 1.3 65.7 + - - +
279J VAL 3.2 1.3 - - - -
280J GLU* 3.2 35.9 + - - +
281J ARG* 4.4 0.9 + - - +
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Residues in contact with LYS 278 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242J THR* 3.8 7.5 + - - -
243J GLY* 3.5 25.9 - - - -
244J MET* 3.5 33.0 - - + +
248J LYS* 3.6 50.4 - - + +
250J LYS* 5.8 2.2 - - - +
274J LYS 4.2 2.8 + - - -
275J MET 4.5 0.6 + - - -
276J LYS 3.6 0.2 - - - -
277J GLU* 1.3 74.4 - - - +
279J VAL* 1.3 58.2 + - - +
280J GLU 2.9 11.5 + - - -
281J ARG* 3.3 20.2 + - + +
282J ILE* 4.0 14.3 + - + +
290J PHE* 3.3 34.6 - - - -
292J ASN* 4.0 5.7 - - - +
304J PHE* 5.1 6.4 - - + -
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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
------------------------------------------------------------
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