Contacts of the helix formed by residues 264 - 276 (chain B) in PDB entry 4NN2
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 ASP 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B VAL* 3.0 21.2 + - + +
252B LEU* 3.7 18.4 - - + +
263B PHE* 1.3 70.0 - - - +
265B ILE* 1.3 61.8 + - - +
266B LYS* 3.0 26.2 + - - +
267B THR* 2.7 49.4 + - + +
268B VAL* 3.3 6.4 + - - +
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Residues in contact with ILE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B PHE* 3.9 51.8 - - + +
243B MET* 4.8 0.7 - - - -
260B PHE* 4.4 11.4 - - + -
263B PHE* 3.1 20.4 + - + +
264B ASP* 1.3 69.8 + - - +
266B LYS* 1.3 65.9 + - - +
268B VAL* 3.0 11.2 + - + +
269B LEU* 2.9 31.9 + - + +
404B GOL 3.8 26.4 + - - +
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Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B ASP* 3.0 15.3 + - - +
265B ILE* 1.3 78.5 - - - +
267B THR* 1.3 57.6 + - + +
269B LEU* 3.3 11.9 + - + +
270B GLN* 3.0 57.6 + - + +
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Residues in contact with THR 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B GLY 3.5 13.9 - - - +
249B THR* 3.7 1.5 - - - -
250B VAL* 3.0 39.9 + - + -
264B ASP* 2.7 37.2 + - - +
266B LYS* 1.3 74.7 - - + +
268B VAL* 1.3 60.9 + - - +
270B GLN* 3.4 18.7 + - - +
271B GLU* 2.9 33.2 + - - +
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B PHE* 4.3 14.6 - - + -
231B PHE* 3.7 31.0 - - + -
243B MET* 3.5 37.9 - - + -
249B THR* 3.9 17.7 - - + +
263B PHE* 5.1 1.8 - - + -
264B ASP 3.8 12.3 - - - +
265B ILE* 3.0 16.4 + - + +
267B THR* 1.3 77.4 + - - +
269B LEU* 1.3 56.2 + - - +
271B GLU* 3.1 8.1 + - - +
272B ILE* 2.9 29.3 + - + +
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B PHE* 4.0 22.0 - - + +
232B ASN* 4.6 12.8 - - - +
236B ALA* 3.8 29.2 - - + -
265B ILE* 2.9 28.4 + - + +
266B LYS* 3.7 10.8 - - + +
268B VAL* 1.3 77.4 - - - +
270B GLN* 1.3 62.2 + - + +
272B ILE* 3.3 11.7 + - + +
273B LYS* 3.1 20.8 + - - +
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Residues in contact with GLN 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B LYS* 3.0 47.5 + - + +
267B THR* 3.6 25.7 - - - +
269B LEU* 1.3 76.1 - - + +
271B GLU* 1.3 60.0 + - + +
273B LYS* 3.3 10.3 + - + +
274B ARG* 2.9 27.2 + - - +
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Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B PHE* 3.7 7.4 - - + -
246B SER* 2.7 31.6 + - - +
248B GLY* 2.8 44.6 + - - -
249B THR* 3.9 3.1 - - - +
267B THR 2.9 17.9 + - - +
268B VAL* 3.1 10.0 + - - +
270B GLN* 1.3 75.8 - - + +
272B ILE* 1.3 59.9 + - - +
274B ARG* 2.8 42.0 + - - +
275B GLY 2.8 24.8 + - - -
289B THR* 3.5 10.4 - - - +
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Residues in contact with ILE 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B GLY* 3.8 27.2 - - - +
214B PHE* 3.6 26.5 - - + -
231B PHE* 4.4 15.5 - - + -
236B ALA* 5.0 3.8 - - + -
237B ALA 3.7 27.6 - - - +
268B VAL 2.9 18.4 + - - +
269B LEU* 3.3 21.3 + - + +
271B GLU* 1.3 75.2 - - - +
273B LYS* 1.3 64.0 + - - +
275B GLY* 3.2 10.4 + - - -
276B LYS* 3.5 22.2 + - - +
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Residues in contact with LYS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B LEU 3.1 13.3 + - - +
270B GLN* 3.5 12.8 - - + +
271B GLU 3.2 0.2 - - - -
272B ILE* 1.3 74.2 - - - +
274B ARG* 1.3 64.4 + - - +
276B LYS* 3.1 36.6 + - + +
277B ARG* 4.4 3.8 + - - +
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Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B SER* 3.9 11.2 - - - -
248B GLY 4.4 0.2 - - - +
270B GLN 2.9 17.2 + - - +
271B GLU* 2.8 46.9 + - - +
273B LYS* 1.3 72.4 - - - +
275B GLY* 1.3 61.6 + - - +
277B ARG* 3.1 55.5 + - - +
278B MET* 3.3 35.1 - - + +
289B THR* 3.0 33.2 + - - +
300B THR* 5.3 1.2 + - - -
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Residues in contact with GLY 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B GLY 6.0 0.2 - - - -
214B PHE* 5.5 0.7 - - - -
271B GLU 2.8 11.3 + - - -
272B ILE 3.6 6.3 - - - -
273B LYS 3.1 1.0 - - - -
274B ARG* 1.3 77.2 - - - +
276B LYS* 1.3 61.2 + - - +
277B ARG 3.1 0.2 - - - -
278B MET* 3.0 12.9 + - - +
286B PRO* 3.6 0.7 - - - +
287B GLY* 2.8 33.4 + - - -
289B THR* 3.5 23.8 - - - -
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Residues in contact with LYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ILE* 3.5 16.5 + - - +
273B LYS* 3.4 29.6 - - + +
274B ARG 3.1 1.2 + - - -
275B GLY* 1.3 77.0 - - - +
277B ARG* 1.3 58.1 + - - +
279B LYS* 6.1 0.2 - - - +
286B PRO* 3.8 17.8 - - - +
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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