Contacts of the helix formed by residues 272 - 288 (chain B) in PDB entry 4NQJ
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 272 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A GLU* 5.5 0.4 - - - -
260B LYS* 2.5 34.8 + - - -
263B GLN* 5.4 2.8 + - - -
268B ASP 3.5 2.6 - - - +
271B LYS* 1.3 89.1 - - + +
273B ILE* 1.3 65.4 + - - +
274B THR* 3.1 4.7 - - - +
275B THR* 3.0 35.8 + - + +
276B LEU* 3.2 6.3 + - - +
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Residues in contact with ILE 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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159A PHE* 3.9 23.3 - - + -
260B LYS* 4.0 31.0 - - + +
269B PHE* 3.7 29.8 + - + +
270B LEU* 3.2 24.2 + - + +
271B LYS 4.1 0.2 + - - -
272B ASP* 1.3 78.5 + - - +
274B THR* 1.3 62.8 + - + +
276B LEU* 3.3 11.9 + - + +
277B LEU* 2.9 49.8 + - + +
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Residues in contact with THR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 3.4 41.6 + - + +
162A GLU* 4.4 18.5 + - - +
163A GLU* 3.5 29.5 + - + +
166A ILE* 3.7 13.0 - - - +
272B ASP* 4.9 1.4 - - - -
273B ILE* 1.3 80.0 - - + +
275B THR* 1.3 61.4 + - - +
277B LEU* 3.9 9.5 - - + +
278B HIS* 3.0 36.3 + - - -
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Residues in contact with THR 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLU* 6.1 2.9 - - + +
166A ILE* 3.9 21.1 - - + -
272B ASP* 3.0 27.0 + - + +
274B THR* 1.3 77.2 - - - +
276B LEU* 1.3 65.9 + - - +
278B HIS* 4.2 1.8 - - - +
279B SER* 2.9 31.9 + - - -
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B SER* 3.7 31.9 - - - +
257B ILE* 4.8 3.8 - - + -
260B LYS* 3.5 45.3 - - + -
272B ASP* 3.2 7.9 + - - +
273B ILE* 3.6 16.2 - - + +
275B THR* 1.3 83.4 + - - +
277B LEU* 1.3 59.0 + - + +
279B SER* 3.0 14.5 + - - +
280B LEU* 2.9 46.0 + - + +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ILE* 2.9 45.0 + - + +
274B THR* 4.0 9.4 - - + +
276B LEU* 1.3 78.1 - - + +
278B HIS* 1.3 64.7 + - + +
280B LEU* 3.4 20.8 + - + +
281B GLU* 3.1 21.5 + - - +
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Residues in contact with HIS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLU* 2.7 38.7 + - - -
166A ILE* 3.5 28.0 - - + +
167A GLN* 3.5 22.7 - - - -
170A GLN* 3.5 11.6 + - - +
274B THR* 3.0 29.6 + - - +
275B THR* 4.2 2.9 - - - +
277B LEU* 1.3 79.7 - - + +
279B SER* 1.3 61.2 + - - +
281B GLU* 3.1 27.0 + - - +
282B GLN* 2.9 32.5 + - - +
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B MET* 4.6 2.4 - - - +
275B THR 2.9 15.9 + - - -
276B LEU* 3.0 21.0 + - - +
278B HIS* 1.3 73.2 - - - +
280B LEU* 1.3 65.7 + - - +
282B GLN* 3.8 7.3 - - - +
283B GLY* 2.8 27.9 + - - -
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B MET* 3.3 30.4 - - + +
256B SER* 4.1 19.7 - - - +
257B ILE* 3.8 32.1 - - + -
276B LEU* 2.9 36.9 + - + +
277B LEU* 3.5 20.0 - - + +
279B SER* 1.3 80.0 + - - +
281B GLU* 1.3 57.2 + - - +
283B GLY 3.2 0.5 + - - -
284B MET* 2.9 36.8 + - + +
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Residues in contact with GLU 281 (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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167A GLN* 5.6 0.9 + - - -
170A GLN* 3.5 16.8 + - - +
277B LEU 3.1 13.6 + - - +
278B HIS* 3.1 35.2 + - - +
280B LEU* 1.3 75.4 - - - +
282B GLN* 1.3 74.9 + - - +
284B MET* 3.4 7.8 + - - +
285B LYS* 3.2 46.1 + - - +
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Residues in contact with GLN 282 (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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170A GLN* 3.7 26.7 - - - +
278B HIS 2.9 19.9 + - - +
279B SER* 3.8 7.0 - - - +
281B GLU* 1.3 97.2 + - - +
283B GLY* 1.3 63.6 + - - +
285B LYS* 3.2 26.6 + - - +
286B VAL* 3.2 19.1 + - - +
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Residues in contact with GLY 283 (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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249B LEU* 3.9 7.4 - - - +
253B MET* 3.7 21.3 - - - -
279B SER 2.8 17.4 + - - -
280B LEU 3.6 1.8 - - - -
282B GLN* 1.3 77.5 - - - +
284B MET* 1.3 61.7 + - - +
286B VAL* 3.1 13.8 + - - +
287B LEU* 3.1 22.9 + - - +
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Residues in contact with MET 284 (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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253B MET* 3.5 9.8 - - + +
280B LEU* 2.9 25.0 + - + +
281B GLU* 3.7 7.4 - - - +
282B GLN 3.3 0.2 - - - -
283B GLY* 1.3 75.2 - - - +
285B LYS* 1.3 59.5 + - + +
287B LEU* 3.1 26.1 + - + +
288B ALA* 2.9 29.7 + - - +
290B ARG* 6.1 1.8 - - - +
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Residues in contact with LYS 285 (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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281B GLU* 3.2 42.0 + - - +
282B GLN* 3.6 24.6 - - - +
283B GLY 3.2 0.8 - - - -
284B MET* 1.3 77.8 - - + +
286B VAL* 1.3 62.2 + - - +
288B ALA* 3.3 16.0 + - + +
289B THR* 3.6 13.9 - - - +
284C MET* 6.3 0.8 - - - +
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B GLN* 2.8 23.2 + - + +
249B LEU* 3.5 26.7 - - + -
282B GLN 3.2 17.7 - - - +
283B GLY* 3.3 10.8 - - - +
285B LYS* 1.3 73.5 - - - +
287B LEU* 1.3 61.4 + - - +
289B THR* 2.8 29.7 + - - +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B GLN* 3.4 40.6 - - + +
249B LEU* 3.8 19.1 - - + -
250B ALA* 4.0 20.4 - - + +
253B MET* 4.0 16.4 - - + -
283B GLY 3.1 14.8 + - - +
284B MET* 3.1 29.1 + - + +
286B VAL* 1.3 77.2 - - - +
288B ALA* 1.3 60.6 + - - +
289B THR 3.3 0.5 + - - -
290B ARG* 2.8 38.1 + - - +
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Residues in contact with ALA 288 (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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284B MET 2.9 15.5 + - - +
285B LYS* 3.6 10.3 - - - +
286B VAL 3.1 0.8 - - - -
287B LEU* 1.3 77.2 - - - +
289B THR* 1.3 59.1 + - + +
290B ARG* 3.2 18.4 + - - +
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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
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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