Contacts of the helix formed by residues 282 - 295 (chain A) in PDB entry 3HU6
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 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A ARG* 3.4 27.8 - - + +
222A SER* 4.1 6.5 - - - -
254A MET* 3.6 38.1 - - + -
257A PHE* 4.2 14.1 - - + -
258A ILE* 3.8 22.4 - - + -
277A ALA* 2.7 19.5 + - - +
280A TYR* 3.4 19.7 - - + +
281A ALA* 1.3 73.6 - - - +
283A GLU* 1.3 52.2 + - - +
284A ARG 3.4 2.0 - - - -
285A LEU* 3.0 23.1 + - + +
286A LYS* 2.8 33.0 + - - +
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ALA 3.5 5.8 + - - +
282A LEU* 1.3 71.5 - - - +
284A ARG* 1.3 64.2 + - - +
286A LYS* 3.0 21.6 + - - +
287A VAL* 3.1 19.8 + - + +
182B PRO* 5.5 3.4 - - + -
185B ARG* 5.6 5.8 - - - +
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Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ARG* 5.2 0.8 - - - +
257A PHE* 3.2 31.9 - - + -
261A GLY* 3.0 34.1 + - - -
282A LEU 3.4 0.6 - - - -
283A GLU* 1.3 77.0 - - - +
285A LEU* 1.3 57.9 + - - +
287A VAL* 3.4 2.8 + - - +
288A MET* 2.9 49.6 + - + +
181B VAL* 4.6 4.2 - - + +
182B PRO* 3.2 42.6 + - + +
183B GLU 3.8 4.9 - - - -
184B CYS* 3.4 38.5 - - - +
185B ARG* 4.4 19.1 - - + +
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A MET* 4.4 5.2 - - + -
257A PHE* 3.7 51.9 - - + -
263A ALA* 4.0 12.3 - - + -
266A LEU* 4.0 10.5 - - + -
273A LEU* 4.0 39.7 - - + -
277A ALA* 3.8 18.6 - - + -
282A LEU* 3.0 21.1 + - + +
284A ARG* 1.3 75.8 - - - +
286A LYS* 1.3 65.4 + - - +
288A MET* 4.0 4.9 - - - -
289A CYS* 3.1 22.9 + - - -
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Residues in contact with LYS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LEU* 3.2 24.4 - - + +
277A ALA* 3.7 12.3 - - + +
278A ASP* 3.6 35.2 - - + +
282A LEU 2.8 10.8 + - - +
283A GLU* 3.0 16.1 + - - +
285A LEU* 1.3 76.9 - - - +
287A VAL* 1.3 51.7 + - + +
289A CYS 3.0 3.1 + - - -
290A GLU* 2.7 48.1 + - - +
312A HIS* 2.9 21.2 + - - -
313A SER* 2.4 32.7 + - - -
314A ALA* 4.0 1.4 - - - +
315A ASP* 5.0 1.0 + - - +
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLU* 3.1 16.4 + - + +
284A ARG 3.8 4.7 - - - +
286A LYS* 1.3 72.7 - - + +
288A MET* 1.3 56.2 + - - +
289A CYS 3.0 1.6 - - - -
290A GLU* 3.8 18.6 - - + +
291A ASP* 2.8 32.6 + - - +
316A GLN* 4.0 4.5 - - - +
179B VAL* 3.5 22.0 - - + -
180B LYS 3.3 27.8 - - - +
181B VAL* 3.9 8.3 - - + -
182B PRO* 3.9 18.2 - - + -
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Residues in contact with MET 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A PHE* 3.6 29.6 - - - -
261A GLY 4.6 6.3 - - - +
262A LYS* 4.7 1.3 - - - -
263A ALA* 4.2 21.1 - - + +
266A LEU* 3.6 33.3 - - + +
284A ARG* 2.9 40.0 + - + +
285A LEU* 3.7 7.4 - - - +
287A VAL* 1.3 76.1 - - - +
289A CYS* 1.3 57.6 + - - +
291A ASP* 3.8 7.0 - - - +
292A ALA* 3.3 15.6 + - - +
181B VAL* 4.2 21.8 - - + -
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Residues in contact with CYS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LEU* 4.0 25.6 - - - -
270A ALA* 3.7 14.5 - - - +
273A LEU* 3.7 35.0 - - - -
274A LEU* 3.7 20.0 - - + -
285A LEU* 3.1 19.2 + - - -
286A LYS 3.0 9.2 + - - +
288A MET* 1.3 76.0 - - - +
290A GLU* 1.3 65.4 + - - +
291A ASP 3.0 1.6 - - - -
292A ALA* 3.7 1.1 - - - +
293A LEU* 2.9 29.6 + - - +
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Residues in contact with GLU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LEU* 3.9 8.3 - - + +
286A LYS* 2.7 45.3 + - - +
287A VAL* 3.5 24.6 - - - +
289A CYS* 1.3 72.2 - - - +
291A ASP* 1.3 56.6 + - - +
294A CYS* 3.1 30.1 + - - +
314A ALA* 3.4 27.5 - - + -
315A ASP* 3.6 2.5 + - - +
316A GLN* 3.3 18.3 + - - +
317A LEU* 3.2 40.2 + - + +
179B VAL* 3.7 10.6 - - + +
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Residues in contact with ASP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A VAL 2.8 16.1 + - - +
288A MET* 3.8 7.4 - - - +
290A GLU* 1.3 75.6 - - - +
292A ALA* 1.3 66.2 + - - +
294A CYS* 3.4 2.1 + - - +
295A SER* 3.2 25.3 + - - -
64B LYS* 2.8 35.4 + - - -
178B MET* 3.6 29.8 - - - +
179B VAL* 3.4 23.2 + - + +
181B VAL* 4.3 11.7 - - + +
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LEU* 3.3 35.0 - - + -
267A ASP* 4.6 12.3 - - - +
270A ALA* 3.9 10.1 - - + -
288A MET 3.3 4.1 + - - +
289A CYS 3.1 4.8 + - - +
291A ASP* 1.3 80.8 - - - +
293A LEU* 1.3 63.7 + - - +
295A SER* 3.3 12.8 + - - -
296A ASN* 3.6 20.0 + - - +
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ALA* 3.9 20.0 - - + +
271A ASP* 4.3 25.4 - - + +
274A LEU* 4.0 20.2 - - + -
289A CYS 2.9 17.6 + - - +
292A ALA* 1.3 76.4 - - - +
294A CYS* 1.3 62.2 + - - +
296A ASN* 3.1 21.6 + - + +
297A LEU* 3.5 7.8 + - - +
305A ILE* 3.9 31.7 - - + +
308A LEU* 5.1 7.2 - - + -
317A LEU* 3.6 31.9 - - + -
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Residues in contact with CYS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A GLU 3.1 20.0 + - - +
291A ASP* 3.7 5.6 - - - +
293A LEU* 1.3 78.2 - - - +
295A SER* 1.3 61.5 + - - +
296A ASN 3.1 1.6 + - - -
297A LEU* 3.3 24.1 + - - +
317A LEU* 3.5 15.0 - - + +
320A GLN* 3.1 46.0 - - + -
178B MET* 5.4 5.6 - - - -
179B VAL* 4.2 13.2 - - + -
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A ASP* 3.2 19.6 + - - -
292A ALA* 3.7 10.8 - - - -
293A LEU 3.3 0.2 - - - -
294A CYS* 1.3 77.8 - - - +
296A ASN* 1.3 64.2 + - - +
297A LEU 3.5 1.4 - - - +
178B MET* 5.2 6.1 - - - +
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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