Contacts of the helix formed by residues 279 - 296 (chain A) in PDB entry 4I6J
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 SER 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ARG* 3.5 21.4 - - - +
34A HIS* 3.2 30.4 + - - -
35A ASP* 2.9 28.5 + - - -
278A LEU* 1.3 73.0 - - - +
280A CYS* 1.3 62.2 + - - +
281A ARG 3.1 2.1 + - - -
282A LEU* 2.9 23.8 + - - +
283A PHE* 3.2 18.9 + - - +
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Residues in contact with CYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A SER 4.1 7.7 + - - -
148A HIS 3.4 24.7 + - - +
149A THR 3.6 16.8 - - - -
150A LEU* 3.5 25.0 - - + +
273A LEU* 3.9 18.6 - - + -
278A LEU 3.4 4.4 + - - -
279A SER* 1.3 72.6 + - - +
281A ARG* 1.3 61.3 + - - +
283A PHE* 3.6 4.2 - - - +
284A TYR* 3.1 23.9 + - - +
308A LEU* 3.7 8.6 - - + +
311A ARG* 3.4 21.3 - - - +
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Residues in contact with ARG 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASP* 4.1 16.5 + - - +
37A PRO* 5.6 2.8 - - - +
146A ASN* 2.7 39.4 + - - +
147A SER* 3.7 16.7 - - - +
149A THR 3.1 17.2 + - - -
150A LEU* 3.1 28.0 + - + +
151A TYR* 4.7 1.4 - - - +
181A PRO* 5.1 0.9 - - + -
182A LYS* 3.1 57.9 + - - +
183A LYS 4.4 4.6 + - - -
184A PRO* 3.9 8.7 - - + -
279A SER* 3.1 5.2 + - - +
280A CYS* 1.3 84.7 - - - +
282A LEU* 1.3 66.8 + - - +
284A TYR* 3.0 9.3 + - + +
285A TYR* 2.9 28.0 + - + -
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A HIS* 3.6 27.8 - - + +
184A PRO* 3.5 25.5 - - + +
236A LEU* 3.8 22.2 - - + -
239A LEU* 3.9 15.0 - - + -
278A LEU* 4.6 0.7 - - + -
279A SER* 2.9 23.1 + - - +
281A ARG* 1.3 74.2 - - - +
283A PHE* 1.3 64.5 + - - +
285A TYR* 3.0 3.8 + - + -
286A ARG* 3.0 45.6 + - + +
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Residues in contact with PHE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 3.7 23.9 - - + +
242A HIS* 4.0 21.5 - + - -
243A LEU* 4.8 0.9 - - + -
269A LEU* 3.7 26.7 - - + -
273A LEU* 4.2 15.0 - - + -
278A LEU* 4.1 9.4 - - + -
279A SER 3.2 9.2 + - - +
280A CYS* 3.6 9.4 - - - +
282A LEU* 1.3 79.5 - - - +
284A TYR* 1.3 62.8 + - - +
286A ARG* 4.1 0.3 - - - +
287A LEU* 3.1 42.8 + - + +
307A GLN* 3.9 24.9 - - + -
308A LEU* 3.7 33.9 - - + -
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Residues in contact with TYR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU* 3.9 24.7 - - + -
151A TYR* 4.9 3.7 + - - -
180A LEU* 4.3 12.3 - - + +
181A PRO* 3.8 33.6 - - + +
280A CYS 3.1 14.8 + - - +
281A ARG* 3.0 14.0 + - - +
283A PHE* 1.3 77.0 - - - +
285A TYR* 1.3 79.4 + + + +
287A LEU* 3.2 7.7 - - - +
288A TRP* 3.0 42.9 + + - +
302A LEU* 5.6 3.5 - - - +
305A PHE* 3.4 50.2 - + + -
308A LEU* 3.9 9.6 - - + -
309A LEU* 5.4 3.6 - - + -
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Residues in contact with TYR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 3.5 22.7 - - + +
181A PRO* 2.5 31.5 + - + -
182A LYS 3.5 11.9 - - - -
183A LYS* 3.6 39.3 + - + +
184A PRO* 4.0 9.2 - - + -
281A ARG* 2.9 20.0 + - + +
282A LEU* 4.2 2.0 - - + +
284A TYR* 1.3 87.7 - + - +
286A ARG* 1.3 56.9 + - - +
287A LEU 3.1 1.8 - - - -
288A TRP* 2.9 32.3 + + + +
289A ASP* 2.7 48.3 + - - +
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 4.2 12.4 - - + +
240A ASP* 2.7 44.7 + - - +
243A LEU* 3.3 57.0 - - + +
282A LEU* 3.0 40.7 + - + +
283A PHE 4.2 2.5 - - - +
285A TYR* 1.3 75.5 - - - +
287A LEU* 1.3 62.4 + - - +
289A ASP* 3.6 12.4 + - - +
290A LEU* 3.2 20.3 + - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A HIS* 5.4 1.1 - - + +
243A LEU* 3.5 25.1 - - + +
248A TRP* 4.2 15.1 - - + +
283A PHE* 3.1 37.2 + - + +
284A TYR* 3.2 11.9 - - - +
285A TYR 3.1 0.2 - - - -
286A ARG* 1.3 76.7 - - - +
288A TRP* 1.3 65.5 + - - +
290A LEU* 3.3 3.3 + - + +
291A TYR* 3.1 23.2 + - - +
304A LEU* 3.3 46.1 - - + +
305A PHE* 3.7 20.0 - - + -
308A LEU* 5.5 2.0 - - + -
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Residues in contact with TRP 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 3.9 23.2 - - + +
284A TYR* 3.0 25.2 + + - +
285A TYR* 2.9 38.1 + + + +
287A LEU* 1.3 77.9 - - - +
289A ASP* 1.3 68.6 + - - +
291A TYR* 3.0 7.1 + + + +
292A LYS* 2.9 51.9 + - + +
298A SER 3.5 14.4 - - - -
299A THR* 3.7 18.6 - - + -
300A PRO* 3.1 39.9 - - + -
304A LEU* 4.8 0.4 - - - -
305A PHE* 4.3 11.3 - + + -
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Residues in contact with ASP 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A TYR* 2.7 34.3 + - - +
286A ARG* 3.8 14.2 - - - +
288A TRP* 1.3 76.8 - - - +
290A LEU* 1.3 60.8 + - - +
292A LYS* 3.2 7.8 - - - +
293A LYS* 2.7 51.4 + - - +
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.4 35.4 - - + +
245A ARG* 4.2 24.0 - - + +
248A TRP* 3.5 41.7 - - + -
286A ARG 3.2 16.2 + - - +
287A LEU* 3.8 3.6 - - + +
289A ASP* 1.3 76.2 - - - +
291A TYR* 1.3 66.6 + - - +
293A LYS* 3.2 12.5 + - + -
294A VAL* 3.0 31.8 + - + +
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Residues in contact with TYR 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TRP* 4.2 19.3 - + + -
287A LEU 3.1 12.7 + - - +
288A TRP* 3.0 10.9 + + - +
290A LEU* 1.3 75.5 - - - +
292A LYS* 1.3 69.6 + - - +
294A VAL* 3.1 4.9 + - + +
295A LYS* 2.8 77.9 + - + +
296A ARG 3.6 1.0 + - - -
298A SER* 4.0 6.5 - - - -
300A PRO* 3.3 38.8 - - + -
301A PRO* 3.5 17.4 - - + +
304A LEU* 3.9 25.8 - - + -
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Residues in contact with LYS 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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288A TRP* 2.9 37.5 + - + +
289A ASP* 3.2 15.5 - - - +
291A TYR* 1.3 80.3 - - - +
293A LYS* 1.3 62.5 + - + +
296A ARG* 2.8 49.9 + - - +
297A ASN* 3.4 28.3 - - - +
298A SER 3.5 12.6 + - - +
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Residues in contact with LYS 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ARG* 3.5 20.3 + - - +
289A ASP* 2.7 53.4 + - - +
290A LEU* 3.6 12.3 - - + +
291A TYR 3.2 0.2 - - - -
292A LYS* 1.3 81.7 - - + +
294A VAL* 1.3 59.0 + - - +
296A ARG* 2.9 29.8 + - - +
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ARG* 3.6 24.9 - - + +
248A TRP* 4.7 7.4 - - + -
249A VAL* 4.2 28.9 - - + -
290A LEU* 3.0 34.6 + - + +
291A TYR* 3.1 5.1 + - + +
293A LYS* 1.3 76.1 - - - +
295A LYS* 1.3 67.6 + - + +
296A ARG* 3.0 19.6 + - - +
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Residues in contact with LYS 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A TYR* 2.8 50.5 + - + +
294A VAL* 1.3 76.7 - - + +
296A ARG* 1.3 69.2 + - - +
297A ASN 4.3 1.7 - - - +
298A SER* 2.1 43.6 + - - -
299A THR 4.1 5.7 + - - -
300A PRO* 4.7 0.2 - - - +
301A PRO* 5.2 1.4 - - - +
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Residues in contact with ARG 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ARG* 4.9 6.7 - - - +
291A TYR* 3.6 1.3 + - - +
292A LYS* 2.8 38.8 + - - +
293A LYS* 2.9 31.8 + - - +
294A VAL* 3.0 12.5 + - - +
295A LYS* 1.3 79.2 - - - +
297A ASN* 1.3 65.0 + - + +
298A SER* 2.3 29.1 + - - +
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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
------------------------------------------------------------
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