Contacts of the helix formed by residues 282 - 296 (chain G) in PDB entry 3SZ9
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 282 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G ASP 3.8 0.6 + - - -
281G ALA* 1.3 70.2 - - - +
283G MET* 1.3 52.5 + - - +
284G ASP* 3.4 11.4 + - - +
285G TRP* 3.1 36.0 + - + +
286G ALA* 2.8 36.0 + - - +
432G PHE* 6.2 0.4 - - - -
434G LYS* 3.9 26.5 + - + +
454G ASN* 5.9 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 283 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G ILE* 6.0 0.7 - - - -
281G ALA* 3.2 8.4 + - - +
282G ASP* 1.3 70.9 + - - +
284G ASP* 1.3 66.8 + - - +
286G ALA* 3.9 3.3 - - - -
287G VAL* 3.0 39.9 + - - +
314G ILE* 3.6 49.6 - - + +
317G GLU* 3.8 23.8 - - + +
318G PHE* 4.0 19.5 - - + -
321G ARG* 3.5 31.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 284 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G ASP* 3.4 7.7 + - - +
283G MET* 1.3 77.9 - - - +
285G TRP* 1.3 62.5 + - - +
287G VAL* 3.9 2.8 - - - +
288G GLU* 3.1 23.8 + - - +
321G ARG* 3.0 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 285 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G ASP* 3.1 29.4 + - + +
284G ASP* 1.3 74.9 - - - +
286G ALA* 1.3 57.5 + - - +
288G GLU* 3.3 10.9 + - + +
289G GLN* 2.9 68.6 + - + +
432G PHE* 3.8 17.0 - + - -
454G ASN* 2.8 28.6 + - + -
455G CYS* 5.1 3.1 - - + -
150H PHE* 6.6 0.2 - + - -
494H LYS* 3.7 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 286 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G ILE* 3.8 31.9 - - + +
281G ALA* 4.2 6.1 - - + -
282G ASP 2.8 22.6 + - - +
283G MET* 4.0 4.0 - - - +
285G TRP* 1.3 74.0 - - - +
287G VAL* 1.3 57.2 + - - +
289G GLN* 4.2 0.3 - - - +
290G ALA* 2.9 32.2 + - - +
318G PHE* 3.8 5.6 - - + -
432G PHE* 3.9 25.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 287 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G MET* 3.0 31.7 + - - +
284G ASP* 3.9 4.7 - - - +
286G ALA* 1.3 74.8 - - - +
288G GLU* 1.3 67.4 + - - +
290G ALA* 3.4 1.7 + - - +
291G HIS* 3.0 22.2 + - - +
318G PHE* 3.7 31.9 - - + +
321G ARG* 3.9 44.4 - - + +
322G SER* 4.2 9.0 + - - +
325G ARG* 4.7 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 288 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284G ASP 3.1 15.7 + - - +
285G TRP* 3.3 11.4 + - + +
287G VAL* 1.3 80.4 - - + +
289G GLN* 1.3 66.6 + - + +
291G HIS* 3.3 7.6 - - - +
292G PHE* 3.0 28.9 + - + +
325G ARG* 2.9 48.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 289 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G ASN* 4.8 1.1 - - - -
285G TRP* 2.9 65.8 + - + +
288G GLU* 1.3 78.5 - - + +
290G ALA* 1.3 55.1 + - - +
292G PHE* 3.6 15.5 - - - +
293G ALA* 2.6 36.5 + - - +
432G PHE* 3.5 22.0 - - + -
455G CYS* 3.7 5.5 - - - +
456G TYR* 3.4 33.2 + - + +
458G VAL* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 290 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G ASN* 3.5 23.7 + - - +
277G ILE* 4.9 1.6 - - + -
286G ALA 2.9 20.7 + - - +
287G VAL 3.9 1.6 - - - +
289G GLN* 1.3 75.9 - - - +
291G HIS* 1.3 63.9 + - - +
293G ALA* 3.4 2.4 + - - +
294G LEU* 3.2 17.7 + - - +
305G GLY 5.1 0.9 - - - +
308G THR* 4.0 11.2 + - + +
318G PHE* 3.6 24.0 - - + -
405G MET* 3.3 15.7 - - + +
432G PHE* 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 291 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G VAL 3.0 14.4 + - - +
288G GLU* 3.3 11.2 - - - +
290G ALA* 1.3 78.7 - - - +
292G PHE* 1.3 59.7 + - + +
295G PHE* 2.9 63.3 + + - +
322G SER* 4.9 3.3 + - - -
325G ARG* 3.3 66.1 + - + +
326G ALA* 3.9 9.4 + - - +
329G ARG* 3.0 36.8 + - - -
405G MET* 4.0 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 292 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G GLU* 3.0 19.5 + - + +
289G GLN* 3.6 20.4 - - - +
291G HIS* 1.3 79.3 - - + +
293G ALA* 1.3 67.0 + - - +
295G PHE* 5.3 0.2 - - - -
296G PHE* 3.0 71.3 + + + +
329G ARG* 5.9 0.9 - - - +
456G TYR* 4.1 10.1 - - + -
457G ASP* 3.6 35.7 - - + -
8001G I3E 5.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 293 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G ASN* 4.0 4.9 - - - +
289G GLN 2.6 21.7 + - - +
290G ALA* 3.5 12.1 - - - +
291G HIS 3.3 0.2 - - - -
292G PHE* 1.3 75.0 - - - +
294G LEU* 1.3 58.8 + - - +
296G PHE* 4.9 1.0 + - - +
301G CYS* 5.7 0.9 - - - +
304G ALA* 3.5 8.7 - - - +
305G GLY* 2.9 23.5 + - - +
456G TYR* 3.4 46.1 - - + -
457G ASP* 4.2 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G ALA 3.2 14.7 + - - +
291G HIS 4.1 0.2 - - - +
292G PHE 3.1 0.4 - - - -
293G ALA* 1.3 79.6 - - - +
295G PHE* 1.3 87.1 + - + +
296G PHE 3.4 1.9 + - - +
299G GLY* 3.4 18.9 - - - -
304G ALA* 4.3 9.5 - - + +
305G GLY 3.6 22.9 - - - +
306G SER* 3.6 20.2 - - - -
402G GLY 4.2 5.2 - - - +
403G PRO 4.1 0.2 - - - -
404G VAL 3.4 39.9 - - - +
405G MET* 3.6 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 295 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G HIS* 2.9 56.3 + + - +
292G PHE* 5.3 0.2 - - - -
294G LEU* 1.3 85.9 - - + +
296G PHE* 1.3 69.3 + - - +
298G GLN* 3.3 12.0 + - - -
299G GLY 3.3 4.3 + - - +
322G SER 5.9 0.2 - - - -
326G ALA* 4.3 10.1 - - + -
329G ARG* 3.1 42.2 + - - +
341G GLN* 4.3 1.0 - - - +
383G PRO* 3.8 18.4 - - + -
384G THR 3.9 18.8 - - - -
385G VAL* 4.3 0.9 - - + -
403G PRO* 3.3 39.3 - - + -
405G MET* 4.1 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 296 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G LYS* 6.2 0.2 - - - -
116G ILE* 3.9 28.9 - - + -
120G VAL* 4.1 27.8 - - + -
121G ASP* 5.3 0.4 - - - -
170G PHE* 3.8 22.2 - + - -
292G PHE* 3.0 53.4 + + + +
293G ALA 5.2 0.9 - - - +
294G LEU 3.4 2.1 - - - +
295G PHE* 1.3 75.1 - - - +
297G ASN* 1.3 72.0 + - + +
299G GLY* 2.9 19.2 + - - -
301G CYS* 3.6 29.0 - - - -
329G ARG* 4.5 4.7 - - - +
457G ASP* 4.0 15.5 - - - +
8001G I3E 3.4 25.1 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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