Contacts of the helix formed by residues 293 - 311 (chain G) in PDB entry 2NZV
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 PRO 293 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G ILE* 3.3 24.5 - - + -
291G VAL* 4.2 10.5 - - + +
292G GLN* 1.3 79.6 - - + +
294G MET* 1.3 66.0 + - - +
295G TYR 3.4 2.5 - - - -
296G ASP* 2.9 35.3 + - + +
297G ILE* 2.8 30.9 + - + +
321G LEU* 4.3 7.2 - - + -
322G PRO* 4.1 9.2 - - + +
15L HIS* 5.2 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 294 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G PHE* 3.2 59.0 - - + +
77G GLU* 3.4 25.0 + - + +
78G LEU* 3.5 20.9 - - + +
275G ASP* 3.6 30.1 - - + +
277G THR* 3.9 13.9 - - + -
292G GLN* 3.1 32.3 + - - +
293G PRO* 1.3 69.0 - - - +
295G TYR* 1.3 65.0 + - - +
297G ILE* 2.9 9.7 + - - +
298G GLY 2.8 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 295 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G GLU* 3.0 30.6 + - - +
80G ARG* 3.5 22.9 - - + -
81G GLY* 3.3 32.8 - - - -
84G ASP* 2.6 35.5 + - + +
85G ILE* 4.8 0.2 - - + -
293G PRO 3.4 0.6 - - - -
294G MET* 1.3 78.0 - - - +
296G ASP* 1.3 58.3 + - - +
298G GLY* 3.0 1.6 + - - -
299G ALA* 2.7 44.1 + - + -
16L ALA* 3.1 34.3 - - + -
17L ARG* 3.3 15.6 - - + +
20L THR* 3.0 30.1 + - - +
51L MET* 5.4 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 296 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293G PRO* 2.9 27.9 + - + +
295G TYR* 1.3 77.5 - - - +
297G ILE* 1.3 65.9 + - - +
300G VAL* 2.9 29.8 + - - +
321G LEU* 3.6 16.8 - - + +
15L HIS* 3.0 33.8 + - - +
16L ALA* 3.1 22.0 + - - +
51L MET* 3.5 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 297 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G LEU* 3.9 10.8 - - + -
145G ALA* 4.6 1.1 - - - -
146G ALA* 3.8 18.8 - - + +
157G VAL* 3.3 34.6 - - + +
158G THR* 3.8 14.1 - - - +
159G ILE* 3.7 34.5 - - + -
161G TYR* 6.2 0.2 - - - +
292G GLN* 4.7 9.0 - - + +
293G PRO* 2.8 36.1 + - + +
294G MET* 3.3 9.4 - - + +
296G ASP* 1.3 71.0 - - - +
298G GLY* 1.3 67.1 + - - +
301G ALA* 2.8 24.1 + - - +
321G LEU* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 298 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G LEU* 3.4 17.4 - - - +
82G ILE* 3.2 29.4 - - - +
294G MET 2.8 11.8 + - - -
295G TYR 3.0 4.8 + - - -
297G ILE* 1.3 74.9 - - - +
299G ALA* 1.3 67.2 + - - +
301G ALA* 2.7 20.3 + - - +
302G MET 3.2 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G GLY 3.6 14.2 - - - -
82G ILE* 4.9 0.2 - - - +
85G ILE* 3.8 28.8 - - + +
295G TYR* 2.7 26.6 + - + +
296G ASP 3.7 2.9 - - - +
298G GLY* 1.3 72.8 - - - +
300G VAL* 1.3 63.1 + - - +
302G MET* 3.0 4.2 + - - +
303G ARG* 2.9 23.7 + - - +
20L THR* 5.5 0.2 - - - +
47L ILE* 4.9 4.0 - - + -
51L MET* 4.1 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 300 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G VAL* 3.7 24.5 - - + -
296G ASP 2.9 18.0 + - - +
299G ALA* 1.3 77.9 - - - +
301G ALA* 1.3 56.3 + - - +
303G ARG* 3.8 8.2 - - - +
304G LEU* 3.0 27.7 + - - +
319G VAL* 4.7 2.2 - - + -
321G LEU* 4.0 16.4 - - + -
47L ILE* 4.5 1.3 - - + +
48L MET* 3.4 33.2 - - + -
51L MET* 3.4 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 301 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G ILE* 4.4 1.8 - - + -
121G ILE* 3.5 10.5 - - + +
143G VAL* 3.4 31.6 - - + +
145G ALA* 4.0 22.7 - - + -
157G VAL* 3.5 19.5 - - + +
297G ILE 2.8 21.7 + - - +
298G GLY* 2.7 14.3 + - - +
300G VAL* 1.3 73.3 - - - +
302G MET* 1.3 57.0 + - - +
304G LEU* 4.1 0.3 - - - +
305G LEU 3.4 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 302 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G VAL* 4.1 21.1 - - + -
65G VAL* 5.2 0.9 - - + -
82G ILE* 3.7 25.5 - - + +
85G ILE* 3.4 22.7 - - + -
86G ALA* 3.5 30.7 - - + +
91G TYR* 5.2 1.8 - - - -
93G ILE* 5.2 1.3 - - + -
121G ILE* 3.5 27.8 - - + -
298G GLY 3.2 4.6 + - - +
299G ALA 3.0 7.9 + - - +
301G ALA* 1.3 76.3 - - - +
303G ARG* 1.3 55.1 + - - +
305G LEU* 2.6 21.9 + - + +
306G THR* 2.6 42.9 + - + +
309G MET* 5.0 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 303 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G ILE* 3.9 7.6 - - + +
89G TYR* 3.1 37.3 + - - -
299G ALA 2.9 12.5 + - - +
300G VAL 3.8 3.6 - - - +
302G MET* 1.3 77.6 - - - +
304G LEU* 1.3 61.7 + - - +
306G THR* 2.2 44.0 + - - -
307G LYS* 3.0 20.6 + - - +
312G GLU* 2.6 37.6 + - - -
46L SEP 2.9 36.8 + - - -
47L ILE* 3.3 32.5 - - + -
48L MET* 3.5 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G VAL* 3.5 37.0 - - + -
155G PRO* 3.9 9.9 - - + -
157G VAL* 4.8 3.4 - - + -
300G VAL 3.0 18.8 + - - +
301G ALA 4.1 0.9 - - - +
303G ARG* 1.3 76.6 - - - +
305G LEU* 1.3 60.8 + - - +
307G LYS* 3.3 8.5 + - + +
308G TYR* 2.9 36.0 + - + +
314G VAL* 4.4 6.1 - - + -
316G SER 3.8 12.1 - - - +
317G SER* 3.8 17.7 - - - +
319G VAL* 3.7 28.0 - - + -
48L MET* 3.5 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G VAL* 3.4 31.6 - - + -
119G GLY* 4.0 0.2 - - - -
120G ILE 3.7 18.6 - - - +
121G ILE* 4.2 4.0 - - + -
141G PRO* 3.4 42.2 - - + +
142G VAL 4.1 0.2 - - - +
143G VAL* 3.4 26.2 - - + -
301G ALA 3.4 5.1 + - - +
302G MET* 2.6 32.6 + - + +
304G LEU* 1.3 73.1 - - - +
306G THR* 1.3 52.9 + - - +
308G TYR* 3.2 4.2 + - + +
309G MET* 2.7 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 306 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G ILE* 4.5 1.3 - - + -
89G TYR* 3.5 35.0 - - + -
91G TYR* 5.5 3.4 - - + -
302G MET* 2.6 39.4 + - + +
303G ARG* 2.2 50.4 + - - -
305G LEU* 1.3 71.8 - - - +
307G LYS* 1.3 56.5 + - - +
309G MET* 3.6 12.2 - - + +
310G ASN* 2.7 43.4 + - - +
312G GLU* 4.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 307 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303G ARG* 3.0 38.2 + - - +
304G LEU* 3.4 8.5 - - + +
306G THR* 1.3 80.8 + - - +
308G TYR* 1.3 64.8 + - - +
309G MET 3.0 0.2 + - - -
311G LYS* 2.8 21.5 + - - -
312G GLU* 3.1 42.4 + - + +
313G THR 4.5 17.0 + - - +
314G VAL* 4.7 16.2 - - + -
315G ASP* 5.8 3.0 - - - +
46L SEP 2.8 28.3 + - - -
48L MET* 3.8 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 308 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G PRO* 3.9 29.8 - - + +
155G PRO* 3.5 27.4 - - + +
304G LEU* 2.9 30.4 + - + +
305G LEU* 3.2 7.2 + - + +
307G LYS* 1.3 77.7 - - - +
309G MET* 1.3 58.1 + - - +
311G LYS* 3.8 13.1 + - - +
314G VAL* 3.6 29.6 - - + +
317G SER* 3.5 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 309 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G VAL* 3.4 19.1 - - + -
91G TYR* 3.3 34.9 + - + +
118G ASP* 3.3 48.7 - - + +
119G GLY* 3.3 6.7 - - - -
141G PRO* 3.8 19.1 - - + -
302G MET* 5.0 4.0 - - - -
305G LEU* 2.7 38.4 + - + +
306G THR* 3.7 7.4 - - + +
308G TYR* 1.3 72.3 - - - +
310G ASN* 1.3 60.8 + - - +
311G LYS* 3.1 10.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 310 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G TYR* 4.7 10.7 - - - -
91G TYR* 3.1 35.6 + - - -
306G THR 2.7 22.0 + - - +
307G LYS 4.5 0.4 - - - +
309G MET* 1.3 74.0 + - - +
311G LYS* 1.3 71.9 + - - +
312G GLU* 3.6 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 311 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307G LYS 2.8 7.9 + - - -
308G TYR* 4.2 12.1 - - - +
309G MET 3.1 8.0 - - - +
310G ASN* 1.3 84.0 - - - +
312G GLU* 1.3 63.6 + - - +
----------------------------------------------------------
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