Contacts of the helix formed by residues 274 - 292 (chain B) in PDB entry 3GZN
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 274 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ASP* 3.4 23.0 + - - +
273B ASP* 1.3 75.4 - - - +
275B PRO* 1.4 70.3 - - - +
276B GLU* 2.7 55.8 + - - +
277B HIS* 3.3 29.8 + - + +
278B ILE* 3.2 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ASP 3.4 9.2 - - - +
274B ASP* 1.4 89.9 - - - +
276B GLU* 1.3 60.8 + - + +
278B ILE* 4.1 3.1 - - + -
279B GLN* 3.2 25.8 + - - +
299B TYR* 3.8 18.9 + - - +
303B GLN* 6.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PHE* 3.8 30.0 - - + -
274B ASP* 2.7 29.6 + - - +
275B PRO* 1.3 75.0 - - + +
277B HIS* 1.3 64.8 + - - +
279B GLN* 3.2 8.1 + - - +
280B TRP* 2.9 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B TRP* 3.1 35.5 - + + -
264B PHE* 4.0 30.4 - + + +
268B VAL* 4.3 8.2 - - + +
269B PRO 3.9 10.3 + - - -
270B LEU* 4.0 7.4 - - + -
271B ASP* 3.6 35.3 + - + +
274B ASP* 3.3 34.1 + - + +
276B GLU* 1.3 79.6 - - - +
278B ILE* 1.3 62.3 - - - +
280B TRP* 3.1 17.8 + - - +
281B ILE* 3.1 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 5.3 0.4 - - + -
271B ASP 4.6 1.8 - - - +
272B GLY* 3.3 35.2 - - - +
273B ASP 4.9 0.7 - - - +
274B ASP 3.2 19.6 + - - +
275B PRO* 4.2 0.9 - - + +
277B HIS* 1.3 75.2 - - - +
279B GLN* 1.3 62.9 + - - +
281B ILE* 3.4 9.4 + - + +
282B PHE* 2.9 22.7 + - - +
299B TYR* 3.7 35.0 - - + +
302B THR* 4.1 16.7 - - + +
303B GLN* 4.5 24.9 - - + +
306B VAL* 4.4 22.0 - - + -
307B LYS* 5.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B PRO 3.2 14.9 + - - +
276B GLU* 3.2 12.9 + - - +
278B ILE* 1.3 78.7 - - - +
280B TRP* 1.3 63.7 + - - +
282B PHE* 3.1 30.2 + - - +
283B GLN* 3.1 26.0 + - + +
299B TYR* 4.3 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B VAL* 3.5 22.7 - - + -
257B GLN* 4.0 25.1 - - - -
258B TRP* 3.6 32.1 - + + -
261B GLU* 3.7 11.0 - - - -
263B PRO* 3.7 29.2 - - + +
264B PHE* 3.8 24.5 - + + -
276B GLU 2.9 12.6 + - - +
277B HIS* 3.1 8.3 + - - +
279B GLN* 1.3 76.7 - - - +
281B ILE* 1.3 76.2 + - + +
283B GLN* 3.5 4.7 + - + +
284B LYS* 3.1 62.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ILE* 3.7 24.9 - - + +
253B VAL* 3.9 22.4 - - + +
254B ARG* 5.1 0.9 - - - +
258B TRP* 4.2 8.3 - - + -
270B LEU* 3.6 38.4 - - + -
277B HIS 3.1 25.8 + - - +
278B ILE* 3.8 8.5 - - + +
280B TRP* 1.3 93.6 - - + +
282B PHE* 1.3 55.4 + - - +
284B LYS* 3.2 2.6 + - - +
285B SER* 2.7 46.6 + - - +
302B THR* 3.8 7.4 - - + -
306B VAL* 4.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ILE 2.9 15.2 + - - +
279B GLN* 3.1 30.7 + - - +
281B ILE* 1.3 76.4 - - - +
283B GLN* 1.3 63.4 + - + +
285B SER* 3.2 5.0 + - - -
286B LEU* 3.1 41.4 + - + +
297B VAL* 3.3 22.0 - - + -
298B THR* 3.3 23.8 - - - -
299B TYR* 3.8 27.4 - + + -
302B THR* 3.5 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B GLN* 3.1 16.3 + - + +
280B TRP* 4.0 4.0 - - - +
282B PHE* 1.3 77.8 - - + +
284B LYS* 1.3 59.7 + - + +
286B LEU* 3.0 28.8 + - - +
287B GLU* 3.1 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B VAL* 3.8 24.5 - - + +
257B GLN* 3.3 29.7 + - - +
261B GLU* 3.6 19.2 + - - -
280B TRP* 3.1 49.5 + - + +
281B ILE 3.2 4.7 + - - +
283B GLN* 1.3 76.7 - - + +
285B SER* 1.3 58.4 + - - +
287B GLU* 3.4 29.3 + - - +
288B ARG* 3.6 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B CYS* 4.0 3.3 - - - +
250B ILE* 3.6 24.7 - - - +
253B VAL* 3.3 18.9 - - - +
281B ILE* 2.7 25.9 + - - +
282B PHE* 3.5 6.5 - - - -
283B GLN 3.0 0.2 - - - -
284B LYS* 1.3 75.1 - - - +
286B LEU* 1.3 60.9 + - - +
287B GLU 3.3 1.1 - - - -
288B ARG* 3.9 3.1 - - - +
289B ALA* 2.9 31.2 + - - +
297B VAL* 3.8 20.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PHE* 3.1 46.4 + - + +
283B GLN* 3.0 12.2 + - - +
285B SER* 1.3 75.0 - - - +
287B GLU* 1.3 58.4 - - - +
289B ALA* 4.0 4.8 - - + +
290B SER* 3.0 32.6 + - - -
294B ILE 6.1 0.9 - - - +
297B VAL* 3.8 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLN* 3.1 21.0 + - - +
284B LYS* 3.4 41.2 + - - +
286B LEU* 1.3 77.8 - - - +
288B ARG* 1.3 63.9 + - - +
290B SER* 3.2 3.9 + - - -
291B GLN* 3.1 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ILE 4.2 3.0 + - - -
240B ALA 4.4 4.8 + - - -
241B SER* 4.5 4.8 - - - +
243B PRO* 3.7 20.4 - - - +
249B CYS* 4.1 20.0 - - + +
252B TYR* 3.4 69.7 + - - +
253B VAL* 5.3 0.2 - - + -
257B GLN* 5.2 3.5 - - - +
284B LYS 3.6 13.8 + - - +
285B SER* 3.6 5.5 + - - +
287B GLU* 1.3 78.8 - - - +
289B ALA* 1.3 61.3 + - - +
291B GLN* 3.4 13.4 + - - +
292B TYR* 3.0 72.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B CYS* 3.8 15.9 - - - -
285B SER 2.9 20.5 + - - +
286B LEU* 4.0 5.6 - - + +
288B ARG* 1.3 75.0 - - - +
290B SER* 1.3 58.4 + - - +
292B TYR 3.1 3.8 + - - -
293B ASN 2.9 10.6 + - - -
294B ILE* 2.7 49.6 + - + +
297B VAL* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 3.0 20.9 + - - -
287B GLU* 3.7 4.3 - - - -
289B ALA* 1.3 76.6 - - - +
291B GLN* 1.3 65.0 + - - +
293B ASN* 3.4 16.1 + - - +
294B ILE 4.7 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLU 3.1 12.0 + - - +
288B ARG* 3.4 19.6 + - - +
289B ALA 3.1 0.2 - - - -
290B SER* 1.3 79.7 - - - +
292B TYR* 1.3 86.8 + - + +
293B ASN* 3.3 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A SER* 3.2 34.3 - - - -
344A GLY* 6.0 0.2 - - - -
347A ILE* 3.3 17.8 - - - +
241B SER* 4.4 15.4 - - - -
243B PRO* 4.0 14.8 - - + -
288B ARG* 3.0 66.2 + - + +
289B ALA 3.1 4.1 + - - -
291B GLN* 1.3 100.9 + - + +
293B ASN* 1.3 70.3 + - - +
294B ILE* 3.5 20.4 - - + +
----------------------------------------------------------
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