Contacts of the helix formed by residues 262 - 276 (chain P) in PDB entry 5G04
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 262 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P GLU* 4.4 10.3 + - - +
58P LEU* 3.8 23.1 - - - +
60P PHE* 6.4 1.3 - - - -
61P SER* 3.0 29.3 + - - +
259P PHE* 3.1 11.7 + - - -
260P SER 3.8 0.2 - - - +
261P LYS* 1.3 74.1 - - - +
263P SER* 1.3 64.2 + - - +
264P TYR* 3.3 12.6 + - - +
265P ILE* 3.5 17.3 + - - +
266P VAL* 3.3 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 263 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C PHE* 6.5 1.8 - - - -
57P GLU* 4.3 11.9 + - - +
261P LYS 3.4 5.2 + - - -
262P SER* 1.3 71.9 + - - +
264P TYR* 1.3 65.6 + - - +
266P VAL* 3.2 7.1 + - - -
267P SER* 2.9 20.4 + - - -
289P LEU* 3.5 13.1 - - - +
292P GLN* 4.8 10.5 - - - -
293P ASP* 4.0 21.6 - - - +
296P ARG* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 264 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P TRP* 3.8 39.5 - + + +
57P GLU* 5.0 10.6 + - + +
58P LEU* 4.5 10.1 - - + -
203P TRP* 3.9 11.0 - + - -
232P PHE* 4.6 12.9 + + - +
236P HIS* 3.1 28.6 + + - +
251P TYR* 3.6 21.6 + + - -
262P SER* 3.3 8.5 + - - +
263P SER* 1.3 79.5 - - - +
265P ILE* 1.3 67.1 + - + +
267P SER* 3.3 6.1 + - - -
268P GLN* 2.8 52.9 + - + +
296P ARG* 3.7 19.6 - - - +
298P GLU* 5.3 7.4 - - - -
299P ASN* 5.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 265 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58P LEU* 4.7 1.3 - - + -
232P PHE* 4.2 24.9 - - + -
251P TYR* 4.4 19.1 - - + +
254P LEU* 4.6 3.4 - - + -
255P ILE* 4.0 35.0 - - + +
259P PHE* 3.3 31.0 - - + +
260P SER* 4.0 5.4 - - - +
262P SER* 3.5 23.6 + - - +
263P SER 3.3 0.8 - - - -
264P TYR* 1.3 83.7 - - + +
266P VAL* 1.3 64.3 - - + +
268P GLN* 3.2 5.9 + - - +
269P ILE* 2.8 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255P ILE* 5.7 5.2 - - + -
260P SER 4.1 10.5 - - - +
262P SER 3.3 19.7 - - - +
263P SER* 3.2 7.1 + - - +
265P ILE* 1.3 76.9 - - + +
267P SER* 1.3 66.9 + - - +
269P ILE* 3.2 10.3 + - + +
270P ALA* 3.2 18.2 + - - +
285P ILE* 3.6 23.0 - - + +
288P GLU* 4.3 25.1 - - + +
289P LEU* 3.6 15.0 - - + -
292P GLN* 4.5 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 267 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263P SER 2.9 13.2 + - - -
264P TYR* 3.5 9.0 - - - -
266P VAL* 1.3 77.2 - - - +
268P GLN* 1.3 65.0 + - - +
270P ALA* 3.2 6.3 + - - +
271P VAL* 3.0 24.7 + - - +
286P PHE* 4.8 1.6 - - - -
289P LEU* 3.2 16.7 - - - +
296P ARG* 3.7 8.5 - - - -
299P ASN* 2.6 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 268 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236P HIS* 3.5 19.8 + - - +
239P THR* 3.6 20.3 - - + +
251P TYR* 3.2 38.6 - - + +
264P TYR* 2.8 50.7 + - + +
265P ILE 3.5 5.2 - - - +
267P SER* 1.3 73.9 + - - +
269P ILE* 1.3 52.6 + - - +
271P VAL* 3.2 24.5 + - - +
272P ALA* 2.7 36.5 + - - +
299P ASN* 5.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 269 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248P LEU* 4.0 17.7 - - + -
251P TYR* 3.3 42.4 - - + +
252P GLN* 5.2 8.3 - - - +
255P ILE* 6.0 6.1 - - + -
265P ILE* 2.8 33.7 + - + +
266P VAL* 3.2 10.1 + - - +
268P GLN* 1.3 75.5 - - - +
270P ALA* 1.3 51.4 + - - +
272P ALA* 3.1 8.6 + - + +
273P TYR* 2.8 59.7 + - + -
285P ILE* 4.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 270 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266P VAL 3.2 7.4 + - - +
267P SER* 3.2 9.8 + - - +
269P ILE* 1.3 74.9 - - - +
271P VAL* 1.3 57.4 + - - +
273P TYR* 3.3 6.8 + - - +
274P HIS* 2.9 28.1 + - - +
282P ALA* 4.2 9.1 - - - +
285P ILE* 3.6 24.0 - - + +
286P PHE* 3.6 39.0 - - + +
289P LEU* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 271 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239P THR* 4.5 6.1 - - + +
267P SER* 3.0 17.9 + - - +
268P GLN* 3.5 23.8 - - - +
270P ALA* 1.3 74.9 - - - +
272P ALA* 1.3 58.0 + - - +
274P HIS* 3.2 2.5 + - + +
275P ASN* 2.9 44.5 + - - +
286P PHE* 4.2 2.9 - - + -
299P ASN* 4.4 11.4 - - + -
302P THR* 3.4 42.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239P THR* 3.4 22.6 + - - +
244P ILE* 3.7 24.9 - - + +
247P ALA* 5.7 5.6 - - + -
248P LEU* 5.4 8.3 - - + +
251P TYR* 6.0 4.9 - - + -
268P GLN* 2.7 17.5 + - + +
269P ILE* 3.2 15.7 - - + +
271P VAL* 1.3 73.7 - - - +
273P TYR* 1.3 60.3 - - - +
275P ASN* 3.2 15.0 + - - +
276P ILE 3.4 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 273 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244P ILE* 4.8 6.7 - - + -
248P LEU* 3.7 35.7 - - + +
269P ILE* 2.8 39.5 + - + +
270P ALA 3.7 1.8 - - - +
272P ALA* 1.3 70.6 - - - +
274P HIS* 1.3 54.8 + - - +
276P ILE* 2.7 27.0 + - + +
278P ASP* 3.1 47.8 + - - +
281P LYS* 4.7 8.9 - - + +
282P ALA* 3.4 25.4 - - + +
285P ILE* 3.6 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 274 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270P ALA 2.9 14.0 + - - +
271P VAL* 3.2 8.0 + - + +
273P TYR* 1.3 72.9 - - - +
275P ASN* 1.3 66.1 + - - +
276P ILE 2.4 20.2 - - - +
277P ARG* 4.6 6.5 - - - +
278P ASP 6.3 0.2 - - - -
279P ILE* 6.1 1.4 - - - +
282P ALA* 4.0 1.9 - - - +
302P THR* 3.6 25.1 - - - +
305P ASN* 4.0 16.6 + - + +
306P LEU* 3.2 53.7 - - + +
309P VAL* 6.1 3.6 - - + -
400P ARG* 6.0 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 275 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239P THR* 2.6 32.8 + - - +
240P GLU* 4.8 2.6 - - - +
241P LEU 4.6 3.9 + - - +
244P ILE* 4.6 9.9 - - + -
271P VAL* 2.9 27.6 + - - +
272P ALA* 3.2 10.9 + - - +
274P HIS* 1.3 83.8 - - - +
276P ILE* 1.3 64.3 + - - +
277P ARG* 4.8 3.8 - - - +
429P ARG* 3.6 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 276 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244P ILE* 3.4 37.9 - - + -
245P GLU* 4.9 11.4 - - + +
272P ALA 3.4 3.2 + - - -
273P TYR* 2.7 19.0 + - + +
274P HIS* 2.4 27.4 - - - +
275P ASN* 1.3 78.2 - - - +
277P ARG* 1.3 74.6 + - - +
278P ASP* 3.9 20.2 - - + +
----------------------------------------------------------
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