Contacts of the strand formed by residues 300 - 307 (chain P) in PDB entry 5C7O
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 LEU 300 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375O LEU* 3.8 6.7 - - - +
229P LEU* 4.7 8.7 - - + -
233P ALA* 4.6 7.2 - - + -
242P ILE* 4.3 15.7 - - + -
245P GLY* 3.4 25.1 - - - +
286P ALA* 3.8 17.9 - - + +
287P LYS* 3.8 19.8 - - - +
289P VAL* 3.8 29.6 - - + -
290P THR* 3.9 11.8 - - + +
296P LEU* 4.0 18.0 + - + -
298P GLY* 3.7 1.8 - - - -
299P LYS* 1.3 93.0 + - + +
301P THR* 1.3 64.6 + - - +
317P LEU* 4.4 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 301 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373O ILE* 3.5 25.3 - - + +
374O ALA 4.0 12.6 - - - +
375O LEU* 4.0 14.3 - - + +
245P GLY 3.5 4.4 + - - -
246P LEU* 3.3 27.4 - - + -
247P MET* 2.9 19.9 + - - +
283P THR 5.3 1.9 + - - -
286P ALA* 3.3 17.2 - - - +
287P LYS* 4.3 16.6 + - - +
300P LEU* 1.3 75.6 - - - +
302P GLY* 1.3 65.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 302 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373O ILE* 3.5 24.9 - - - +
246P LEU* 4.7 1.1 - - - -
247P MET* 3.0 16.6 - - - -
282P SER* 5.6 0.2 - - - -
283P THR* 3.6 20.1 + - - +
286P ALA* 3.7 7.3 - - - +
301P THR* 1.3 84.7 + - - +
303P MET* 1.3 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 303 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371O ALA 3.8 25.8 - - - +
373O ILE* 4.3 8.5 - - + -
381O LYS* 3.7 23.1 - - + -
383O ILE* 4.4 5.6 - - + -
247P MET* 2.9 11.7 + - - +
248P THR* 3.3 19.4 - - - -
249P THR 3.1 20.3 + - - -
280P PRO* 4.2 10.1 - - + -
281P ALA 3.8 9.2 - - - +
282P SER* 5.1 2.5 - - - -
283P THR* 3.7 12.1 - - - +
302P GLY* 1.3 75.5 - - - +
304P ALA* 1.3 78.9 + - - +
305P PHE* 3.7 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 304 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249P THR* 3.3 25.4 - - + +
251P HIS* 5.1 4.5 - - + -
280P PRO* 3.4 4.5 - - - +
281P ALA* 2.8 48.2 + - + +
282P SER 5.2 0.2 - - - +
283P THR* 4.1 10.8 - - + -
303P MET* 1.3 83.9 - - - +
305P PHE* 1.3 65.4 + - - +
306P ARG* 5.0 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 305 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250O VAL* 4.0 21.1 - - + -
314O VAL* 3.9 23.8 - - + -
316O ASP* 3.7 24.2 - - + -
383O ILE* 3.9 21.3 - - + -
385O TRP* 5.0 0.2 - + - -
248P THR* 3.6 15.3 - - + -
249P THR 2.9 9.7 + - - +
250P VAL* 3.6 4.9 - - + -
251P HIS* 2.8 27.4 + - - -
278P ILE* 3.8 28.5 - - + -
279P ILE 3.4 2.5 - - - -
280P PRO* 4.0 25.8 - - + -
303P MET* 3.7 25.1 - - + -
304P ALA* 1.3 73.3 - - - +
306P ARG* 1.3 61.6 + - - +
307P VAL* 3.7 7.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 306 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251P HIS* 3.3 26.8 + - - +
252P SER 3.4 14.1 - - - -
253P TYR* 5.0 0.7 - - - -
254P THR* 2.9 32.3 + - - +
256P THR* 4.2 1.6 + - - -
257P GLN* 2.9 48.4 + - - +
270P ASP* 5.3 2.7 - - - +
274P ALA 5.8 0.4 - - - -
277P ASN 3.4 5.2 - - - +
278P ILE* 3.5 2.1 - - - -
279P ILE* 2.8 50.3 + - + +
281P ALA* 4.7 15.3 - - + +
304P ALA* 4.1 5.2 - - + +
305P PHE* 1.3 71.5 - - - +
307P VAL* 1.3 58.9 + - - +
502P SO4 2.7 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 307 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250O VAL* 4.2 18.4 - - + -
278O ILE* 3.9 12.6 - - + -
307O VAL* 4.2 11.4 - - + -
308O PRO* 5.0 0.2 - - + -
250P VAL* 3.9 31.2 - - + -
251P HIS 2.9 15.9 + - - +
253P TYR* 3.5 20.3 + - - +
274P ALA 4.4 2.0 - - - -
277P ASN 3.9 2.0 - - - -
278P ILE* 4.2 15.0 - - + -
305P PHE* 4.1 4.7 - - + +
306P ARG* 1.3 77.6 - - - +
308P PRO* 1.3 64.0 - - + +
309P THR* 2.8 31.3 + - + +
----------------------------------------------------------
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