Contacts of the strand formed by residues 270 - 275 (chain P) in PDB entry 1SXG
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 GLU 270 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172P LEU* 3.9 15.3 - - + +
175P SER* 3.7 15.0 + - - -
177P HIS* 3.1 33.8 + - + +
241P THR 2.9 7.8 + - - +
242P ALA* 3.0 4.4 - - + +
243P ILE 2.8 25.8 + - - +
266P PRO* 3.5 19.0 - - + +
269P LEU* 1.3 72.2 - - - +
271P ILE* 1.3 62.0 + - - +
272P ILE* 4.6 1.1 - - - -
330P SER 3.3 14.6 - - - +
331P THR* 3.6 11.2 - - + -
332P LYS* 3.2 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 271 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243P ILE* 3.4 14.1 - - + +
245P VAL* 4.3 12.3 - - + -
251P ALA* 4.4 4.5 - - + +
254P VAL* 3.7 31.2 - - + -
255P ILE* 3.5 35.0 - - + -
265P VAL* 3.9 13.5 - - + -
269P LEU* 3.6 25.6 - - + -
270P GLU* 1.3 86.4 - - - +
272P ILE* 1.3 74.1 + - - +
287P LEU* 4.3 9.6 - - + -
288P THR* 3.9 0.3 + - - -
330P SER* 2.9 29.9 + - - -
331P THR* 3.6 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 272 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168P ALA* 4.3 14.6 - - + +
171P SER* 5.2 3.8 - - - +
172P LEU* 3.2 48.9 - - + -
243P ILE 3.2 6.4 + - - +
244P PHE* 3.6 19.9 - - + -
245P VAL* 2.8 28.9 + - - +
271P ILE* 1.3 86.6 - - - +
273P GLY* 1.3 71.0 + - - +
287P LEU* 4.4 2.5 - - - -
288P THR* 3.3 26.5 - - - +
289P SER* 4.2 3.4 - - - -
290P VAL* 4.5 4.0 - - + +
325P ILE* 4.9 6.3 - - + -
327P PHE* 5.7 2.0 - - + -
331P THR* 3.5 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244P PHE* 4.1 1.2 - - - -
245P VAL 3.4 8.7 - - - +
248P ASP* 4.0 8.5 - - - -
251P ALA* 4.0 17.3 - - - -
272P ILE* 1.3 80.2 - - - +
274P PHE* 1.3 62.1 + - - +
287P LEU* 3.8 4.9 - - - +
288P THR 3.0 11.3 + - - -
289P SER* 3.4 7.8 - - - -
290P VAL* 3.1 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 274 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159P ILE* 3.9 8.3 - - + -
161P TYR* 3.9 19.3 - + - -
164P ALA* 3.4 40.6 - - + -
165P ALA* 4.2 3.4 - - - -
196P LYS* 4.1 19.7 - - + -
244P PHE* 3.8 15.5 - + - -
245P VAL 3.5 3.3 + - - +
246P GLY 3.1 25.1 - - - +
247P THR* 3.7 0.3 - - - -
248P ASP* 3.2 23.6 + - - +
273P GLY* 1.3 71.5 - - - -
275P ASP* 1.3 103.0 + - - +
289P SER* 3.5 4.9 - - - -
290P VAL* 3.7 26.0 - - + +
292P GLN* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 275 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P ASN* 4.9 2.4 + - - +
73P ILE* 5.3 2.6 - - - +
74P PHE* 3.4 39.6 - - + +
196P LYS* 5.0 2.0 + - - -
246P GLY 5.1 0.4 - - - -
247P THR* 4.1 13.3 + - - -
248P ASP* 4.6 1.3 + - + -
274P PHE* 1.3 91.7 - - - +
276P ASN* 1.3 70.8 + - - +
277P THR* 3.4 10.5 + - - +
290P VAL 2.9 13.3 + - - -
292P GLN* 2.7 44.5 + - - +
294P MET* 3.9 12.3 - - - +
----------------------------------------------------------
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