Contacts of the strand formed by residues 270 - 275 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 3.7 17.7 - - + +
175A SER* 3.8 18.7 + - - +
177A HIS* 2.7 35.0 + - + +
241A THR 2.9 7.5 + - - +
242A ALA* 3.1 4.6 - - - +
243A ILE 2.9 24.9 + - - -
266A PRO* 3.5 22.9 - - + +
269A LEU* 1.3 73.7 - - - +
271A ILE* 1.3 62.2 + - - +
330A SER 3.4 7.0 - - - +
331A THR* 3.2 12.5 - - - +
332A LYS* 2.8 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ILE 3.4 14.8 - - - +
245A VAL* 4.1 15.0 - - + -
251A ALA* 4.8 2.5 - - + -
254A VAL* 3.6 26.2 - - + -
255A ILE* 3.4 39.3 - - + -
265A VAL* 3.9 12.6 - - + -
269A LEU* 3.9 18.6 - - + +
270A GLU* 1.3 81.7 - - - +
272A ILE* 1.3 78.1 + - - +
287A LEU* 4.1 10.2 - - + +
330A SER* 2.8 37.0 + - - +
331A THR* 4.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ALA* 4.4 17.9 - - + +
171A SER* 4.6 6.1 - - - +
172A LEU* 3.2 49.6 - - + -
243A ILE 3.3 6.0 + - - +
244A PHE* 3.6 17.6 - - + -
245A VAL* 2.8 29.1 + - - +
271A ILE* 1.3 76.5 - - - +
273A GLY* 1.3 74.6 + - - +
288A THR* 3.2 27.4 - - - +
289A SER* 4.1 5.6 - - - -
290A VAL* 4.3 5.2 - - + +
325A ILE* 5.0 4.5 - - + -
327A PHE* 5.3 3.4 - - + -
331A THR* 3.4 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PHE* 4.2 1.4 - - - -
245A VAL 3.5 9.3 - - - +
248A ASP* 3.9 7.2 - - - -
251A ALA* 4.0 18.4 - - - -
272A ILE* 1.3 84.2 - - - +
274A PHE* 1.3 63.9 + - - +
287A LEU* 3.6 3.7 - - - +
288A THR 3.1 10.7 + - - -
289A SER* 3.6 5.6 - - - -
290A VAL* 3.1 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 3.9 4.3 - - + -
161A TYR* 3.7 29.8 - + - -
164A ALA* 3.6 18.8 - - + -
165A ALA 4.4 2.5 - - - -
196A LYS* 3.7 25.8 - - + -
244A PHE* 3.9 19.3 - + - -
245A VAL 3.6 3.0 + - - +
246A GLY 2.9 23.3 - - - +
247A THR* 3.2 0.7 - - - -
248A ASP* 2.9 29.2 + - - +
273A GLY* 1.3 71.9 - - - -
275A ASP* 1.3 103.6 + - - +
276A ASN 3.4 4.9 - - - -
289A SER* 3.5 2.2 - - - -
290A VAL* 3.4 40.6 - - + -
292A GLN* 3.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASN* 4.0 3.3 + - - +
74A PHE* 3.3 35.8 - - + +
196A LYS* 4.9 2.4 + - - -
247A THR* 3.6 22.3 - - - +
248A ASP* 4.6 0.7 - - - +
274A PHE* 1.3 97.8 - - - +
276A ASN* 1.3 71.9 + - - +
277A THR* 3.5 20.4 + - + +
290A VAL 2.9 11.8 + - - -
291A VAL* 5.4 0.2 - - - +
292A GLN* 3.1 42.2 + - - +
294A MET* 5.0 2.9 - - - +
----------------------------------------------------------
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