Contacts of the strand formed by residues 283 - 287 (chain A) in PDB entry 2XTJ
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 283 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLU* 3.7 18.2 - - + -
183A TYR* 3.7 31.4 - - + +
271A ILE* 4.4 13.7 - - + +
275A GLN* 3.6 42.6 - - + +
280A VAL* 5.8 7.6 - - + -
281A GLY 3.5 11.1 + - - +
282A PRO* 1.3 75.1 - - - +
284A VAL* 1.3 63.6 + - - +
285A VAL* 5.4 0.9 - - + -
308A GLY 5.1 4.8 + - - +
309A VAL* 3.8 24.5 - - + +
310A VAL* 2.9 30.6 + - - +
400A LEU* 4.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A VAL* 4.3 10.5 - - + -
181A GLU 3.0 12.5 + - - +
182A VAL* 4.4 12.8 - - + -
183A TYR* 2.7 32.9 + - - +
283A LEU* 1.3 77.5 - - - +
285A VAL* 1.3 64.3 + - - +
310A VAL* 3.4 17.7 - - + +
312A VAL* 4.0 24.9 - - + -
393A ALA* 4.2 21.1 - - + +
396A ALA* 4.5 8.3 - - + -
397A ALA* 4.5 5.8 - - - +
400A LEU* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A TYR* 3.4 8.1 - - + +
185A LEU* 4.0 13.5 - - + -
268A LEU* 4.6 3.4 - - + -
271A ILE* 3.8 41.3 - - + -
283A LEU* 5.2 1.3 - - + -
284A VAL* 1.3 79.3 - - - +
286A LEU* 1.3 62.5 + - - +
287A LEU* 4.3 11.7 - - + +
304A LEU* 4.7 1.3 - - + -
309A VAL* 3.5 26.5 - - + -
310A VAL 2.8 11.4 + - - +
311A LEU* 3.6 18.8 - - + +
312A VAL* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A VAL* 4.9 6.3 - - + +
183A TYR 2.7 15.4 + - - +
184A LEU* 3.9 20.6 - - + -
185A LEU* 3.2 20.8 + - - +
230A LEU* 4.9 5.4 - - + +
234A VAL* 3.9 18.2 - - + -
247A MET* 5.4 1.3 - - + -
284A VAL 4.3 0.2 - - - -
285A VAL* 1.3 73.3 - - - +
287A LEU* 1.3 61.6 + - - +
288A PRO* 3.2 21.9 - - + +
312A VAL* 3.5 12.3 - - + +
386A SER 4.9 1.1 - - - +
389A ALA* 3.7 36.6 - - + +
390A ALA* 3.7 21.8 - - + +
393A ALA* 4.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 4.0 31.6 - - + -
264A THR* 4.3 16.8 - - + -
268A LEU* 4.3 11.4 - - + -
285A VAL* 4.3 5.2 - - + +
286A LEU* 1.3 75.4 - - - +
288A PRO* 1.3 57.5 - - - +
289A LEU* 2.8 19.7 + - + -
297A LEU* 6.1 0.2 - - + -
301A CYS* 4.6 7.4 - - - -
311A LEU* 3.8 34.1 - - + -
312A VAL 2.7 16.3 + - - +
313A THR* 2.6 43.0 + - - +
314A ALA 3.3 0.9 + - - -
327A PRO* 4.4 17.9 - - + -
333A VAL* 5.1 0.7 - - + -
----------------------------------------------------------
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