Contacts of the strand formed by residues 310 - 314 (chain A) in PDB entry 2W2P
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 VAL 310 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU 3.0 17.7 + - - +
284A VAL* 3.3 8.7 - - + +
285A VAL 2.8 31.7 + - - +
308A GLY 4.2 7.2 - - - +
309A VAL* 1.3 69.9 - - - +
311A LEU* 1.3 58.1 + - - +
312A VAL* 4.3 10.8 - - + -
334A ILE* 3.8 16.8 - - + -
396A ALA* 4.6 8.3 - - + -
400A LEU* 4.1 15.7 - - + -
407A THR 6.2 0.2 - - - -
408A LEU* 3.7 23.3 - - + -
411A LEU* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 4.5 10.5 - - + -
285A VAL* 3.4 9.6 - - + +
287A LEU* 3.6 26.0 - - + -
301A CYS* 3.8 45.1 - - + +
304A LEU* 4.2 6.7 - - + -
305A ALA* 4.0 11.2 - - + +
309A VAL* 3.5 33.4 + - + +
310A VAL* 1.3 73.7 - - - +
312A VAL* 1.3 61.1 + - - +
332A GLU 5.3 2.2 + - - -
333A VAL* 3.5 17.8 - - + +
334A ILE* 2.9 32.4 + - - +
408A LEU* 5.1 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A VAL* 4.3 11.7 - - + -
285A VAL 2.9 8.5 + - - +
286A LEU* 3.4 10.2 - - + +
287A LEU* 2.7 33.6 + - - +
310A VAL* 4.3 11.0 - - + -
311A LEU* 1.3 77.0 - - - +
313A THR* 1.3 56.4 + - - +
333A VAL* 4.6 0.2 - - - -
334A ILE* 3.4 9.6 - - + +
336A VAL* 3.9 18.8 - - + -
389A ALA* 3.3 33.0 - - + +
392A VAL* 4.0 11.2 - - + +
393A ALA* 3.9 23.8 - - + +
396A ALA* 5.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 3.0 18.5 + - - -
289A LEU 3.8 2.6 + - - -
312A VAL* 1.3 74.5 - - - +
314A ALA* 1.3 75.3 + - - +
327A PRO* 3.3 22.7 - - - +
328A ALA* 3.9 13.2 + - - +
333A VAL* 3.4 25.1 - - + -
334A ILE 2.9 8.6 + - - +
335A THR* 3.5 20.0 - - - +
336A VAL* 3.0 25.3 + - - +
389A ALA* 3.5 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU 3.3 4.0 + - - -
288A PRO* 4.2 9.6 - - + -
289A LEU 4.2 8.2 - - - +
290A ALA* 4.9 1.6 - - - +
313A THR* 1.3 86.3 + - - +
315A ALA* 1.3 63.9 + - - +
316A GLY 3.3 0.6 + - - -
328A ALA* 3.7 11.8 - - - +
335A THR* 4.6 0.2 - - - -
336A VAL 3.9 0.4 - - - -
385A THR* 3.4 38.6 - - - +
386A SER* 3.8 7.2 - - - +
389A ALA* 3.9 1.4 - - + +
152P GLN* 3.9 16.6 - - + -
----------------------------------------------------------
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