Contacts of the strand formed by residues 61 - 65 (chain D) in PDB entry 2W3S
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 61 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D VAL 3.2 27.1 - - - +
56D ARG* 3.8 13.2 - - - +
58D SER* 3.2 19.2 + - - +
59D PRO 3.2 3.3 - - - +
60D GLY* 1.3 77.7 - - - +
62D ILE* 1.3 68.3 + - - +
63D ALA* 3.9 8.5 - - - +
64D VAL* 3.8 24.7 - - + -
101D VAL* 4.2 6.7 - - + -
102D ALA 3.7 6.1 - - - +
103D ALA* 4.0 3.8 - - + -
112D ALA* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU* 3.8 40.4 - - + -
60D GLY 3.7 14.4 - - - +
61D VAL* 1.3 83.6 - - - +
63D ALA* 1.3 59.1 + - + +
102D ALA 2.7 16.4 + - - +
103D ALA* 4.3 0.9 - - - -
104D THR* 4.0 12.6 - - + -
249D THR* 4.2 12.3 - - + -
251D ARG* 4.1 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ARG* 6.5 0.2 - - - +
61D VAL* 3.9 1.4 - - - +
62D ILE* 1.3 80.7 - - + +
64D VAL* 1.3 68.8 - - - +
65D PHE* 3.7 28.9 - - + -
102D ALA* 2.9 30.4 + - + +
248D ALA* 5.7 0.2 - - + -
249D THR* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 3.7 34.8 - - + -
55D VAL* 3.7 29.8 - - + -
56D ARG* 3.8 33.8 + - + +
61D VAL* 3.8 14.4 - - + -
63D ALA* 1.3 81.0 - - - +
65D PHE* 1.3 69.1 + - - +
69D ASP* 3.9 8.7 - - - +
99D PHE* 4.3 9.0 - - + -
100D LEU 3.3 7.2 - - - +
101D VAL* 4.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ALA* 3.7 28.3 - - + -
64D VAL* 1.3 79.9 - - - +
66D THR* 1.3 64.2 + - - +
69D ASP* 3.5 22.2 - - + -
70D LEU* 5.3 2.5 - - + -
86D LEU* 4.0 7.6 - - + -
99D PHE* 3.0 13.0 - - - +
100D LEU* 2.8 64.7 + - + +
102D ALA* 4.5 4.0 - - + -
244D VAL* 4.2 17.3 - - + -
245D ALA* 3.7 26.7 - - + -
248D ALA* 3.4 34.5 - - + -
249D THR* 4.8 0.2 - - + -
----------------------------------------------------------
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