Contacts of the strand formed by residues 32 - 36 (chain D) in PDB entry 5BXD
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 32 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ALA* 3.8 10.8 - - + +
31D PRO* 1.3 76.7 - - - +
33D HIS* 1.3 63.9 + - - +
34D ILE* 3.7 10.6 + - + +
42D THR* 3.4 3.2 - - - +
43D SER 2.7 36.9 + - - +
44D SER* 4.0 10.8 - - - -
45D LEU* 4.0 23.6 - - + +
48D LEU* 3.9 21.8 - - + -
60D PHE* 4.1 3.8 - - + -
75D TYR* 3.6 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PRO* 4.3 12.1 - - + +
32D VAL* 1.3 75.0 - - - +
34D ILE* 1.3 61.7 + - - +
41D TYR 3.6 4.2 + - - +
42D THR* 3.5 26.1 + - + +
73D GLN 3.5 23.6 - - - +
74D HIS* 3.2 10.3 - - + -
75D TYR* 2.8 28.9 + - - -
35E ASP* 4.2 6.5 - - - -
69E ASP* 3.2 27.7 + - - -
71E LEU* 6.2 5.5 - - + +
72E LYS* 4.8 15.0 - - + +
74E HIS* 5.8 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D VAL* 3.7 16.6 - - + +
33D HIS* 1.3 80.9 - - - +
35D ASP* 1.3 63.7 + - - +
36D VAL* 3.6 24.0 + - + -
39D HIS 3.6 1.4 - - - +
40D MET* 3.4 6.7 - - - +
41D TYR* 2.8 43.5 + - + +
43D SER* 4.8 6.3 - - - +
48D LEU* 3.7 28.7 - - + -
60D PHE* 3.7 24.9 - - + -
74D HIS* 4.2 3.4 - - - -
75D TYR* 3.4 10.8 - - + +
77D ILE* 4.2 16.4 - - + -
84D PHE* 4.5 11.7 - - + -
88D LEU* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PRO* 5.7 1.2 - - - +
33C HIS* 4.9 6.9 + - - -
42C THR* 4.5 7.6 + - - +
34D ILE* 1.3 70.7 - - - +
36D VAL* 1.3 60.8 + - - +
37D GLY 3.7 0.5 + - - -
38D GLY* 2.7 37.6 + - - -
39D HIS 3.8 2.5 - - - -
40D MET* 3.4 25.9 - - - +
69D ASP* 5.5 0.2 - - - +
74D HIS* 3.6 24.2 - - - +
75D TYR 2.6 14.5 + - - +
76D PHE* 3.2 20.9 - - + -
77D ILE 2.8 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ILE* 3.6 24.0 - - + -
35D ASP* 1.3 70.8 - - - +
37D GLY* 1.3 64.6 + - - +
38D GLY 3.1 0.4 - - - -
39D HIS 2.9 23.3 + - - +
41D TYR* 4.1 5.8 - - + -
77D ILE* 3.3 17.3 - - + +
79D ARG* 3.5 21.8 - - + +
80D ASP 4.0 5.2 - - - +
81D GLY* 3.0 14.6 - - - -
84D PHE* 3.6 55.6 - - + -
----------------------------------------------------------
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