Contacts of the strand formed by residues 53 - 57 (chain A) in PDB entry 1XWD
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 53 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 4.4 3.8 - - + -
37A TYR 3.8 6.1 - - - +
39A THR* 3.1 7.7 + - - -
51A LYS* 3.1 3.7 - - - +
52A ASN* 1.3 86.0 - - + +
54A THR* 1.3 73.4 + - - +
27B TRP* 3.6 41.7 - - + -
53B PHE* 4.3 9.4 - - + -
56B LEU* 3.8 18.2 - - + -
58B TYR* 5.5 0.4 - - - +
77B PRO* 4.2 5.8 - - + -
91B SER* 3.4 14.9 + - - +
92B THR* 3.3 17.2 - - + +
93B ASP* 2.9 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG 4.1 0.3 - - - +
36A ALA* 3.2 3.5 - - - +
37A TYR* 2.8 72.7 + - + +
39A THR* 2.8 30.6 + - - +
40A PRO* 4.6 2.0 - - + +
43A SER* 5.5 1.0 + - - -
53A VAL* 1.3 74.1 + - - +
55A SER* 1.3 65.1 + - - +
56A GLU* 4.3 0.7 - - + -
93B ASP* 3.7 21.0 + - - +
95B THR* 4.2 14.4 - - - +
98B GLY* 4.3 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG 3.3 9.6 + - - -
36A ALA* 4.5 7.6 - - - -
54A THR* 1.3 76.4 - - - +
56A GLU* 1.3 68.0 + - - +
57A SER* 4.1 4.3 + - - -
50B THR* 4.1 18.9 - - - +
51B CYS 5.1 0.7 - - - -
52B THR* 5.2 2.0 - - - -
87B CYS* 4.3 10.1 - - - +
92B THR* 3.5 20.8 - - - +
93B ASP 2.9 7.6 + - - +
94B CYS* 4.6 2.5 - - - +
95B THR* 3.1 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 5.7 0.7 - - - -
34A SER* 3.4 3.4 - - - -
35A ARG* 2.9 64.0 + - + +
37A TYR* 2.6 42.0 + - + +
54A THR* 4.7 1.1 - - + -
55A SER* 1.3 77.7 + - - +
57A SER* 1.3 60.1 + - - +
50B THR* 4.4 0.2 + - - -
95B THR 3.4 5.2 - - - -
96B VAL 3.0 18.1 - - - +
97B ARG* 4.2 8.8 - - - +
98B GLY 2.8 23.3 + - - +
100B GLY 4.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE 4.3 0.7 - - - -
34A SER* 3.7 7.2 - - - +
55A SER* 4.1 5.1 + - - -
56A GLU* 1.3 74.3 - - - +
58A THR* 1.3 64.5 + - - +
85A SER 4.6 0.2 - - - +
86A THR* 5.1 0.3 - - - -
87A CYS* 4.0 17.5 + - - +
90A HIS* 3.6 24.4 + - - -
50B THR* 2.6 34.0 + - - -
95B THR 3.4 8.0 + - - +
96B VAL* 3.9 20.7 + - - +
----------------------------------------------------------
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