Contacts of the strand formed by residues 32 - 39 (chain B) in PDB entry 1CDT
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.1 39.8 + - + +
28B SER* 5.0 9.4 - - - +
29B LYS* 5.2 10.8 - - - +
30B LYS 2.7 11.3 + - - +
31B MET* 1.3 72.0 - - - +
33B PRO* 1.3 78.6 - - + +
34B VAL* 3.8 9.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.9 14.4 - - + +
23B LYS* 3.7 30.1 - - + -
24B MET 3.4 7.9 - - - +
25B MET* 3.9 4.0 - - + -
31B MET 3.5 7.6 - - - +
32B VAL* 1.3 95.7 - - + +
34B VAL* 1.3 64.8 + - - +
35B LYS 4.9 2.2 - - - +
36B ARG* 4.1 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.8 19.9 - - - +
24B MET* 2.6 46.1 + - + +
25B MET* 4.4 1.8 - - - -
26B LEU* 4.0 32.8 - - + -
32B VAL* 3.9 15.5 - - + +
33B PRO* 1.3 79.3 - - - +
35B LYS* 1.3 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.8 7.9 - - - +
22B TYR* 3.1 26.2 - - + +
23B LYS* 4.8 0.3 - - - +
24B MET* 2.9 58.1 + - + +
33B PRO* 3.8 0.6 - - - +
34B VAL* 1.3 79.2 + - - +
36B ARG* 1.3 67.9 - - - +
61B PO4 4.5 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASN* 3.5 16.4 - - - +
5B LYS* 3.2 25.8 + - - +
6B LEU* 3.1 27.4 + - + +
8B PRO* 3.0 29.9 - - - +
12B LYS* 5.0 0.9 + - - -
22B TYR* 3.6 13.7 + - - +
23B LYS* 3.4 34.8 - - + +
33B PRO* 4.1 21.7 - - + +
35B LYS* 1.3 83.3 - - - +
37B GLY* 1.3 58.0 - - - +
60B ASN* 2.7 45.0 + - - +
61B PO4 4.5 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B CYS* 3.6 6.0 - - - -
4B ASN 3.9 7.9 - - - -
12B LYS* 4.1 14.4 - - - -
21B CYS* 3.4 2.8 - - - -
22B TYR* 3.1 40.8 + - - -
36B ARG* 1.3 76.4 - - - +
38B CYS* 1.3 60.8 + - - -
60B ASN* 3.1 9.6 + - - +
61B PO4 4.1 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B CYS* 3.6 7.0 - - - -
12B LYS* 3.6 26.2 - - + +
14B CYS* 2.0 53.6 - - + -
15B PRO* 4.5 1.8 - - + -
18B LYS* 3.7 22.5 + - + +
20B LEU 3.2 6.7 - - - +
22B TYR* 3.5 2.8 - - - -
37B GLY* 1.3 74.3 - - - -
39B ILE* 1.3 63.2 - - - +
61B PO4 3.2 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LYS* 3.4 17.4 - - - +
20B LEU* 2.8 50.5 + - + +
21B CYS 4.3 0.7 - - - +
22B TYR* 3.2 40.1 - - + -
38B CYS* 1.3 71.9 - - - +
40B ASN* 1.3 82.8 + - - +
41B VAL* 3.4 30.3 - - + +
42B CYS* 4.3 0.9 - - - +
43B PRO* 4.1 14.8 - - + -
53B CYS* 4.4 2.9 - - - -
----------------------------------------------------------
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