Contacts of the strand formed by residues 20 - 27 (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 LEU 20 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A CYS* 3.8 36.8 - - + +
44A LYS* 5.0 4.9 - - + -
1B LEU* 4.2 4.3 - - - +
3B CYS* 3.8 3.8 - - - -
18B LYS 3.5 0.2 - - - -
19B ASN* 1.3 98.2 - - + +
21B CYS* 1.3 62.4 + - - +
38B CYS* 3.2 10.0 - - - +
39B ILE* 2.8 46.5 + - + +
40B ASN 3.7 12.3 - - - +
41B VAL* 4.1 0.7 - - - -
42B CYS* 3.6 30.7 - - + +
53B CYS* 4.3 6.1 - - + -
54B CYS 4.0 4.9 - - - +
55B SER* 3.9 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LEU* 3.7 14.6 - - - -
2B LYS 3.5 13.9 - - - -
3B CYS* 2.0 48.9 - - - -
20B LEU* 1.3 75.0 - - - +
22B TYR* 1.3 64.0 + - - +
37B GLY 3.4 2.0 - - - -
53B CYS* 3.2 8.7 - - - +
54B CYS 2.8 35.4 + - - +
56B THR 4.4 0.2 - - - -
59B CYS* 4.0 11.7 - - - -
60B ASN* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B CYS* 1.3 78.2 - - - +
23B LYS* 1.3 73.3 + - - +
24B MET* 4.0 19.5 - - + -
35B LYS* 3.1 30.3 - - + +
36B ARG* 3.6 3.4 - - - -
37B GLY 3.1 50.3 + - - -
38B CYS 3.5 11.2 - - - -
39B ILE* 3.2 32.3 - - + -
43B PRO* 4.9 1.8 - - + -
51B TYR* 4.3 13.0 - + - -
52B VAL 3.2 8.3 - - - +
53B CYS* 3.6 20.9 - - - -
54B CYS 4.9 0.2 - - - +
60B ASN* 3.2 23.7 + - - +
61B PO4 2.9 17.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 1.3 83.8 - - - +
24B MET* 1.3 58.8 + - - +
25B MET* 3.6 31.2 - - + -
31B MET 5.8 0.2 - - - -
33B PRO* 3.7 15.9 - - + -
35B LYS 3.9 2.2 - - - -
36B ARG* 3.4 29.4 - - + +
50B LYS 4.2 0.7 - - - -
51B TYR* 3.3 5.7 - - - -
52B VAL* 2.8 49.8 + - + +
59B CYS 5.8 0.6 + - - -
60B ASN* 3.2 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 4.0 4.5 - - + -
23B LYS* 1.3 74.8 - - - +
25B MET* 1.3 58.3 + - - +
26B LEU* 5.3 2.7 - - + -
33B PRO* 3.4 2.4 - - - +
34B VAL* 2.6 53.9 + - + +
35B LYS* 2.9 44.1 + - + +
49B VAL* 4.4 19.3 - - + -
50B LYS 3.2 5.8 - - - +
51B TYR* 3.6 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS* 3.6 35.7 - - + -
24B MET* 1.3 80.1 - - - +
26B LEU* 1.3 64.3 + - - +
31B MET* 3.3 42.4 - - + +
32B VAL 3.4 9.4 - - - +
33B PRO* 3.9 7.4 - - + -
34B VAL* 4.5 0.7 - - - -
48B LEU 3.4 2.3 - - - +
49B VAL* 3.6 2.9 - - - +
50B LYS* 2.8 57.9 + - + +
51B TYR 5.0 0.2 - - - -
52B VAL* 3.4 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B MET* 5.3 2.7 - - + -
25B MET* 1.3 72.6 - - - +
27B ALA* 1.3 62.5 - - - +
28B SER* 3.0 18.7 + - - +
30B LYS 4.2 0.7 - - - -
31B MET* 3.4 20.6 + - - -
32B VAL* 3.1 26.2 + - + +
34B VAL* 4.0 28.9 - - + -
48B LEU* 3.3 17.7 - - + +
49B VAL* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET 3.9 1.2 + - - -
26B LEU* 1.3 71.4 - - - +
28B SER* 1.3 49.5 + - - +
29B LYS 2.5 31.5 + - - +
30B LYS* 4.5 0.2 - - - -
31B MET* 3.4 25.8 - - + +
47B ALA 3.9 9.0 - - - +
48B LEU* 2.8 32.5 + - + +
50B LYS* 4.2 5.2 - - - -
----------------------------------------------------------
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