Contacts of the strand formed by residues 25 - 31 (chain A) in PDB entry 1JGK
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 TYR 25 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A CYS* 5.7 0.4 - - - -
23A GLU 5.1 2.2 - - - -
24A LYS* 1.3 78.4 - - - +
26A CYS* 1.3 71.2 + - - +
27A PHE* 4.1 9.2 - - + -
43A CYS* 3.4 3.7 - - - -
44A ALA 2.7 35.8 + - - +
45A ALA* 2.7 26.6 + - + -
46A THR 2.6 35.8 + - - -
47A CYS* 2.7 32.7 + - + +
59A CYS* 4.0 6.3 - - + -
60A CYS 3.1 15.0 - - - +
61A THR* 4.2 9.9 - - - +
66A ASN* 2.9 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A CYS* 2.0 52.0 - - - -
5A ILE* 5.0 7.2 - - - -
25A TYR* 1.3 76.0 - - - +
27A PHE* 1.3 60.3 + - - +
28A LYS* 4.1 16.1 + - + -
42A GLY 3.8 4.7 - - - -
43A CYS* 3.8 17.3 - - - +
59A CYS* 3.2 3.6 - - - -
60A CYS* 2.8 28.5 + - + +
65A CYS 3.1 13.0 - - - +
66A ASN* 2.5 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.9 13.0 + - + +
26A CYS* 1.3 75.4 - - - +
28A LYS* 1.3 67.1 + - - +
29A GLU* 3.7 33.1 - - + +
40A GLU 3.9 0.7 - - - +
41A ARG* 3.5 18.5 - - - -
42A GLY 2.7 25.0 + - - +
44A ALA* 5.1 6.1 - - + +
46A THR 3.8 11.9 - - - +
47A CYS* 3.5 23.3 - - - -
48A PRO* 3.5 40.6 - - + -
57A VAL* 4.0 8.7 - - + -
58A LEU 3.8 21.1 - - - -
59A CYS* 3.8 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A CYS* 4.1 10.5 - - - -
4A LYS 3.4 24.7 + - - -
5A ILE* 5.0 3.0 - - + +
6A CYS 5.6 1.5 - - - +
26A CYS* 4.3 14.8 - - + -
27A PHE* 1.3 87.1 - - - +
29A GLU* 1.3 61.7 + - - +
39A ILE* 5.7 5.2 - - + -
40A GLU 3.5 2.9 - - - +
41A ARG* 4.3 22.4 - - + -
42A GLY 5.2 0.4 - - - +
56A TYR* 5.4 0.5 - - - -
57A VAL 3.6 0.2 - - - -
58A LEU* 2.7 52.7 + - + +
60A CYS* 4.7 16.2 - - - -
64A ASP 6.1 0.2 - - - -
65A CYS* 5.5 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 3.7 32.8 - - + +
28A LYS* 1.3 76.5 - - - +
30A SER* 1.3 64.3 + - - +
31A TRP* 3.2 37.4 - - - -
39A ILE* 3.2 8.7 - - - +
40A GLU* 2.8 55.6 + - + +
41A ARG 5.8 0.4 - - - +
55A LEU* 3.9 6.9 - - - +
56A TYR* 2.7 18.4 - - - +
57A VAL* 4.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 1.3 79.0 - - - +
31A TRP* 1.3 61.4 + - - +
32A ARG* 3.7 0.9 + - - +
37A THR* 3.9 20.1 + - - -
38A ARG 3.3 6.3 + - - -
39A ILE* 3.8 19.9 - - - +
54A GLY 4.3 0.5 - - - +
55A LEU* 2.8 8.8 - - - -
56A TYR* 2.7 50.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 3.2 35.6 + - - -
30A SER* 1.3 74.3 - - - +
32A ARG* 1.3 79.9 + - - +
33A GLU* 5.4 0.2 - - - +
37A THR* 3.3 4.7 - - - -
38A ARG* 2.8 43.0 + - + +
40A GLU* 4.4 14.5 + - - +
53A TYR* 3.8 28.7 - + + -
55A LEU* 3.8 27.6 - - + -
----------------------------------------------------------
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