Contacts of the strand formed by residues 31 - 38 (chain E) in PDB entry 1J8H
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 ASN 31 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA* 4.5 2.4 - - - +
99D ASN 3.2 20.0 + - - -
102D GLU* 3.8 2.4 - - - +
29E HIS* 3.4 0.9 - - - +
30E GLU* 1.3 86.3 - - - +
32E MET* 1.3 66.1 + - - +
33E PHE* 3.8 11.9 - - + -
49E SER 3.3 2.7 - - - -
50E TYR* 3.5 34.0 - - + +
94E SER* 3.0 5.5 - - - -
95E SER* 2.7 52.3 + - - +
97E THR* 3.2 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 32 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E CYS* 3.5 42.2 - - - +
25E GLN* 3.9 18.6 - - + +
29E HIS 4.9 0.4 - - - +
30E GLU 4.0 0.2 + - - -
31E ASN* 1.3 80.5 - - - +
33E PHE* 1.3 65.1 + - - +
48E PHE* 3.4 0.7 - - - -
49E SER 2.9 32.2 + - - +
69E ARG* 3.5 31.9 - - - +
72E LYS 3.6 13.0 - - - +
73E GLU 3.8 11.4 - - - +
75E PHE* 3.4 33.4 - - + -
92E CYS* 4.2 1.1 - - - -
93E ALA 3.2 6.3 - - - +
94E SER* 4.0 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ASN 3.9 6.1 - - - -
102D GLU 4.0 0.2 - - - -
103D LYS* 3.3 36.1 - - + -
31E ASN* 3.8 26.9 - - + -
32E MET* 1.3 75.0 - - - +
34E TRP* 1.3 62.2 + - - +
35E TYR* 3.6 18.2 - - + -
45E LEU* 4.0 7.9 - - + -
47E TYR 3.7 4.9 - - - -
48E PHE* 3.5 17.5 - - + -
50E TYR* 3.8 13.0 - + - -
75E PHE* 3.9 3.4 - - - -
91E LEU 3.8 0.4 - - - +
92E CYS* 3.4 10.6 - - - -
93E ALA* 2.8 43.3 + - + +
95E SER* 3.7 13.9 - - - -
106E TYR* 3.4 37.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E GLN* 3.6 23.8 - - - -
21E LEU* 3.8 29.2 - - + -
22E GLU 3.8 7.0 - - - -
23E CYS* 3.5 21.7 - - + +
33E PHE* 1.3 74.2 - - - +
35E TYR* 1.3 63.8 + - - +
45E LEU* 3.6 4.3 - - - +
46E ILE* 2.8 27.0 + - + -
47E TYR* 2.9 19.1 + - + +
67E VAL* 4.5 0.7 - - + -
75E PHE* 3.0 49.2 + + - -
77E LEU* 3.5 49.9 - - + +
90E TYR* 3.6 25.6 - - + -
91E LEU 3.4 23.8 - - - -
92E CYS* 3.9 5.8 - - + -
112E THR* 5.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D LYS* 4.4 0.3 - - - -
104D LEU 2.9 25.6 + - - -
106D PHE* 3.8 15.0 - + - -
33E PHE* 3.6 20.4 - - + -
34E TRP* 1.3 79.1 - - - +
36E ARG* 1.3 58.2 + - - +
43E LEU* 4.0 28.9 - - + -
44E ARG 3.2 9.2 - - - +
45E LEU* 3.5 40.0 - - + +
46E ILE* 4.1 4.5 - - - +
90E TYR* 3.4 6.1 - - - +
91E LEU* 2.7 45.6 + - + +
93E ALA* 4.7 5.4 - - + -
106E TYR* 2.4 46.3 + + - -
108E PHE* 5.2 6.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 36 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E TYR* 1.3 75.3 - - - +
37E GLN* 1.3 60.6 + - - +
38E ASP* 2.9 37.3 + - - +
42E GLY 3.6 1.0 - - - +
43E LEU* 3.6 2.7 - - - -
44E ARG* 3.0 43.2 + - - +
46E ILE* 3.7 12.7 - - + +
60E ILE* 3.7 30.9 - - + +
65E TYR* 2.8 37.0 + - - -
85E ASN* 3.0 29.7 + - - -
86E GLN* 3.7 5.4 - - - +
87E THR 3.5 9.1 + - - -
88E SER* 3.5 13.7 + - - +
89E MET 3.2 5.8 - - - +
90E TYR* 3.9 8.5 - - + -
91E LEU* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D GLN* 3.0 34.6 + - - +
43D LEU* 4.4 1.0 - - - +
87D GLU* 4.2 5.3 + - - -
89D PHE* 3.5 20.7 - - + -
36E ARG* 1.3 74.8 - - - +
38E ASP* 1.3 66.3 + - - +
39E PRO* 4.6 0.3 - - - +
42E GLY* 3.3 6.7 - - - +
43E LEU* 3.4 24.2 - - + -
88E SER* 3.0 12.5 + - - -
89E MET* 2.6 41.6 + - + +
91E LEU* 3.6 21.6 - - + +
113E ARG* 4.4 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E ARG* 2.9 44.7 + - - +
37E GLN* 1.3 77.6 + - - +
39E PRO* 1.3 70.0 - - + +
40E GLY 3.3 0.2 + - - -
41E LEU* 2.9 40.5 + - + +
42E GLY* 3.2 13.9 + - - +
44E ARG* 3.3 11.6 + - - -
87E THR 3.7 2.9 - - - +
88E SER* 2.7 24.8 + - - -
113E ARG* 5.8 0.2 + - - -
----------------------------------------------------------
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