Contacts of the helix formed by residues 36 - 45 (chain A) in PDB entry 7A62
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 36 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.9 20.6 - - + -
33A PRO* 2.8 29.5 + - + +
35A PHE* 1.3 98.0 - + + +
37A ASN* 1.3 64.1 + - - +
38A ASP 3.1 3.4 - - - -
39A TRP* 3.0 55.6 + + + +
40A MET* 3.1 12.1 + - - +
65A LEU* 4.3 7.2 - - + -
66A SER 2.7 30.0 + - - -
67A ILE* 3.4 8.3 + - - -
69A HIS* 3.2 34.7 + - + +
70A LEU* 3.6 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO 4.0 1.0 + - - -
34A ASP* 3.1 22.8 + - + +
35A PHE 3.4 1.4 + - - -
36A TYR* 1.3 76.5 - - - +
38A ASP* 1.3 66.3 + - - +
40A MET* 3.0 10.8 + - - +
41A PHE* 2.7 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE 4.9 2.1 + - - -
36A TYR 3.1 1.0 - - - -
37A ASN* 1.3 85.3 - - - +
39A TRP* 1.3 63.5 + - - +
41A PHE* 4.0 3.5 + - - +
42A ILE* 3.2 28.8 + - - +
62A LEU* 3.7 20.4 - - + +
63A ASN* 5.3 8.5 + - - +
65A LEU* 4.6 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.5 8.7 - - + -
36A TYR* 3.0 45.1 + + + +
38A ASP* 1.3 76.2 - - - +
40A MET* 1.3 65.7 + - - +
42A ILE* 3.1 5.8 + - - +
43A ALA* 3.0 19.2 + - - +
62A LEU* 4.3 21.0 - - + +
63A ASN 4.9 1.8 + - - -
65A LEU* 3.6 45.6 - - + +
67A ILE* 4.5 6.1 - - + -
70A LEU* 5.0 2.0 - - + -
79A ALA* 4.6 13.0 - - + -
82A VAL* 3.8 15.5 - - + -
83A LEU* 3.5 41.7 - - + -
86A ILE* 3.7 10.9 - - + +
106A ASN 4.9 4.6 + - - -
107A ILE* 4.2 12.2 - - + +
110A PRO* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU 4.5 7.4 - - - +
31A ASN* 5.0 0.9 - - - -
32A LEU* 3.5 50.9 - - + +
36A TYR 3.1 7.6 + - - +
37A ASN* 3.0 16.6 + - - +
39A TRP* 1.3 78.5 - - - +
41A PHE* 1.3 65.7 + - - +
43A ALA* 3.2 1.2 + - - +
44A LYS* 2.9 40.6 + - + +
78A LEU* 4.3 5.4 - - + -
82A VAL* 3.7 15.7 - - + +
152A PHE* 4.0 24.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 2.7 34.3 + - - +
38A ASP* 4.4 4.3 - - - +
40A MET* 1.3 73.9 - - - +
42A ILE* 1.3 70.6 + - + +
44A LYS* 4.8 1.8 - - - -
45A HIS* 2.9 64.2 + + + +
49A LEU* 4.9 8.3 - - + -
58A ARG* 3.6 29.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP 3.2 17.7 - - - +
39A TRP 3.1 6.6 + - - +
41A PHE* 1.3 84.8 - - + +
43A ALA* 1.3 62.5 + - - +
45A HIS 3.2 11.6 + - - -
46A LEU* 3.3 13.9 + - + +
49A LEU* 3.9 11.6 - - + +
55A LEU* 3.6 28.3 - - + -
58A ARG* 3.8 38.8 - - + +
59A VAL* 4.3 5.6 - - + +
62A LEU* 3.9 22.7 - - + -
86A ILE* 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TRP 3.0 14.8 + - - +
40A MET 3.8 2.2 - - - +
42A ILE* 1.3 77.0 - - - +
44A LYS* 1.3 63.5 + - - +
45A HIS 3.2 0.9 + - - -
46A LEU* 3.4 25.7 + - - +
47A PRO* 5.3 0.2 - - - +
82A VAL* 3.7 28.3 - - + +
85A CYS* 5.1 3.4 - - + -
86A ILE* 4.3 4.0 - - + +
152A PHE* 3.6 34.2 - - + +
153A SER 4.6 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 5.1 8.6 + - - +
40A MET* 2.9 37.6 + - + +
41A PHE* 4.8 0.7 - - - -
43A ALA* 1.3 75.9 - - - +
45A HIS* 1.3 78.4 + - + +
46A LEU 3.6 0.8 + - - -
47A PRO* 4.6 6.0 - - - +
151A LEU* 3.0 37.2 + - - +
152A PHE* 3.5 24.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 2.9 59.9 + + + +
42A ILE 3.2 5.6 + - - -
43A ALA 3.1 0.8 - - - -
44A LYS* 1.3 91.3 + - + +
46A LEU* 1.3 64.3 + - - +
47A PRO* 3.4 4.5 - - - -
48A ASP* 3.4 23.6 + - + +
49A LEU* 2.9 34.9 + - + +
----------------------------------------------------------
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