Contacts of the helix formed by residues 36 - 45 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 3.7 22.4 - - + -
33D PRO* 2.9 24.1 + - + +
35D PHE* 1.3 97.8 - + + +
37D ASN* 1.3 64.6 + - - +
38D ASP 3.1 2.9 - - - -
39D TRP* 2.9 55.4 + + + +
40D MET* 3.1 11.9 + - - +
65D LEU* 4.2 7.2 - - + -
66D SER 2.6 30.1 + - - -
67D ILE* 3.5 1.7 - - - -
69D HIS* 3.3 32.8 + - + +
70D LEU* 3.4 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU 5.1 1.9 - - - +
33D PRO 4.2 2.4 - - - +
34D ASP* 3.0 42.4 + - - +
35D PHE 3.4 1.4 + - - -
36D TYR* 1.3 77.8 - - - +
38D ASP* 1.3 62.2 + - - +
40D MET* 3.1 3.5 + - - -
41D PHE* 2.9 32.7 + - - +
503D GOL 3.6 36.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D PHE 4.9 1.9 + - - -
36D TYR 2.9 1.2 + - - -
37D ASN* 1.3 83.8 - - - +
39D TRP* 1.3 62.2 + - - +
41D PHE* 3.7 4.3 + - - +
42D ILE* 3.3 26.7 + - - +
62D LEU* 3.6 21.8 - - + +
63D ASN* 5.2 8.0 + - - +
65D LEU* 4.5 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 4.5 9.0 - - + -
36D TYR* 2.9 44.9 + + + +
38D ASP* 1.3 74.9 - - - +
40D MET* 1.3 65.9 + - - +
42D ILE* 3.2 3.1 + - - -
43D ALA* 3.0 19.1 + - - +
62D LEU* 4.0 25.9 - - + +
63D ASN 4.9 2.2 + - - -
65D LEU* 3.5 48.4 - - + +
67D ILE* 4.4 6.1 - - + -
70D LEU* 5.0 3.1 - - + -
79D ALA* 4.6 11.9 - - + -
82D VAL* 3.9 14.8 - - + -
83D LEU* 3.8 34.1 - - + -
86D ILE* 3.5 14.8 - - + +
106D ASN 4.8 3.8 + - - -
107D ILE* 4.4 7.5 - - + +
110D PRO* 4.1 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D GLU 4.5 11.7 - - - +
31D ASN* 5.6 0.2 - - - +
32D LEU* 3.4 55.4 - - + +
36D TYR 3.1 7.9 + - - +
37D ASN* 3.1 7.8 + - - +
39D TRP* 1.3 79.4 - - - +
41D PHE* 1.3 58.2 + - - +
43D ALA* 3.3 3.0 + - - +
44D LYS* 2.9 42.2 + - + +
78D LEU* 4.8 2.2 - - + -
82D VAL* 3.9 20.4 - - + -
152D PHE* 4.2 15.9 - - - -
503D GOL 3.2 33.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ASN 2.9 12.4 + - - +
38D ASP* 4.2 5.2 - - - +
39D TRP 3.2 0.2 - - - -
40D MET* 1.3 77.9 - - - +
42D ILE* 1.3 71.6 + - + +
44D LYS* 4.5 0.9 - - - -
45D HIS* 2.8 69.0 + + + +
49D LEU* 4.2 20.4 - - + -
58D ARG* 4.5 21.5 - - - -
503D GOL 3.2 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ASP 3.3 16.2 - - - +
39D TRP 3.2 6.3 + - - +
41D PHE* 1.3 84.4 - - + +
43D ALA* 1.3 61.5 + - - +
45D HIS 3.2 11.4 + - - -
46D LEU* 3.4 14.6 + - + +
49D LEU* 4.0 10.2 - - + +
55D LEU* 3.6 28.0 - - + -
58D ARG* 3.8 42.8 - - + +
59D VAL* 4.3 3.4 - - + +
62D LEU* 3.9 24.0 - - + -
86D ILE* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D TRP 3.0 15.2 + - - +
40D MET 3.9 2.2 - - - +
42D ILE* 1.3 77.6 - - - +
44D LYS* 1.3 61.8 + - - +
45D HIS 3.4 0.5 + - - -
46D LEU* 3.6 21.4 + - - +
82D VAL* 3.7 27.4 - - + +
85D CYS* 5.1 3.4 - - + -
86D ILE* 4.1 12.9 - - + +
152D PHE* 3.4 32.1 - - + +
153D SER 4.6 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D GLU 5.5 2.0 - - - -
31D ASN* 4.1 13.8 - - - +
40D MET* 2.9 27.2 + - + +
42D ILE 3.2 0.2 - - - -
43D ALA* 1.3 77.3 - - - +
45D HIS* 1.3 80.0 + - + +
46D LEU 3.6 0.9 - - - -
47D PRO* 4.8 4.3 - - - +
151D LEU 5.3 2.9 - - - +
152D PHE* 4.1 18.6 - - + -
503D GOL 2.4 48.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PHE* 2.8 60.9 + + + +
42D ILE 3.2 5.8 + - - -
43D ALA 3.2 0.6 - - - -
44D LYS* 1.3 101.1 + - + +
46D LEU* 1.3 63.6 + - - +
47D PRO* 3.4 4.9 - - - -
48D ASP* 3.4 21.6 + - + +
49D LEU* 3.0 35.2 + - + +
503D GOL 5.4 1.8 - - - -
----------------------------------------------------------
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