Contacts of the helix formed by residues 35 - 44 (chain A) in PDB entry 2M9W
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 35 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.6 7.9 + - - +
22A THR* 4.5 8.6 + - - +
23A LEU* 3.0 40.4 + - + +
25A ARG* 2.7 36.5 + - - +
34A CYS* 1.3 70.6 - - - +
36A ALA* 1.3 62.7 + - - +
38A GLY* 3.3 2.3 + - - -
39A LEU* 3.1 49.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 5.2 0.2 + - - -
34A CYS* 3.3 11.0 - - - +
35A ASN* 1.3 84.0 - - - +
37A CYS* 1.4 59.8 + - - +
39A LEU* 3.8 8.5 + - - +
40A TYR* 3.6 13.9 + - - +
48A ARG* 3.4 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A CYS* 3.2 8.7 - - - -
15A ASN* 3.2 28.3 - - + +
16A CYS* 3.0 10.8 - - - -
27A ASN* 5.8 0.6 - - - +
33A VAL* 3.9 9.6 - - + -
34A CYS* 2.9 10.1 + - - +
36A ALA* 1.4 75.7 - - - +
38A GLY* 1.3 65.3 + - - +
40A TYR* 3.4 14.9 + - - +
41A MET* 3.7 12.1 + - - +
47A PRO* 4.5 5.9 - - + +
48A ARG* 4.1 14.8 - - - +
101A ZN 1.9 38.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 4.5 11.9 - - - -
26A ARG 4.8 7.1 - - - +
27A ASN* 5.3 0.9 - - - -
33A VAL* 3.8 17.0 - - - +
34A CYS 3.1 10.4 + - - -
35A ASN 3.3 3.1 + - - -
37A CYS* 1.3 75.8 - - - +
39A LEU* 1.3 64.0 + - - +
41A MET* 3.3 14.9 + - - +
42A LYS* 3.2 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 3.4 31.9 - - - +
35A ASN* 3.1 41.5 + - - +
36A ALA* 4.0 8.1 - - - +
37A CYS 3.4 0.2 - - - -
38A GLY* 1.3 75.8 - - - +
40A TYR* 1.3 56.9 + - - +
42A LYS* 3.1 16.2 + - + +
43A LEU* 2.9 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA 3.6 5.8 + - - +
37A CYS 3.4 11.2 + - - +
38A GLY 3.3 0.8 - - - -
39A LEU* 1.3 78.9 - - - +
41A MET* 1.4 57.5 + - - +
43A LEU* 4.3 11.2 - - + -
44A HIS* 2.9 53.2 + + - +
46A VAL* 3.1 33.0 - - + +
47A PRO 3.4 21.1 - - - -
48A ARG* 3.6 28.9 - - + +
49A PRO* 4.1 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN* 3.3 26.0 - - + +
28A ALA* 3.0 40.6 - - + +
29A GLU* 4.2 10.5 - - - +
37A CYS 3.7 9.8 + - - +
38A GLY 3.3 9.5 + - - +
39A LEU 3.2 0.2 - - - -
40A TYR* 1.4 76.7 - - - +
42A LYS* 1.3 65.1 + - + +
43A LEU 3.3 0.4 - - - -
44A HIS 3.5 2.1 - - - -
45A GLY* 3.1 39.2 + - - +
46A VAL 3.4 11.4 - - - +
47A PRO* 3.6 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 5.8 7.9 - - - +
26A ARG 4.9 11.4 - - - -
38A GLY 3.2 20.9 - - - +
39A LEU* 3.1 22.6 + - + +
41A MET* 1.3 79.7 - - + +
43A LEU* 1.3 63.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 2.9 28.1 + - + +
40A TYR* 3.7 13.5 - - + +
42A LYS* 1.3 81.0 - - + +
44A HIS* 1.4 83.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 2.9 56.0 + + - +
41A MET 3.5 3.9 + - - +
42A LYS 5.2 0.2 - - - -
43A LEU* 1.4 101.8 + - + +
45A GLY* 1.3 58.1 + - - +
46A VAL* 4.4 14.4 - - + +
----------------------------------------------------------
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