Contacts of the helix formed by residues 36 - 47 (chain A) in PDB entry 1GZ0
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 LEU 36 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.3 37.2 - - + -
27A ILE* 5.3 9.0 - - + -
28A LEU 5.8 0.2 - - - +
31A ARG* 3.0 36.6 - - - +
33A ASP* 2.9 19.9 + - + +
35A ARG* 1.3 81.7 - - + +
37A LEU* 1.3 52.4 + - + +
38A PRO* 3.2 2.7 - - - -
39A LEU* 2.6 34.7 + - + +
40A ILE* 2.6 32.5 + - + +
68A GLN 4.3 7.9 - - - +
69A GLY 4.5 8.7 - - - +
70A ILE* 4.6 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU* 3.6 35.9 - - - +
33A ASP 3.4 20.4 + - - +
34A LYS* 5.1 8.5 - - + -
36A LEU* 1.3 73.9 - - + +
38A PRO* 1.3 61.1 - - + +
39A LEU 2.6 10.7 + - - -
40A ILE* 3.6 23.8 - - + -
41A HIS* 2.8 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN* 4.7 10.7 + - - +
34A LYS* 3.5 27.6 - - + +
35A ARG 4.3 2.7 - - - +
36A LEU 3.4 4.9 - - - +
37A LEU* 1.3 93.2 - - + +
39A LEU* 1.3 56.0 + - - -
41A HIS* 4.6 4.7 - - + -
42A ALA* 4.1 12.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
8A ILE* 4.2 13.7 - - + -
11A VAL* 3.5 14.8 - - + -
12A GLN* 3.5 42.6 - - + +
15A LEU* 3.4 14.6 - - + -
35A ARG 4.7 0.9 - - - +
36A LEU* 2.6 26.1 + - + +
37A LEU 2.6 0.6 + - - -
38A PRO* 1.3 74.6 - - - +
40A ILE* 1.3 62.9 + - + +
41A HIS 3.1 1.1 - - - -
42A ALA* 3.0 5.5 + - - +
43A LEU* 2.8 52.2 + - + +
70A ILE* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 4.5 29.2 - - + -
32A GLU* 5.7 0.9 - - - +
36A LEU* 2.6 30.8 + - + +
37A LEU* 3.5 41.1 - - + +
39A LEU* 1.3 74.1 - - + +
41A HIS* 1.3 60.8 + - + +
43A LEU* 3.3 15.8 + - + +
44A GLU* 2.9 49.3 + - - +
50A ILE* 3.8 12.1 - - + +
70A ILE* 6.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 2.8 42.9 + - + +
38A PRO* 5.0 3.6 - - + -
40A ILE* 1.3 79.1 - - + +
42A ALA* 1.3 53.5 + - - +
44A GLU* 3.0 22.4 + - - +
45A SER* 2.7 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.7 25.1 - - + -
38A PRO 4.1 12.9 + - - +
39A LEU* 3.0 9.8 + - - +
41A HIS* 1.3 78.1 - - - +
43A LEU* 1.3 58.0 + - - +
45A SER* 3.2 8.7 + - - -
46A GLN* 2.9 32.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
15A LEU* 3.9 12.8 - - + -
22A PHE* 3.6 34.8 - - + -
25A VAL* 3.9 29.2 - - + -
27A ILE* 5.4 1.8 - - + -
39A LEU* 2.8 42.2 + - + +
40A ILE* 3.4 17.9 - - + +
42A ALA* 1.3 76.1 - - - +
44A GLU* 1.3 61.9 + - - +
46A GLN* 3.2 7.0 + - - +
47A GLY 3.1 4.2 + - - -
48A VAL* 3.0 36.2 + - + -
50A ILE* 4.3 11.9 - - + -
70A ILE* 4.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 2.9 36.6 + - - +
41A HIS* 3.0 36.1 + - - +
43A LEU* 1.3 77.0 - - - +
45A SER* 1.3 60.9 + - - +
47A GLY* 3.0 13.5 + - - -
48A VAL 4.7 4.3 - - - -
50A ILE* 3.4 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A HIS* 2.7 29.3 + - - +
42A ALA* 3.2 9.2 + - - -
44A GLU* 1.3 73.7 - - - +
46A GLN* 1.3 62.7 + - - +
47A GLY* 3.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.7 22.2 + - + +
19A PRO* 3.2 37.2 - - + +
20A GLU* 4.9 0.5 + - - -
42A ALA 2.9 18.4 + - - +
43A LEU* 3.2 6.9 + - - +
45A SER* 1.3 76.2 - - - +
47A GLY* 1.3 61.1 + - - +
48A VAL* 3.8 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU 3.0 15.2 + - - -
45A SER 3.1 1.4 - - - -
46A GLN* 1.3 80.8 - - - +
48A VAL* 1.3 64.4 + - - +
49A VAL* 3.7 5.2 + - - +
----------------------------------------------------------
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