Contacts of the helix formed by residues 7 - 18 (chain H) 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 GLY 7 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H TYR* 1.3 78.6 - - - +
8H ILE* 1.3 65.4 + - - -
9H HIS 3.5 1.8 - - - -
10H ALA 4.2 0.9 - - - -
11H VAL* 3.1 27.4 + - - +
66H VAL 4.4 2.2 - - - -
67H HIS* 3.0 23.3 + - - -
68H GLN* 4.0 3.4 - - - -
70H ILE* 3.2 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 8 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H GLY* 1.3 69.8 - - - +
9H HIS* 1.3 68.0 + - - +
12H GLN* 3.1 32.4 + - - +
33H ASP* 5.0 2.7 - - - +
35H ARG* 3.0 67.1 - - + +
36H LEU* 4.0 26.5 - - + -
39H LEU* 4.0 17.0 - - + +
67H HIS 3.9 0.2 + - - -
68H GLN* 2.9 34.1 + - + +
70H ILE* 4.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 9 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H GLY 3.5 0.4 - - - -
8H ILE* 1.3 80.8 - - - +
10H ALA* 1.3 62.5 + - + +
12H GLN* 3.8 5.2 + - - +
13H ALA* 2.8 40.1 + - + +
68H GLN* 4.3 1.8 + - - -
140H LYS 5.7 0.9 - - - -
143H CYS* 3.6 54.0 - - + -
144H GLY* 4.2 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ILE* 4.0 12.4 - - + +
6H TYR 3.5 29.8 - - - +
7H GLY 3.7 1.2 + - - -
8H ILE 3.3 0.4 - - - -
9H HIS* 1.3 84.8 - - + +
11H VAL* 1.3 62.9 + - - +
13H ALA* 3.4 7.0 + - - +
14H LEU* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 11 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ILE* 4.1 14.8 - - + -
6H TYR 4.6 0.9 - - - -
7H GLY 3.1 23.1 + - - +
8H ILE 4.0 2.0 - - - +
10H ALA* 1.3 76.6 - - - +
12H GLN* 1.3 62.6 + - - +
14H LEU 3.6 0.2 + - - -
15H LEU* 3.2 6.6 + - - +
22H PHE* 3.2 36.4 - - + -
25H VAL* 5.2 0.4 - - + -
39H LEU* 4.1 13.5 - - + -
43H LEU* 4.6 4.3 - - + -
70H ILE* 3.7 44.0 - - + +
72H ALA* 4.4 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 12 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ILE* 3.1 30.5 + - - +
9H HIS* 3.9 5.0 + - - +
11H VAL* 1.3 76.4 - - - +
13H ALA* 1.3 67.2 + - - +
15H LEU* 3.2 8.9 + - + +
16H GLU* 3.0 51.6 + - + +
39H LEU* 3.9 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C VAL* 5.3 1.3 - - + -
9H HIS* 2.8 31.1 + - + +
10H ALA* 3.6 8.5 - - - +
12H GLN* 1.3 75.6 - - - +
14H LEU* 1.3 57.0 + - - +
16H GLU* 3.4 9.7 + - - +
17H ARG* 2.9 41.7 + - - +
143H CYS 5.1 0.2 - - - +
144H GLY* 4.1 26.0 - - - -
147H GLU* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ILE* 3.7 14.8 - - + -
10H ALA 3.1 13.8 + - - +
11H VAL 3.8 4.3 - - - +
12H GLN 3.1 0.4 - - - -
13H ALA* 1.3 78.0 - - - +
15H LEU* 1.3 62.2 + - - +
17H ARG* 2.9 2.1 + - - +
18H ALA* 2.5 52.8 + - + +
21H ARG* 3.8 21.8 - - + +
22H PHE* 3.9 13.5 - - + -
74H VAL* 3.4 39.5 - - + -
147H GLU* 3.6 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H VAL 3.2 9.4 + - - +
12H GLN* 3.2 11.6 + - + +
14H LEU* 1.3 77.2 - - - +
16H GLU* 1.3 62.2 + - + +
19H PRO* 3.2 40.9 - - + +
22H PHE* 3.2 17.4 - - + -
39H LEU* 4.4 7.9 - - + +
42H ALA* 3.5 34.5 - - + -
43H LEU* 3.5 32.1 - - + +
46H GLN* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 16 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C VAL* 3.0 38.3 - - + +
12H GLN* 3.0 52.0 + - + +
13H ALA* 3.8 5.5 - - - +
15H LEU* 1.3 83.5 - - + +
17H ARG* 1.3 61.0 + - - +
19H PRO* 4.7 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 17 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C VAL* 3.4 48.1 + - + +
223C SER* 3.9 1.0 - - - +
224C SER 5.1 0.6 - - - +
13H ALA* 2.9 23.7 + - - +
14H LEU* 2.9 5.4 + - - -
16H GLU* 1.3 83.0 - - + +
18H ALA* 1.3 60.6 + - + +
19H PRO* 3.8 3.6 - - - +
20H GLU* 4.7 0.5 - - - +
117H ASP* 2.9 40.6 + - - -
143H CYS 4.4 6.9 + - - -
144H GLY* 3.4 31.9 + - - -
145H ALA* 4.2 5.1 - - - +
147H GLU* 4.5 12.0 - - + +
148H SER* 2.8 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LEU* 2.5 28.1 + - + +
17H ARG* 1.3 78.4 - - + +
19H PRO* 1.3 60.0 - - - +
20H GLU* 3.1 26.0 - - - +
21H ARG* 2.9 44.4 + - - +
22H PHE 4.3 0.2 + - - -
147H GLU 4.9 7.9 - - - +
----------------------------------------------------------
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