Contacts of the helix formed by residues 36 - 46 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F ILE* 5.9 3.6 - - + -
27F ILE* 4.5 8.7 - - + -
28F LEU* 3.5 30.1 - - + -
33F ASP* 2.8 41.0 + - + +
35F ARG* 1.3 83.3 - - + +
37F LEU* 1.3 52.1 + - - +
38F PRO 3.4 0.2 - - - -
39F LEU* 3.1 9.0 + - + +
40F ILE* 2.6 58.6 + - + +
68F GLN 4.4 7.4 - - - +
69F GLY* 4.5 3.6 - - - +
70F ILE* 3.2 34.3 - - + -
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Residues in contact with LEU 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ASP 3.4 8.6 + - - +
34F LYS* 4.5 6.1 - - - +
36F LEU* 1.3 74.5 - - - +
38F PRO* 1.3 68.4 - - + +
39F LEU 2.8 6.3 + - - -
40F ILE* 4.3 12.6 - - + +
41F HIS* 3.0 53.9 + - + +
44F GLU* 5.9 2.0 - - - +
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Residues in contact with PRO 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F GLN* 4.2 10.0 - - - +
34F LYS 3.1 23.1 - - - +
35F ARG* 3.3 21.3 - - + +
37F LEU* 1.3 92.5 - - + +
39F LEU* 1.3 57.5 + - - +
41F HIS* 3.8 16.3 - - + +
42F ALA* 4.1 6.4 + - - +
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Residues in contact with LEU 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ILE* 5.2 4.3 - - + -
11F VAL* 4.1 18.2 - - + +
12F GLN* 3.2 42.8 - - + +
15F LEU* 3.7 4.3 - - + +
27F ILE* 6.2 0.2 - - + -
35F ARG 4.2 6.5 - - - +
36F LEU* 3.1 16.4 + - + +
37F LEU 2.8 1.2 + - - -
38F PRO* 1.3 78.6 - - + +
40F ILE* 1.3 57.9 + - + +
41F HIS 2.6 15.9 + - - -
42F ALA 3.0 12.1 + - - -
43F LEU* 3.3 34.2 + - + -
70F ILE* 3.8 33.2 - - + -
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Residues in contact with ILE 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F ILE* 3.2 41.1 - - + -
28F LEU* 6.0 0.2 - - + -
36F LEU* 2.6 45.6 + - + +
37F LEU* 3.7 13.0 - - + +
39F LEU* 1.3 73.0 - - + +
41F HIS* 1.3 57.4 + - - +
43F LEU* 4.0 14.8 - - + -
44F GLU* 2.8 34.6 - - + +
50F ILE* 3.4 29.6 - - + -
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Residues in contact with HIS 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F LEU* 3.0 45.7 + - + +
38F PRO* 3.8 12.2 - - + +
39F LEU 2.6 5.9 + - - -
40F ILE* 1.3 75.2 - - - +
42F ALA* 1.3 62.7 + - - +
43F LEU 3.0 5.1 + - - -
44F GLU* 3.1 21.2 + - - +
45F SER* 3.2 15.9 + - - -
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Residues in contact with ALA 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F GLN* 5.3 2.9 - - - +
15F LEU* 3.4 32.5 - - + +
38F PRO 4.1 6.9 + - - +
39F LEU 3.0 3.7 + - - +
41F HIS* 1.3 79.5 - - - +
43F LEU* 1.3 60.5 + - - +
45F SER* 3.8 9.1 + - - -
46F GLN* 3.3 27.9 + - - +
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F VAL* 5.1 2.7 - - + -
15F LEU* 3.4 24.5 - - + -
22F PHE* 4.0 29.4 - - + -
25F VAL* 3.7 35.4 - - + -
27F ILE* 6.2 0.2 - - + -
39F LEU* 3.3 29.5 + - + +
40F ILE* 4.1 11.2 - - + -
41F HIS 3.0 0.6 - - - -
42F ALA* 1.3 77.0 - - - +
44F GLU* 1.3 64.7 + - - +
46F GLN* 3.3 7.8 + - + +
48F VAL* 3.2 35.6 + - + +
50F ILE* 3.5 18.6 - - + -
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Residues in contact with GLU 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F LEU* 5.9 1.6 - - - +
40F ILE* 2.8 36.4 - - - +
41F HIS* 3.1 14.6 + - - +
43F LEU* 1.3 74.9 - - - +
45F SER* 1.3 62.2 + - - +
47F GLY* 2.9 19.9 + - - -
48F VAL 4.7 3.8 - - - +
50F ILE* 3.4 16.8 - - + -
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Residues in contact with SER 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F HIS 3.2 12.2 + - - -
42F ALA* 3.9 11.5 - - - -
44F GLU* 1.3 80.3 - - - +
46F GLN* 1.3 56.9 + - - +
47F GLY* 3.1 3.9 + - - -
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Residues in contact with GLN 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU* 5.1 9.4 - - + +
19F PRO* 4.0 34.9 + - + +
20F GLU* 5.6 0.6 - - - +
42F ALA 3.3 17.2 + - - +
43F LEU* 3.3 8.4 + - + +
44F GLU 3.1 0.6 - - - -
45F SER* 1.3 79.3 - - - +
47F GLY* 1.3 62.9 + - - +
48F VAL* 3.5 15.5 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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