Contacts of the helix formed by residues 36 - 47 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C ILE* 3.1 31.0 - - + -
27C ILE* 5.3 7.2 - - + -
28C LEU* 5.5 7.4 - - + +
31C ARG 5.9 1.1 - - - +
33C ASP* 2.5 39.7 + - + +
35C ARG* 1.3 75.1 - - + +
37C LEU* 1.3 55.7 + - + +
38C PRO* 3.3 0.7 - - - -
39C LEU* 2.6 33.0 + - + +
40C ILE* 2.8 24.9 + - + +
68C GLN 4.0 9.9 - - - +
69C GLY* 4.0 21.1 - - - +
70C ILE* 3.7 23.6 - - + -
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLU* 4.2 21.3 - - + +
33C ASP* 2.8 48.4 + - + +
34C LYS* 4.0 16.4 - - + +
36C LEU* 1.3 70.7 - - - +
38C PRO* 1.3 70.6 - - + +
40C ILE* 3.0 16.3 + - + +
41C HIS* 2.8 44.9 + - + -
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Residues in contact with PRO 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LYS 3.0 28.5 - - - +
35C ARG* 3.7 10.3 - - - +
36C LEU 3.4 0.4 - - - -
37C LEU* 1.3 87.5 - - + +
39C LEU* 1.3 57.9 + - + +
41C HIS* 3.8 8.2 - - + +
42C ALA* 3.1 27.7 + - - +
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.6 27.1 - - + +
11C VAL* 3.6 25.6 - - + -
12C GLN* 4.1 26.0 - - - +
15C LEU* 3.8 25.4 - - + -
35C ARG 4.5 3.6 - - - +
36C LEU* 2.6 22.8 + - + +
38C PRO* 1.3 73.4 - - - +
40C ILE* 1.3 64.8 + - + -
42C ALA* 3.3 4.6 + - - +
43C LEU* 3.0 28.9 + - + +
70C ILE* 3.4 31.0 - - + -
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Residues in contact with ILE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ILE* 4.1 34.1 - - + -
36C LEU* 2.8 36.5 + - + +
37C LEU* 3.4 16.6 - - + +
39C LEU* 1.3 75.7 - - + +
41C HIS* 1.3 64.0 + - + +
43C LEU* 2.9 14.6 + - + +
44C GLU* 2.9 42.7 + - + +
50C ILE* 3.6 18.4 - - + -
70C ILE* 6.1 1.3 - - + -
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Residues in contact with HIS 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LEU* 2.8 46.4 + - + +
38C PRO* 3.8 8.1 - - + +
40C ILE* 1.3 81.9 - - + +
42C ALA* 1.3 57.0 + - - +
44C GLU* 3.4 17.8 + - - +
45C SER* 2.8 33.5 + - - +
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Residues in contact with ALA 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.5 28.5 - - + -
38C PRO 3.1 17.1 + - - +
39C LEU* 3.7 1.3 - - - +
41C HIS* 1.3 75.7 - - - +
43C LEU* 1.3 60.6 + - - +
45C SER* 3.3 8.1 + - - -
46C GLN* 2.8 33.6 + - - +
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C VAL* 4.6 4.9 - - + -
15C LEU* 4.6 8.1 - - + -
22C PHE* 4.0 25.6 - - + -
25C VAL* 3.8 42.2 - - + -
27C ILE* 5.6 0.7 - - + -
39C LEU* 3.0 29.9 + - + +
40C ILE* 2.9 11.0 + - + +
42C ALA* 1.3 72.8 - - - +
44C GLU* 1.3 62.5 + - - +
46C GLN* 2.8 22.4 + - - +
47C GLY 2.9 9.2 + - - -
48C VAL* 3.0 25.6 + - + -
50C ILE* 3.8 19.7 - - + -
70C ILE* 4.6 5.6 - - + -
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Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ILE* 2.9 28.5 + - - +
41C HIS* 3.6 21.0 + - - +
43C LEU* 1.3 73.9 - - - +
45C SER* 1.3 59.7 + - - +
47C GLY* 2.8 20.8 + - - -
48C VAL 4.4 7.2 - - - +
50C ILE* 3.7 17.3 - - + +
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Residues in contact with SER 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C HIS* 2.8 24.7 + - - +
42C ALA* 3.4 9.5 - - - -
44C GLU* 1.3 76.0 - - - +
46C GLN* 1.3 59.2 + - - +
47C GLY* 3.0 4.7 + - - -
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Residues in contact with GLN 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.5 23.0 - - + +
19C PRO* 3.6 32.8 - - + +
42C ALA 2.8 16.9 + - - +
43C LEU* 2.8 12.5 + - - +
45C SER* 1.3 74.5 - - - +
47C GLY* 1.3 58.4 + - - +
48C VAL* 3.2 17.4 + - + +
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Residues in contact with GLY 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C GLU* 2.8 17.2 + - - -
45C SER 3.0 2.3 - - - -
46C GLN* 1.3 78.8 - - - +
48C VAL* 1.3 62.7 + - - +
49C VAL* 3.6 8.0 + - - +
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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