Contacts of the helix formed by residues 42 - 48 (chain B) in PDB entry 1GZY
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 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B PHE 3.0 13.9 - - - -
26B ASN* 4.0 2.2 + - - -
27B LYS* 4.5 2.2 - - - -
41B THR* 1.3 80.2 + - - +
43B ILE* 1.3 66.1 + - - -
44B VAL 3.4 2.2 - - - -
45B ASP* 3.1 16.2 + - - +
46B GLU* 3.3 13.6 + - - +
60B TYR* 3.1 22.8 + - - -
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 3.7 19.5 - - + -
14B LEU* 3.4 34.8 - - + -
24B TYR 4.6 0.2 - - - +
25B PHE* 2.7 48.4 + - + +
42B GLY* 1.3 68.5 - - - -
44B VAL* 1.3 62.6 + - + +
46B GLU 3.2 1.1 + - - +
47B CYS* 2.7 49.3 + - - +
57B LEU* 4.0 13.9 - - + +
60B TYR* 3.1 40.8 - - + -
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLY 6.1 1.6 - - - +
10B LEU* 4.0 18.8 - - + -
25B PHE* 4.7 8.3 + - + -
42B GLY 3.4 0.4 - - - -
43B ILE* 1.3 83.7 - - + +
45B ASP* 1.3 62.9 + - - +
48B CYS* 2.7 45.3 + - + +
49B PHE* 3.0 38.4 + - + -
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Residues in contact with ASP 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLN 5.2 0.7 - - - +
41B THR* 3.4 25.4 + - - +
42B GLY* 3.1 25.2 + - - +
43B ILE 3.2 0.8 - - - -
44B VAL* 1.3 83.0 - - - +
46B GLU* 1.3 61.4 + - + +
49B PHE* 3.5 28.6 - - + +
50B ARG* 3.2 41.9 + - - +
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS* 4.1 19.4 + - - -
41B THR* 5.4 3.9 + - - +
42B GLY* 3.3 11.0 + - - +
43B ILE 3.2 2.7 + - - +
45B ASP* 1.3 80.0 - - + +
47B CYS* 1.3 60.7 + - - +
50B ARG* 3.1 10.2 - - - +
51B SER 3.3 0.9 - - - +
52B CYS* 2.8 10.6 - - - +
56B ARG* 2.7 65.9 + - - +
59B MET* 5.1 8.9 - - - +
60B TYR* 3.0 28.6 + - - +
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Residues in contact with CYS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B GLU 3.7 1.7 - - - +
4B THR* 3.5 1.9 - - - -
5B LEU* 2.7 32.7 + - + -
10B LEU* 4.0 12.1 - - + -
43B ILE* 2.7 42.0 + - + +
46B GLU* 1.3 73.7 - - - +
48B CYS* 1.3 50.7 + - - +
50B ARG 2.8 13.3 - - - +
52B CYS* 2.0 46.0 - - - -
56B ARG* 3.4 14.4 - - - -
57B LEU* 4.2 8.1 - - + -
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Residues in contact with CYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B THR* 3.5 22.2 + - - +
5B LEU 3.3 12.1 - - - +
6B CYS* 2.0 48.2 - - - -
7B GLY 5.1 0.9 - - - -
10B LEU* 5.0 0.4 - - + -
44B VAL* 2.7 37.8 + - + +
47B CYS* 1.3 72.1 - - - +
49B PHE* 1.3 78.5 + - - +
50B ARG 3.1 1.3 + - - -
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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