Contacts of the helix formed by residues 54 - 62 (chain K) in PDB entry 1ZGL
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 54 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76J ARG* 4.6 3.4 - - - -
37K ASP* 3.7 19.2 + - - -
38K LEU* 3.6 10.0 - - - +
49K ALA* 4.2 5.8 - - - -
51K THR 2.8 9.9 + - - -
52K GLU 2.5 10.7 + - - -
53K LEU* 1.3 76.3 - - - +
55K ARG* 1.3 63.6 + - - +
56K PRO* 3.1 4.7 - - - -
57K ASP* 3.0 9.1 + - - +
58K ALA* 2.9 19.1 + - - +
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Residues in contact with ARG 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K ALA* 3.8 26.6 - - + +
52K GLU* 2.7 30.3 + - + +
54K GLY* 1.3 71.3 - - - +
56K PRO* 1.3 63.9 - - + +
58K ALA* 3.5 4.4 - - - +
59K GLU* 3.0 52.3 + - - +
41M GLU* 2.5 30.7 + - - -
110P GLN* 2.5 46.9 + - - +
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Residues in contact with PRO 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76J ARG* 3.8 36.1 - - - +
52K GLU 3.7 6.3 - - - +
53K LEU 4.3 1.3 - - - -
54K GLY* 3.1 8.3 - - - +
55K ARG* 1.3 95.8 - - + +
57K ASP* 1.3 60.1 + - - +
59K GLU* 4.0 8.8 - - - +
60K TYR* 3.3 23.7 + - - +
12L THR* 4.3 2.5 - - - +
1P GLY* 5.6 0.7 - - - -
2P GLY* 4.4 14.8 - - - +
3P GLY 3.9 13.5 + - - +
5P THR* 5.5 6.7 - - + -
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Residues in contact with ASP 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J ASN* 5.0 9.3 + - - -
73J MET* 4.6 5.1 - - - +
76J ARG* 2.6 36.6 + - - -
30K ASP* 6.5 0.9 - - - -
38K LEU* 3.9 24.1 - - + +
54K GLY* 3.0 10.2 + - - +
56K PRO* 1.3 76.7 - - - +
58K ALA* 1.3 70.1 + - - +
60K TYR* 4.1 0.3 - - - +
61K TRP* 3.1 32.9 + - + -
11L ARG* 5.7 0.3 - - - -
12L THR* 2.8 33.7 + - - +
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Residues in contact with ALA 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K LEU* 3.5 16.1 - - + +
47K TYR* 4.4 17.7 - - - +
49K ALA* 4.3 16.4 - - + +
54K GLY 2.9 11.9 + - - +
55K ARG* 3.5 14.8 - - + +
57K ASP* 1.3 72.9 - - - +
59K GLU* 1.3 70.5 + - + +
61K TRP* 2.7 18.2 + - - +
62K ASN* 3.0 16.5 + - - +
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Residues in contact with GLU 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K ARG* 3.0 49.1 + - + +
56K PRO* 4.0 5.2 - - - +
58K ALA* 1.3 78.0 - - + +
60K TYR* 1.3 61.1 + - - +
62K ASN* 3.6 7.3 + - - +
63K SER* 3.4 22.9 + - - -
3P GLY* 3.7 10.2 - - - +
4P VAL* 3.7 33.2 - - + +
26P ILE* 4.3 6.3 - - + +
108P PHE 4.2 3.8 - - - +
109P GLY* 3.5 27.9 - - - -
110P GLN* 4.1 4.9 + - - +
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Residues in contact with TYR 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K PRO 3.3 15.8 + - - +
57K ASP 4.1 0.2 - - - +
58K ALA 2.7 5.7 + - - -
59K GLU* 1.3 76.6 - - - +
61K TRP* 1.3 82.7 + + - +
63K SER* 2.9 10.3 + - - -
64K GLN* 2.5 49.6 + - - -
12L THR* 3.4 24.5 - - + -
13L PRO* 3.7 21.7 - - + +
2P GLY 4.0 16.8 - - - +
3P GLY* 4.8 1.1 - - - -
26P ILE* 3.9 21.1 - - + -
27P SER* 4.0 24.9 - - - -
30V ARG* 3.0 21.7 + - - -
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Residues in contact with TRP 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K LEU* 5.0 10.0 - - + +
47K TYR* 4.2 18.2 - + + -
57K ASP* 3.1 31.1 + - + +
58K ALA 2.7 9.0 + - - +
60K TYR* 1.3 96.0 - + - +
62K ASN* 1.3 55.9 + - - +
63K SER 2.9 5.2 - - - -
64K GLN* 2.9 46.8 + - + +
67K PHE* 3.3 42.4 - + + -
68K LEU* 3.8 8.2 - - - +
9L THR* 4.3 13.0 + - - -
10L PRO* 3.2 42.0 + - + -
11L ARG 4.6 2.5 - - - -
12L THR* 4.4 6.9 - - - +
30V ARG* 3.8 20.6 - - - -
98V ASP* 4.0 14.4 - - - -
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Residues in contact with ASN 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K GLU* 3.0 38.2 + - - +
47K TYR* 3.1 33.3 + - - +
58K ALA* 3.0 19.4 + - - +
59K GLU* 4.0 6.0 - - - +
61K TRP* 1.3 76.6 - - - +
63K SER* 1.3 59.7 + - - +
64K GLN 3.3 0.2 - - - -
65K LYS* 3.7 17.7 - - - +
68K LEU* 3.1 11.9 - - - +
44M GLN* 5.7 3.4 - - - +
107P PHE* 4.3 7.7 - - - -
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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