Contacts of the helix formed by residues 35 - 42 (chain A) in PDB entry 1ZD4
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 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLU* 2.4 27.6 + - - -
34A ARG* 1.3 67.1 - - - +
36A LEU* 1.3 64.6 + - - +
37A LEU 3.1 3.1 - - - -
38A ASN* 2.8 11.7 + - - -
39A ASP* 2.7 37.3 + - - +
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU* 3.5 0.6 + - + -
32A LEU* 4.6 8.5 - - + -
33A PRO* 2.6 43.0 + - + +
34A ARG 3.5 0.8 + - - -
35A GLY* 1.3 72.2 - - - +
37A LEU* 1.3 80.1 + - + +
39A ASP* 3.7 8.3 + - - +
40A ALA* 3.4 18.5 + - - +
71A CYS* 4.6 8.1 - - + +
74A CYS* 3.1 39.5 - - + +
75A SER* 3.4 12.6 - - - +
78A ALA* 4.4 9.4 - - + -
82A LEU* 4.2 20.0 - - + -
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.3 39.2 - - + +
26A THR* 3.4 31.6 - - + -
27A GLU* 3.1 23.1 + - + +
32A LEU* 4.1 8.7 - - + -
36A LEU* 1.3 90.3 - - + +
38A ASN* 1.3 66.4 + - - +
40A ALA* 3.5 5.0 + - - +
41A PHE* 3.1 22.5 + - - +
67A MET* 4.1 2.9 - - + +
71A CYS* 4.2 9.2 - - - -
82A LEU* 5.4 0.2 - - + -
86A PHE* 3.5 31.9 - - + -
88A ILE* 5.3 2.2 - - + -
91A ILE* 5.2 1.6 - - + -
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Residues in contact with ASN 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 3.7 20.0 - - - -
23A LEU* 3.8 19.0 - - + +
24A GLY* 5.9 0.7 - - - +
27A GLU* 3.2 9.3 + - - +
35A GLY* 2.8 16.6 + - - +
37A LEU* 1.3 74.7 - - - +
39A ASP* 1.3 66.2 + - - +
41A PHE* 3.1 12.6 - - - +
42A GLN* 3.1 34.5 + - - +
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Residues in contact with ASP 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG 5.0 0.7 - - - +
35A GLY* 2.7 35.0 + - - +
36A LEU* 3.7 5.6 + - - +
38A ASN* 1.3 70.4 - - - +
40A ALA* 1.3 59.0 + - - +
41A PHE 2.9 4.7 - - - -
42A GLN* 2.8 22.0 + - - +
43A LYS* 2.9 14.5 + - - +
74A CYS* 3.8 16.6 - - - -
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU 3.4 8.8 + - - +
37A LEU 3.9 2.0 - - - +
38A ASN 3.5 0.2 - - - -
39A ASP* 1.3 79.1 - - - +
41A PHE* 1.3 59.9 + - - +
43A LYS* 3.8 6.0 + - - -
67A MET* 3.6 6.6 - - - +
70A ASN* 3.3 49.9 + - + +
71A CYS* 3.4 29.8 - - - -
74A CYS* 3.3 13.9 - - - -
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Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 3.3 37.5 - + - -
23A LEU* 3.7 12.8 - - + -
37A LEU 3.1 14.3 + - - +
38A ASN 3.1 11.0 - - - +
39A ASP 2.9 0.6 + - - -
40A ALA* 1.3 79.5 - - - +
42A GLN* 1.3 72.3 + - + +
43A LYS 3.5 0.7 + - - -
50A THR* 2.7 51.0 + - + -
54A MET* 4.9 9.0 - - + -
63A TRP* 3.4 28.5 - + - -
67A MET* 3.3 25.6 - - + -
92A PHE* 4.0 15.7 - + - -
126A TRP* 6.5 1.1 - + - -
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Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 3.6 22.3 - - - -
38A ASN* 3.1 28.1 + - - +
39A ASP* 2.8 7.9 + - - +
41A PHE* 1.3 94.3 - - + +
43A LYS* 1.3 62.6 + - - +
44A GLY 3.3 3.8 + - - -
45A GLY* 3.5 12.9 + - - -
50A THR* 5.2 2.9 - - + -
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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