Contacts of the helix formed by residues 37 - 45 (chain A) in PDB entry 1ZJA
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 LYS 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PHE* 3.7 17.5 - - + -
21A LYS* 4.0 24.2 - - + +
33A GLY 3.3 16.6 - - - +
34A LEU 3.0 7.6 + - - +
36A GLU* 1.3 87.5 + - - +
38A LEU* 1.3 62.9 + - - +
39A ASP 3.2 2.9 - - - +
40A TYR* 3.2 18.2 + - + +
41A LEU* 3.2 15.7 + - - +
423A TRP* 3.6 56.4 - - + +
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Residues in contact with LEU 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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34A LEU* 3.6 21.1 - - + +
35A THR* 3.3 19.0 + - - +
36A GLU 3.5 0.4 - - - -
37A LYS* 1.3 76.3 - - - +
39A ASP* 1.3 60.7 + - - +
41A LEU* 3.3 4.1 + - + +
42A LYS* 2.9 31.2 + - - +
49A ILE* 3.9 17.5 - - + -
85A LEU* 4.2 9.4 - - + +
88A GLU* 3.7 32.3 - - + -
89A LEU* 3.6 42.6 - - + +
92A ARG* 3.9 19.5 - - - +
94A MET* 4.3 4.5 - - + +
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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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35A THR 5.1 0.2 + - - -
36A GLU 4.8 5.1 + - - +
37A LYS* 3.2 0.8 - - - +
38A LEU* 1.3 77.7 - - - +
40A TYR* 1.3 57.1 + - - +
42A LYS* 3.9 5.3 - - - +
43A GLY* 2.9 26.9 + - - -
92A ARG* 2.9 33.2 + - - +
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Residues in contact with TYR 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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13A TYR* 4.1 1.1 - - - -
37A LYS* 3.2 15.7 + - + +
38A LEU 3.2 0.2 - - - -
39A ASP* 1.3 80.8 - - - +
41A LEU* 1.3 83.4 + - + +
43A GLY* 3.8 1.1 - - - -
44A LEU* 3.1 22.4 + - + +
368A GLU* 2.8 40.4 + - + +
369A LEU* 3.8 4.3 - - - +
421A PHE* 3.7 20.3 - + - -
423A TRP* 3.8 26.7 - + + -
449A ALA* 4.3 8.1 - - + -
453A ILE* 3.8 31.2 - - + -
460A TYR* 3.7 25.1 + + - -
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Residues in contact with LEU 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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13A TYR* 3.5 47.1 - - + +
15A VAL* 4.3 0.9 - - + -
20A PHE* 4.2 10.8 - - + -
34A LEU* 4.2 16.8 - - + -
37A LYS 3.2 12.6 + - - +
38A LEU* 3.3 7.4 + - + +
40A TYR* 1.3 90.5 - - + +
42A LYS* 1.3 67.3 + - - +
44A LEU* 3.2 6.5 + - + +
45A GLY 3.1 5.0 + - - -
46A ILE* 3.1 29.1 + - + +
49A ILE* 3.3 31.4 - - + -
94A MET* 4.0 12.1 - - + -
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Residues in contact with LYS 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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38A LEU 2.9 18.7 + - - +
39A ASP* 3.9 6.7 - - - +
41A LEU* 1.3 75.8 - - - +
43A GLY* 1.3 59.5 + - - +
45A GLY* 2.9 20.8 + - - -
46A ILE 4.4 9.4 + - - +
47A ASP* 5.9 2.0 + - - +
92A ARG* 2.7 39.6 + - + +
93A GLY* 4.5 5.7 + - - -
94A MET* 4.0 22.6 - - + +
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Residues in contact with GLY 43 (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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39A ASP 2.9 18.2 + - - -
40A TYR* 3.8 2.0 - - - -
41A LEU 3.3 0.2 - - - -
42A LYS* 1.3 76.9 - - - +
44A LEU* 1.3 60.1 + - - +
45A GLY* 3.4 0.5 + - - -
460A TYR* 4.0 7.0 - - - -
464A ARG* 3.1 26.0 + - - +
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Residues in contact with LEU 44 (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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13A TYR* 3.8 30.1 - - + -
40A TYR* 3.1 16.8 + - + +
41A LEU* 3.4 12.3 - - + +
43A GLY* 1.3 76.8 - - - +
45A GLY* 1.3 57.7 + - - +
46A ILE* 4.0 13.0 - - + -
363A ILE* 5.5 2.2 - - + -
368A GLU* 4.1 17.7 - - + +
460A TYR* 3.8 29.8 + - + -
463A TYR* 4.3 8.5 - - + -
464A ARG* 3.7 35.3 - - - +
467A ILE* 3.5 26.0 - - + +
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Residues in contact with GLY 45 (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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11A VAL* 4.8 0.9 - - - +
42A LYS* 2.9 14.5 + - - -
43A GLY 3.1 1.5 - - - -
44A LEU* 1.3 80.9 - - - +
46A ILE* 1.3 65.0 + - - +
47A ASP* 3.6 12.3 + - - +
467A ILE* 3.6 24.2 - - - +
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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