Contacts of the helix formed by residues 37 - 45 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.7 16.8 - - + -
21B LYS* 4.2 24.8 - - + +
33B GLY 3.3 13.9 - - - +
34B LEU 2.9 11.4 + - - +
36B GLU* 1.3 87.1 - - + +
38B LEU* 1.3 63.5 + - - +
39B ASP 3.2 2.9 - - - -
40B TYR* 3.0 20.1 + - + +
41B LEU* 3.2 14.6 + - - +
423B TRP* 3.5 57.9 - - + +
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Residues in contact with LEU 38 (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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34B LEU* 3.3 19.3 + - + +
35B THR* 3.3 16.8 + - - +
37B LYS* 1.3 79.1 - - - +
39B ASP* 1.3 58.7 + - - +
41B LEU* 3.2 4.4 + - + +
42B LYS* 2.8 31.0 + - - +
49B ILE* 4.0 16.6 - - + -
85B LEU* 4.2 9.9 - - + +
88B GLU* 3.6 34.3 - - + +
89B LEU* 3.6 43.5 - - + +
92B ARG* 3.8 17.7 - - - +
94B MET* 4.3 4.0 - - - +
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Residues in contact with ASP 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B THR 5.1 0.2 + - - -
36B GLU 4.9 4.8 + - - +
37B LYS* 3.2 1.4 - - - +
38B LEU* 1.3 77.3 - - - +
40B TYR* 1.3 62.9 + - - +
42B LYS* 3.9 5.4 - - - +
43B GLY* 3.0 20.1 + - - -
92B ARG* 2.8 34.9 + - - +
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Residues in contact with TYR 40 (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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13B TYR* 4.2 0.7 - - - -
20B PHE* 5.0 0.2 - + - -
37B LYS* 3.0 16.5 + - + +
39B ASP* 1.3 80.0 - - - +
41B LEU* 1.3 84.5 + - + +
43B GLY* 3.3 2.6 + - - -
44B LEU* 3.2 21.9 + - + +
368B GLU* 2.7 41.6 + - + +
369B LEU* 3.8 7.6 - - - +
421B PHE* 3.8 15.4 - + - -
423B TRP* 3.8 27.1 - + + -
449B ALA* 4.3 7.4 - - + -
453B ILE* 3.6 33.4 - - + -
460B TYR* 3.7 24.3 + + - -
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B TYR* 3.4 51.1 - - + -
15B VAL* 4.4 0.7 - - + -
20B PHE* 4.3 8.3 - - + -
34B LEU* 4.3 16.2 - - + -
37B LYS 3.2 12.1 + - - +
38B LEU* 4.0 7.0 - - + +
40B TYR* 1.3 91.7 - - + +
42B LYS* 1.3 67.2 + - - +
44B LEU* 3.1 14.6 + - + +
45B GLY 3.2 0.3 + - - -
46B ILE* 3.2 26.0 + - + +
49B ILE* 3.4 29.4 - - + -
94B MET* 4.1 11.2 - - + -
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Residues in contact with LYS 42 (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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38B LEU 2.8 17.4 + - - +
39B ASP* 3.9 7.9 - - - +
41B LEU* 1.3 78.3 - - - +
43B GLY* 1.3 57.7 + - - +
45B GLY* 2.9 21.2 + - - -
46B ILE 4.5 8.9 + - - +
47B ASP* 6.4 0.2 - - - +
92B ARG* 3.1 38.9 + - + +
93B GLY* 4.9 3.4 + - - -
94B MET* 4.1 22.9 - - + +
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Residues in contact with GLY 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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39B ASP 3.0 16.4 + - - -
40B TYR 3.3 4.5 + - - -
41B LEU 3.2 0.2 - - - -
42B LYS* 1.3 76.7 - - - +
44B LEU* 1.3 58.3 + - - +
45B GLY* 4.5 0.3 - - - -
460B TYR* 4.1 7.0 - - - -
464B ARG* 3.0 26.7 + - - +
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Residues in contact with LEU 44 (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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13B TYR* 3.9 28.3 - - + -
40B TYR* 3.2 14.8 + - + +
41B LEU* 3.1 13.6 + - + +
43B GLY* 1.3 77.5 - - - +
45B GLY* 1.3 57.0 + - - +
46B ILE* 3.9 15.0 - - + -
363B ILE* 5.2 2.5 - - + -
368B GLU* 4.1 17.5 - - + +
460B TYR* 3.9 29.4 + - + -
463B TYR* 4.2 9.4 - - + -
464B ARG* 3.8 35.4 - - - +
467B ILE* 3.4 24.6 - - + +
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Residues in contact with GLY 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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11B VAL* 4.8 0.7 - - - +
42B LYS* 2.9 13.9 + - - -
43B GLY 3.2 0.6 - - - -
44B LEU* 1.3 80.2 - - - +
46B ILE* 1.3 66.2 + - - +
47B ASP* 3.5 12.6 + - - +
467B ILE* 3.6 23.8 - - - +
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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