Contacts of the helix formed by residues 33 - 44 (chain B) in PDB entry 1ZZJ
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 33 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ILE* 3.2 20.6 - - - -
30B GLY 2.8 15.0 + - - -
32B GLY* 1.3 71.8 - - - +
34B GLN* 1.3 63.7 + - - +
35B ARG 3.2 0.3 + - - -
36B ILE* 3.4 6.4 - - - +
37B LYS* 3.2 23.1 + - - +
7D C 3.6 4.0 - - - -
8D C 3.2 25.3 + - - +
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Residues in contact with GLN 34 (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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29B ILE 3.6 0.8 + - - -
30B GLY 4.2 0.6 + - - -
31B LYS 3.2 20.0 + - - +
32B GLY* 3.2 9.4 + - - -
33B GLY* 1.3 78.2 - - - +
35B ARG* 1.3 57.9 - - + +
37B LYS* 3.4 8.8 + - - +
38B GLN* 3.0 29.4 + - - +
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Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER 3.6 11.2 - - - +
28B ILE 3.1 16.2 - - - +
29B ILE 3.0 14.2 + - - +
30B GLY* 4.1 8.2 - - - -
34B GLN* 1.3 76.2 - - + +
36B ILE* 1.3 65.6 + - - +
38B GLN* 3.3 29.0 + - - +
39B ILE* 3.0 41.7 + - + +
76B LEU* 2.9 42.4 + - - +
79B ASN* 4.4 7.9 + - - +
80B SER* 2.6 29.2 + - - +
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 3.1 24.5 + - + +
29B ILE* 3.1 11.5 + - + +
33B GLY 3.4 10.3 - - - +
35B ARG* 1.3 75.7 - - - +
37B LYS* 1.3 61.0 + - - +
39B ILE* 2.8 23.4 + - + -
40B ARG* 2.9 56.3 + - + +
47B ILE* 4.0 17.7 - - + +
49B ILE* 3.3 29.8 - - + -
77B LEU* 5.5 0.2 - - + -
8D C 3.3 24.5 - - + +
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Residues in contact with LYS 37 (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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33B GLY 3.2 10.6 + - - +
34B GLN* 3.6 15.7 - - - +
36B ILE* 1.3 81.8 - - + +
38B GLN* 1.3 61.6 + - - +
40B ARG* 3.6 15.7 + - - +
41B HIS* 3.3 23.7 + - - +
8D C 6.3 0.9 - - + -
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Residues in contact with GLN 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 GLN 3.0 17.2 + - - +
35B ARG* 3.5 31.8 - - - +
36B ILE 3.1 0.2 - - - -
37B LYS* 1.3 74.7 - - - +
39B ILE* 1.3 65.6 + - + +
41B HIS* 4.0 3.3 - - - -
42B GLU* 2.9 53.8 + - + +
76B LEU* 6.3 1.6 - - + -
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Residues in contact with ILE 39 (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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28B ILE* 3.9 9.9 - - + +
35B ARG* 3.0 39.7 - - + +
36B ILE* 2.8 9.9 + - + +
38B GLN* 1.3 79.7 - - + +
40B ARG* 1.3 54.9 + - - +
43B SER* 2.8 33.3 + - - -
47B ILE* 3.4 23.3 - - + -
73B ALA* 4.2 10.1 - - - +
76B LEU* 3.7 27.8 - - + +
77B LEU* 4.0 16.4 - - + -
80B SER* 3.2 27.1 - - - +
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Residues in contact with ARG 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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36B ILE* 2.9 41.7 + - + +
37B LYS* 3.8 12.4 - - - +
38B GLN 3.3 0.2 - - - -
39B ILE* 1.3 77.7 - - - +
41B HIS* 1.3 58.3 + - + +
43B SER* 4.2 0.4 - - - -
44B GLY* 3.0 27.4 + - - -
45B ALA 3.6 17.0 - - - +
46B SER* 5.2 1.1 - - - +
47B ILE* 2.6 52.7 + - + +
48B LYS* 4.6 0.6 - - - +
8D C 2.7 41.0 + - - +
9D C 3.5 30.1 + - - -
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Residues in contact with HIS 41 (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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37B LYS 3.3 14.8 + - - +
38B GLN* 4.2 4.5 - - - +
39B ILE 3.4 0.2 - - - -
40B ARG* 1.3 78.0 - - - +
42B GLU* 1.3 69.0 + - + +
44B GLY* 3.6 6.9 + - - -
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Residues in contact with GLU 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 GLN* 2.9 46.5 + - + +
41B HIS* 1.3 83.2 - - + +
43B SER* 1.3 59.0 + - - +
72B ASN* 4.0 8.2 - - - +
76B LEU* 3.7 20.9 - - + -
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Residues in contact with SER 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE 2.8 24.1 + - - -
40B ARG 3.9 0.3 + - - -
42B GLU* 1.3 76.8 - - - +
44B GLY* 1.3 55.9 + - - +
45B ALA* 3.0 22.3 + - - +
47B ILE* 4.2 0.7 - - - +
69B GLN* 3.2 31.2 - - - +
72B ASN* 3.7 13.1 - - - +
73B ALA* 3.5 34.3 - - - +
76B LEU* 3.7 5.8 - - - +
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Residues in contact with GLY 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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40B ARG 3.0 15.7 + - - -
41B HIS 3.6 5.4 + - - -
42B GLU 3.4 2.8 - - - -
43B SER* 1.3 76.7 - - - +
45B ALA* 1.3 62.5 + - - +
46B SER 3.9 0.5 + - - -
64B THR 4.7 0.3 - - - +
65B GLY* 5.4 0.2 - - - -
69B GLN* 3.8 21.9 + - - +
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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