Contacts of the helix formed by residues 78 - 92 (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 THR 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B PHE* 4.2 0.9 - - - -
72B VAL* 4.1 9.3 - - - +
77B GLY* 1.3 78.5 - - - +
79B MET* 1.3 64.7 + - - +
80B GLU* 3.3 13.0 + - - +
81B ASP* 2.9 35.9 + - - +
82B PHE* 3.1 11.6 + - - +
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Residues in contact with MET 79 (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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70B ARG 3.5 25.1 - - - +
71B GLU* 4.5 10.3 - - - +
72B VAL* 4.1 18.4 - - + +
78B THR* 1.3 74.7 - - - +
80B GLU* 1.3 57.3 + - - +
82B PHE* 3.1 4.4 + - - +
83B ASP* 2.9 39.6 + - - +
188B PHE* 4.1 12.3 - - + -
189B TRP* 3.9 23.8 - - + -
192B LYS* 3.4 32.5 - - - +
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B THR* 3.1 11.8 + - - +
79B MET* 1.3 79.2 - - - +
81B ASP* 1.3 57.8 + - - +
83B ASP* 3.2 10.5 + - + +
84B ARG* 2.9 46.5 + - - +
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Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 3.9 21.1 - - + +
32B LYS* 3.1 27.2 - - + +
35B THR* 4.6 2.4 + - - -
76B TYR 4.2 0.2 - - - +
77B GLY* 3.2 10.2 - - - -
78B THR* 2.9 38.2 + - - +
80B GLU* 1.3 80.8 - - - +
82B PHE* 1.3 57.1 + - - +
84B ARG* 2.5 38.9 + - - +
85B LEU* 2.9 27.4 + - - +
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Residues in contact with PHE 82 (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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31B PHE* 4.2 17.6 - + + -
51B ILE* 4.3 4.5 - - + -
54B HIS* 3.6 31.4 - + - -
72B VAL* 4.0 19.1 - - + -
78B THR 3.1 3.0 + - - -
79B MET* 3.5 10.1 - - - +
81B ASP* 1.3 79.0 - - - +
83B ASP* 1.3 74.9 + - - +
85B LEU* 3.1 11.0 + - + +
86B MET* 3.0 43.8 + - + +
96B LEU* 3.8 31.6 - - + -
98B VAL* 4.5 1.3 - - + -
189B TRP* 3.5 36.1 - + - -
192B LYS* 4.0 10.1 - - + -
194B VAL* 4.3 8.3 - - + -
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Residues in contact with ASP 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B MET* 2.9 27.2 + - - +
80B GLU* 3.5 9.1 - - - +
82B PHE* 1.3 80.3 - - - +
84B ARG* 1.3 58.3 + - - +
86B MET* 3.3 8.8 + - - +
87B ALA* 2.9 27.9 + - - +
192B LYS* 2.6 34.1 + - - +
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Residues in contact with ARG 84 (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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32B LYS* 3.9 19.0 - - - +
35B THR* 4.7 11.2 + - + +
80B GLU* 2.9 40.4 + - - +
81B ASP* 2.5 35.1 + - - +
82B PHE 3.1 0.2 - - - -
83B ASP* 1.3 75.6 - - - +
85B LEU* 1.3 65.5 + - - +
87B ALA* 3.2 7.4 + - + +
88B GLU* 2.9 40.5 + - + +
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Residues in contact with LEU 85 (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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31B PHE* 4.3 21.1 - - + -
34B LEU* 3.7 39.5 - - + -
35B THR* 3.6 24.8 + - - +
38B LEU* 4.3 10.5 - - + -
51B ILE* 4.8 3.8 - - + -
81B ASP 2.9 13.2 + - - +
82B PHE* 3.3 17.7 - - + +
84B ARG* 1.3 76.1 - - - +
86B MET* 1.3 64.1 + - - +
88B GLU* 3.3 1.2 + - - +
89B LEU* 2.9 47.5 + - + +
96B LEU* 4.5 18.8 - - + -
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Residues in contact with MET 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PHE* 3.0 41.9 + - + +
83B ASP* 3.4 11.0 - - - +
85B LEU* 1.3 76.5 - - - +
87B ALA* 1.3 62.9 + - - +
89B LEU* 3.2 9.1 + - + +
90B LYS* 3.0 25.9 + - + +
96B LEU* 3.4 39.5 - - + +
192B LYS* 4.2 11.9 - - + +
193B GLY* 4.0 27.8 - - - +
194B VAL* 4.4 7.2 - - - +
195B SER* 5.7 0.4 - - - +
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Residues in contact with ALA 87 (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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83B ASP 2.9 17.3 + - - +
84B ARG* 3.2 9.4 + - + +
86B MET* 1.3 77.0 - - - +
88B GLU* 1.3 59.5 + - + +
90B LYS* 3.3 7.8 + - - +
91B LYS* 3.0 40.3 + - - +
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Residues in contact with GLU 88 (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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35B THR* 3.8 20.0 - - + -
38B LEU* 3.6 14.8 - - + -
84B ARG* 2.9 31.8 + - + +
85B LEU 3.9 0.7 - - - +
87B ALA* 1.3 75.2 - - + +
89B LEU* 1.3 65.6 + - - +
91B LYS* 3.2 35.1 + - - +
92B ARG* 2.7 67.1 + - - +
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Residues in contact with LEU 89 (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* 3.6 30.7 - - + -
49B ILE* 3.8 19.5 - - + -
85B LEU* 2.9 34.7 + - + +
86B MET* 3.5 10.3 - - + +
88B GLU* 1.3 76.3 - - - +
90B LYS* 1.3 62.7 + - - +
92B ARG* 3.0 9.0 + - - -
94B MET* 2.8 53.3 + - + +
95B ARG 4.8 2.7 - - - +
96B LEU* 3.7 41.5 - - + +
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Residues in contact with LYS 90 (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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86B MET* 3.0 15.2 + - + +
87B ALA* 3.6 10.5 - - - +
89B LEU* 1.3 74.2 - - - +
91B LYS* 1.3 61.1 + - - +
93B GLY* 2.7 20.7 + - - +
94B MET 4.1 9.2 + - - +
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Residues in contact with LYS 91 (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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87B ALA* 3.0 25.8 + - - +
88B GLU* 3.2 37.8 + - - +
89B LEU 3.3 0.4 - - - -
90B LYS* 1.3 76.0 - - - +
92B ARG* 1.3 63.0 + - + +
93B GLY 3.3 0.6 + - - -
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Residues in contact with ARG 92 (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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35B THR 5.4 3.8 + - - -
38B LEU* 3.8 30.4 - - - +
39B ASP* 2.8 35.1 + - - +
42B LYS* 3.1 37.9 + - + +
88B GLU* 2.7 63.0 + - - +
89B LEU 3.0 7.7 + - - +
90B LYS 3.0 0.6 - - - -
91B LYS* 1.3 80.9 - - + +
93B GLY* 1.3 62.3 + - - +
94B MET* 3.2 18.0 + - + +
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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