Contacts of the helix formed by residues 78 - 92 (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 THR 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A PHE* 4.4 0.2 - - - -
72A VAL* 4.0 11.6 - - - +
77A GLY* 1.3 79.1 - - - +
79A MET* 1.3 66.7 + - - +
80A GLU* 3.3 13.0 + - - +
81A ASP* 2.9 37.4 + - - +
82A PHE 3.0 9.9 + - - -
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Residues in contact with MET 79 (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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70A ARG 3.5 25.6 - - - +
71A GLU* 4.5 8.7 - - - +
72A VAL* 3.9 23.1 - - + +
78A THR* 1.3 75.1 - - - +
80A GLU* 1.3 57.9 + - - +
82A PHE* 3.1 4.6 + - - +
83A ASP* 2.8 39.4 + - - +
188A PHE* 4.1 13.7 - - + -
189A TRP* 3.8 21.3 - - + -
192A LYS* 3.6 31.9 - - - +
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A THR* 3.1 12.1 + - - +
79A MET* 1.3 79.8 - - - +
81A ASP* 1.3 56.9 + - - +
83A ASP* 3.3 10.2 + - + +
84A ARG* 2.9 46.8 + - + +
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Residues in contact with ASP 81 (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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31A PHE* 4.0 21.7 - - + +
32A LYS* 3.3 23.1 - - + +
35A THR* 4.7 1.7 + - - -
76A TYR 4.4 0.7 - - - +
77A GLY* 3.2 9.6 - - - -
78A THR* 2.9 36.2 + - - +
80A GLU* 1.3 73.5 - - - +
82A PHE* 1.3 61.3 + - - +
84A ARG* 2.8 43.6 + - - +
85A LEU* 2.9 27.5 + - - +
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Residues in contact with PHE 82 (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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31A PHE* 3.9 19.4 - + + -
51A ILE* 4.4 3.4 - - + -
54A HIS* 3.6 31.9 - + - -
72A VAL* 4.0 18.6 - - + -
78A THR 3.0 6.6 + - - +
79A MET* 3.5 7.2 - - - +
81A ASP* 1.3 77.2 - - - +
83A ASP* 1.3 73.0 + - - +
85A LEU* 3.0 11.5 + - + +
86A MET* 3.0 39.7 + - + +
96A LEU* 3.8 31.4 - - + -
98A VAL* 4.4 2.0 - - + -
189A TRP* 3.6 29.2 - + - -
192A LYS* 3.9 14.6 - - - -
194A VAL* 4.2 11.0 - - + -
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A MET* 2.8 27.5 + - - +
80A GLU* 3.6 9.1 - - + +
82A PHE* 1.3 79.4 - - - +
84A ARG* 1.3 56.5 + - - +
86A MET* 3.2 8.2 + - - +
87A ALA* 3.0 28.6 + - - +
192A LYS* 2.6 37.3 + - - -
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Residues in contact with ARG 84 (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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31A PHE 6.0 0.2 - - - -
32A LYS* 3.8 25.0 - - - +
35A THR* 4.8 15.1 + - + -
80A GLU* 2.9 41.9 + - + +
81A ASP* 2.8 41.6 + - - +
82A PHE 3.2 0.2 - - - -
83A ASP* 1.3 73.2 - - - +
85A LEU* 1.3 66.0 + - - +
87A ALA* 3.3 6.5 + - + +
88A GLU* 2.9 37.1 + - + +
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Residues in contact with LEU 85 (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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31A PHE* 3.9 26.5 - - + +
34A LEU* 3.8 37.2 - - + -
35A THR* 3.6 25.0 + - - +
38A LEU* 4.2 9.6 - - + -
51A ILE* 4.7 4.5 - - + -
81A ASP 2.9 13.6 + - - +
82A PHE* 3.0 13.4 + - + +
84A ARG* 1.3 76.6 - - - +
86A MET* 1.3 64.9 + - - +
88A GLU* 3.4 1.6 + - - +
89A LEU* 3.0 47.9 + - + +
96A LEU* 4.6 18.4 - - + -
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Residues in contact with MET 86 (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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82A PHE* 3.0 38.7 + - + +
83A ASP* 3.4 9.6 - - - +
84A ARG 3.2 0.2 - - - -
85A LEU* 1.3 76.9 - - - +
87A ALA* 1.3 57.6 + - - +
89A LEU* 3.2 8.8 + - - +
90A LYS* 3.0 28.8 + - - +
96A LEU* 3.3 38.8 - - + -
192A LYS* 3.5 26.0 - - + +
193A GLY* 3.5 25.1 - - - +
194A VAL* 3.7 9.6 - - + +
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Residues in contact with ALA 87 (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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83A ASP 3.0 16.0 + - - +
84A ARG* 3.3 7.4 + - + +
86A MET* 1.3 77.6 - - - +
88A GLU* 1.3 59.1 + - + +
90A LYS* 3.3 9.0 + - - +
91A LYS* 3.0 39.9 + - - +
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Residues in contact with GLU 88 (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* 3.8 18.2 - - + -
38A LEU* 3.7 14.6 - - + -
84A ARG* 2.9 29.9 + - + +
85A LEU 3.9 0.7 - - - +
87A ALA* 1.3 74.2 - - + +
89A LEU* 1.3 65.8 + - - +
91A LYS* 3.0 36.6 + - - +
92A ARG* 2.7 66.5 + - - +
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Residues in contact with LEU 89 (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* 3.6 31.6 - - + +
49A ILE* 4.0 15.9 - - + -
85A LEU* 3.0 34.4 + - + +
86A MET* 3.2 11.0 + - - +
88A GLU* 1.3 76.9 - - - +
90A LYS* 1.3 62.9 + - - +
92A ARG* 3.0 10.3 + - - -
94A MET* 2.8 54.8 + - + +
95A ARG 4.9 1.8 - - - +
96A LEU* 3.6 43.3 - - + +
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Residues in contact with LYS 90 (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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86A MET 3.0 16.8 + - - +
87A ALA* 3.6 8.5 - - - +
89A LEU* 1.3 78.8 - - - +
91A LYS* 1.3 57.6 + - - +
93A GLY* 2.9 20.0 + - - +
94A MET 4.0 7.4 + - - +
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Residues in contact with LYS 91 (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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87A ALA* 3.0 26.5 + - - +
88A GLU* 3.0 39.3 + - - +
89A LEU 3.3 0.2 - - - -
90A LYS* 1.3 74.5 - - - +
92A ARG* 1.3 63.8 + - + +
93A GLY 3.3 0.8 + - - -
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Residues in contact with ARG 92 (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 4.2 + - - -
38A LEU* 3.9 33.6 - - - +
39A ASP* 2.9 37.1 + - - +
42A LYS* 2.7 44.7 + - + +
88A GLU* 2.7 53.5 + - - +
89A LEU 3.0 9.0 + - - +
91A LYS* 1.3 81.2 - - + +
93A GLY* 1.3 58.0 - - - +
94A MET* 3.2 16.0 + - - +
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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