Contacts of the helix formed by residues 83 - 93 (chain A) in PDB entry 1OZJ
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 LEU 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ASP 5.2 2.2 - - - +
73A GLY* 3.9 16.4 - - - +
74A ARG* 4.3 12.1 - - + -
82A GLY* 1.3 71.9 - - - -
84A PRO* 1.3 71.9 - - + +
85A HIS* 3.5 18.4 - - + +
86A VAL* 3.0 16.6 + - + +
87A ILE* 2.9 23.5 + - - +
100A HIS* 3.5 45.5 - - + +
113A PHE* 3.8 23.1 - - + -
2003D A 6.0 0.9 - - - +
2004D T 6.0 2.0 - - - +
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Residues in contact with PRO 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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67A ILE* 4.9 10.8 - - + -
68A PRO 5.9 0.7 - - - +
69A ARG* 6.5 0.7 - - - -
73A GLY 3.2 22.7 - - - +
74A ARG 4.8 0.7 - - - +
75A LEU* 3.9 33.4 - - + -
82A GLY 3.5 3.3 - - - +
83A LEU* 1.3 85.1 - - + +
85A HIS* 1.3 68.2 + - + +
87A ILE* 3.1 12.3 + - + +
88A TYR* 3.1 20.0 + - + -
113A PHE* 4.8 4.7 - - + -
120A VAL* 4.4 14.8 - - + -
122A VAL* 3.8 21.5 - - + -
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Residues in contact with HIS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.6 22.6 - - + +
84A PRO* 1.3 76.7 - - + +
86A VAL* 1.3 69.8 + - + +
88A TYR* 3.5 1.0 + - - +
89A CYS* 3.0 32.3 + - - -
100A HIS* 3.7 23.0 - - + +
103A LEU* 3.4 20.3 - - + +
113A PHE* 3.1 52.2 - + + +
114A ASN* 5.4 1.8 - - - -
120A VAL* 4.9 1.3 - - + +
121A CYS 4.1 4.0 - - - +
122A VAL* 4.1 11.6 - - - +
127A TYR* 3.7 35.7 - + + +
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.0 26.8 + - + +
85A HIS* 1.3 83.3 - - + +
87A ILE* 1.3 64.5 + - + +
90A ARG* 3.1 48.9 + - - +
97A LEU* 3.4 19.6 - - + +
98A HIS 4.6 7.0 - - - +
99A SER* 4.4 2.7 - - - -
100A HIS* 3.6 39.0 - - + +
103A LEU* 4.6 4.3 - - + -
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Residues in contact with ILE 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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30A TRP* 3.8 38.4 - - + -
34A ALA* 4.7 4.0 - - + -
75A LEU* 4.3 22.0 - - + +
77A VAL* 5.2 4.7 - - + -
80A ARG 6.5 0.2 - - - -
81A LYS 5.1 1.3 - - - -
82A GLY* 3.8 28.3 - - - +
83A LEU 2.9 20.2 + - - +
84A PRO 3.1 5.6 + - - +
86A VAL* 1.3 79.6 - - + +
88A TYR* 1.3 79.2 + - + +
90A ARG* 3.9 16.8 - - - +
91A LEU* 3.2 25.3 + - + +
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Residues in contact with TYR 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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34A ALA* 2.7 39.7 + - + +
37A SER* 4.5 1.9 + - - -
38A LEU* 3.6 33.5 + - + +
41A LYS* 5.9 0.2 + - - -
67A ILE* 6.3 0.4 - - + -
75A LEU* 4.0 28.6 - - + +
77A VAL* 4.4 4.2 - - - +
84A PRO 3.1 23.3 + - - +
85A HIS 4.4 1.1 - - - +
87A ILE* 1.3 90.9 - - + +
89A CYS* 1.3 64.8 + - - +
90A ARG 3.3 0.2 - - - -
91A LEU* 3.7 8.3 - - + -
92A TRP* 3.2 58.3 + + + +
122A VAL* 4.0 34.8 - - + +
124A PRO* 4.0 3.7 - - - +
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Residues in contact with CYS 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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85A HIS* 3.0 25.3 + - - +
88A TYR* 1.3 73.7 - - - +
90A ARG* 1.3 60.7 + - - +
93A ARG* 2.8 26.9 + - + +
94A TRP* 2.9 24.5 + - + -
97A LEU* 3.9 15.9 - - + -
103A LEU* 4.1 11.0 - - + -
122A VAL 5.8 1.1 - - - -
124A PRO* 3.9 33.4 - - - -
127A TYR* 4.0 25.4 - - - -
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Residues in contact with ARG 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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19A LYS* 5.0 1.2 - - - +
30A TRP* 5.6 7.2 - - - -
80A ARG* 5.3 9.1 - - - +
86A VAL* 3.1 35.7 + - - +
87A ILE* 3.9 17.5 - - - +
89A CYS* 1.3 80.0 - - - +
91A LEU* 1.3 60.2 + - - +
92A TRP 3.7 0.2 + - - -
94A TRP 3.2 19.2 + - - +
95A PRO* 3.3 37.4 + - + +
97A LEU* 3.4 23.5 + - + +
98A HIS* 3.5 23.0 + - - +
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Residues in contact with LEU 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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16A LEU* 5.7 2.0 - - + +
19A LYS* 2.9 35.8 - - - +
20A LYS 4.2 11.0 - - - +
21A GLY* 5.6 1.7 - - - -
30A TRP* 5.3 2.9 - - + -
31A CYS* 4.1 21.3 - - + +
34A ALA* 4.2 14.8 - - + -
35A VAL* 4.0 24.5 - - + -
87A ILE* 3.2 19.0 + - + +
88A TYR* 3.9 17.5 - - + +
89A CYS 3.2 0.4 - - - -
90A ARG* 1.3 81.3 - - - +
92A TRP* 1.3 87.8 + - + +
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Residues in contact with TRP 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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15A LEU* 3.1 34.3 + - + -
18A TRP* 2.8 38.4 + - + +
19A LYS* 4.3 10.3 + - - +
35A VAL* 4.1 26.9 - - + -
38A LEU* 3.9 22.4 - - + -
51A LEU* 4.5 12.8 - - + -
55A ILE* 3.6 38.3 - - + +
88A TYR* 3.2 52.3 + + + +
91A LEU* 1.3 91.6 - - + +
93A ARG* 1.3 69.3 + - + +
124A PRO* 4.2 12.1 - - + -
125A TYR* 4.2 6.4 + - + +
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Residues in contact with ARG 93 (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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19A LYS* 3.9 8.8 + - - -
89A CYS* 2.8 14.7 + - - +
91A LEU 3.8 0.6 - - - -
92A TRP* 1.3 80.2 - - - +
94A TRP* 1.3 117.8 + - + +
95A PRO* 3.2 13.1 - - - +
124A PRO* 2.4 50.6 + - + +
125A TYR* 3.1 57.5 + - - +
127A TYR 3.8 6.1 + - - -
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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