Contacts of the helix formed by residues 83 - 93 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ASP 5.0 2.0 - - - +
73B GLY* 3.6 20.0 - - - +
74B ARG* 3.9 18.6 - - + -
82B GLY* 1.3 73.1 - - - -
84B PRO* 1.4 61.9 - - + +
85B HIS* 3.5 20.4 - - + +
86B VAL* 3.2 12.9 + - + +
87B ILE* 2.9 29.5 + - - +
100B HIS* 3.2 46.7 - - + +
113B PHE* 3.7 19.3 - - + -
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Residues in contact with PRO 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 5.0 12.1 - - + -
68B PRO 5.8 1.3 - - - +
69B ARG* 6.4 1.1 - - - -
73B GLY 3.4 20.0 - - - +
74B ARG 5.0 0.4 - - - -
75B LEU* 3.9 26.7 - - + -
82B GLY 3.7 2.6 - - - +
83B LEU* 1.4 84.0 - - + +
85B HIS* 1.3 69.1 + - + +
87B ILE* 3.0 10.6 + - + +
88B TYR* 3.0 32.0 + - + -
113B PHE* 4.3 6.3 - - + -
120B VAL* 4.8 11.7 - - + -
122B VAL* 3.6 20.6 - - + -
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Residues in contact with HIS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.7 24.7 - - + +
84B PRO* 1.3 74.7 - - - +
86B VAL* 1.3 69.8 + - + +
88B TYR* 4.5 0.8 - - - +
89B CYS* 3.0 31.0 + - - +
100B HIS* 3.8 21.0 - - + +
103B LEU* 3.9 15.3 - - + +
113B PHE* 3.3 47.5 - + + +
120B VAL* 5.1 0.9 - - + +
121B CYS 4.1 4.9 - - - +
122B VAL* 3.9 10.4 - - - +
127B TYR* 3.6 44.9 - + + +
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.2 19.2 + - + +
84B PRO 3.1 0.6 - - - -
85B HIS* 1.3 85.3 - - - +
87B ILE* 1.3 63.2 + - + +
90B ARG* 3.1 53.5 + - - +
97B LEU* 3.8 9.7 - - + +
99B SER* 4.1 7.2 - - - -
100B HIS* 3.5 41.7 - - + +
103B LEU* 3.8 15.5 - - + -
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Residues in contact with ILE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TRP* 3.6 39.5 - - + -
34B ALA* 4.7 4.9 - - + -
75B LEU* 4.4 22.0 - - + +
77B VAL* 4.8 4.7 - - + -
80B ARG 6.1 0.2 - - - +
81B LYS 5.2 0.7 - - - -
82B GLY* 4.1 27.1 - - - +
83B LEU 2.9 22.1 + - - +
84B PRO* 3.0 6.5 + - + +
86B VAL* 1.3 79.3 - - + +
88B TYR* 1.3 78.5 + - + +
90B ARG* 3.6 15.9 + - - +
91B LEU* 3.1 25.5 + - + +
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Residues in contact with TYR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA* 2.8 34.4 + - - +
35B VAL* 4.8 0.4 - - - -
37B SER* 4.6 2.8 - - - -
38B LEU* 3.5 36.0 + - + +
41B LYS* 5.5 0.5 + - - -
67B ILE* 6.3 0.9 - - + -
75B LEU* 4.1 27.5 - - + +
77B VAL* 4.7 0.7 - - - +
84B PRO* 3.0 23.8 + - + +
85B HIS 4.5 1.1 - - - +
87B ILE* 1.3 87.8 - - + +
89B CYS* 1.3 60.6 + - - +
90B ARG 3.3 0.4 - - - -
91B LEU* 3.4 26.8 - - + +
92B TRP* 3.1 51.5 + + + -
122B VAL* 4.0 33.2 - - + +
124B PRO* 4.0 4.5 - - - +
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Residues in contact with CYS 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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85B HIS* 3.0 25.7 + - - +
88B TYR* 1.3 73.7 - - - +
90B ARG* 1.3 60.9 + - - +
91B LEU 3.1 0.2 - - - -
93B ARG* 2.8 14.7 + - - +
94B TRP* 2.8 39.5 + - + -
97B LEU* 3.9 17.3 - - + -
103B LEU* 4.3 4.0 - - + -
122B VAL 5.6 1.3 - - - -
123B ASN 5.3 0.2 - - - -
124B PRO* 3.8 35.2 - - - -
127B TYR* 4.1 24.0 - - - -
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Residues in contact with ARG 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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20B LYS 4.8 0.5 - - - +
27B GLU* 5.6 5.8 - - - -
30B TRP* 5.8 8.5 - - - -
86B VAL* 3.1 40.8 + - - +
87B ILE* 3.8 14.0 - - - +
89B CYS* 1.3 77.9 - - - +
91B LEU* 1.3 63.5 + - - +
94B TRP 3.2 20.5 + - - +
95B PRO* 3.3 34.0 + - + +
97B LEU* 3.2 31.3 + - + +
98B HIS* 3.4 19.4 + - - +
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Residues in contact with LEU 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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16B LEU* 5.5 1.6 - - + -
19B LYS* 3.5 26.6 - - + +
20B LYS* 3.5 24.3 + - - +
30B TRP* 5.8 3.4 - - + -
31B CYS* 4.3 29.8 - - + +
34B ALA* 4.9 4.9 - - + -
35B VAL* 3.7 29.4 - - + -
87B ILE* 3.1 15.5 + - + +
88B TYR* 3.4 33.9 - - + +
89B CYS 3.1 0.2 - - - -
90B ARG* 1.3 82.4 - - - +
92B TRP* 1.3 74.6 + - + +
93B ARG 3.7 0.2 + - - -
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Residues in contact with TRP 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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15B LEU* 3.1 37.3 + - + -
16B LEU* 5.1 0.6 - - - +
18B TRP* 3.0 32.1 + - + +
19B LYS* 4.1 6.2 + - + +
20B LYS* 3.7 19.6 + - - -
35B VAL* 4.3 12.7 - - + +
38B LEU* 3.8 25.4 - - + -
51B LEU* 4.4 16.6 - - + -
55B ILE* 3.4 36.5 - - + +
88B TYR* 3.1 45.8 + + + +
91B LEU* 1.3 95.7 - - + +
93B ARG* 1.3 66.7 + - + +
122B VAL 5.2 0.4 - - - -
124B PRO* 3.9 15.0 - - + -
125B TYR* 4.1 7.1 + - + +
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Residues in contact with ARG 93 (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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20B LYS* 3.1 25.6 + - - +
89B CYS* 2.8 20.3 + - - +
91B LEU 3.5 1.6 + - - -
92B TRP* 1.3 76.9 - - - +
94B TRP* 1.3 113.6 + - + +
95B PRO* 3.6 1.6 - - - +
124B PRO* 2.5 49.7 + - + +
125B TYR* 3.1 57.5 - - - +
127B TYR 3.7 9.5 + - - -
128B GLN* 5.3 1.2 - - - +
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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
------------------------------------------------------------
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