Contacts of the helix formed by residues 81 - 90 (chain B) in PDB entry 1OCU
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 ARG 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B GLY 4.7 2.4 + - - -
57B PHE* 3.1 52.5 - - + +
58B THR 3.4 22.4 - - - +
59B ASP* 3.9 6.8 - - + +
60B TYR* 4.5 0.9 - - - -
80B ARG* 1.3 75.9 - - - +
82B TYR* 1.3 60.9 + - - +
83B SER* 3.1 13.4 + - - +
84B ASP* 2.8 45.0 + - - +
85B PHE* 3.2 8.5 + - - -
118B ARG* 5.0 0.2 - - - +
1164B PIB 2.8 42.5 + - - +
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Residues in contact with TYR 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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58B THR 4.5 0.2 + - - -
60B TYR* 4.4 8.9 - - + -
81B ARG* 1.3 72.0 - - - +
83B SER* 1.3 57.4 + - - +
85B PHE* 2.8 27.9 + - + +
86B GLU* 2.9 42.9 + - + +
109B LEU* 3.6 15.1 - - + +
110B PRO* 3.9 19.1 - - + -
111B GLY* 2.9 40.0 + - - -
112B LYS* 3.7 3.2 + - + +
127B ARG* 3.4 49.6 - - - +
131B LEU* 4.2 14.4 - - + -
1164B PIB 3.4 32.7 + - - +
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Residues in contact with SER 83 (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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81B ARG* 3.1 16.1 + - - -
82B TYR* 1.3 77.0 - - - +
84B ASP* 1.3 62.9 + - - +
86B GLU* 3.6 21.7 - - - +
87B PHE* 3.1 23.2 + - - +
1164B PIB 3.0 33.8 + - - -
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Residues in contact with ASP 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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79B ARG 4.4 1.6 - - - +
80B ARG* 3.4 29.0 - - + -
81B ARG* 2.8 44.6 + - - +
83B SER* 1.3 78.1 + - - +
85B PHE* 1.3 60.5 + - - +
87B PHE* 3.4 5.4 + - - +
88B PHE* 2.9 30.0 + - - +
154B PHE* 3.6 5.1 - - + -
160B PHE* 4.3 10.1 - - + +
161B VAL* 4.8 15.4 - - - +
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Residues in contact with PHE 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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40B VAL* 4.4 6.5 - - + -
60B TYR* 4.9 1.6 - + - -
62B ILE* 4.1 23.3 - - + -
80B ARG* 3.9 23.6 - - + -
81B ARG 3.2 20.5 + - - -
82B TYR* 2.8 10.7 + - + +
84B ASP* 1.3 80.6 - - - +
86B GLU* 1.3 60.6 + - - +
88B PHE* 3.3 4.9 + - - +
89B ARG* 3.0 18.7 + - - +
109B LEU* 3.5 20.6 - - + +
131B LEU* 3.8 48.9 - - + -
134B TRP* 4.1 19.9 - + - -
135B MET* 4.1 17.0 - - + -
154B PHE* 3.9 27.6 - + - -
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Residues in contact with GLU 86 (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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82B TYR* 2.9 47.2 + - + +
83B SER* 3.6 14.7 - - - +
85B PHE* 1.3 77.0 - - - +
87B PHE* 1.3 62.6 + - - +
89B ARG* 3.3 11.7 + - - +
90B LYS* 3.3 19.0 + - - +
109B LEU* 3.7 11.4 - - + -
112B LYS* 2.9 33.1 + - - +
1164B PIB 2.9 16.5 + - - -
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Residues in contact with PHE 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 SER 3.1 15.6 + - - +
84B ASP* 3.8 4.5 - - - +
85B PHE 3.4 0.2 - - - -
86B GLU* 1.3 78.8 - - - +
88B PHE* 1.3 62.9 + - - +
90B LYS* 3.3 23.6 + - + +
91B CME 3.2 61.1 + - + -
160B PHE* 3.8 20.2 - + - -
161B VAL* 4.0 29.4 - - + -
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Residues in contact with PHE 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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84B ASP 2.9 18.4 + - - +
85B PHE* 3.4 4.0 - - - +
87B PHE* 1.3 77.9 - - - +
89B ARG* 1.3 50.2 + - - +
91B CME 3.3 1.8 + - - +
92B LEU* 2.7 50.0 + - + +
134B TRP* 3.7 35.4 - + - -
135B MET* 4.4 5.4 - - + -
138B VAL* 4.5 1.1 - - + -
150B VAL* 3.3 32.5 - - + -
151B LEU* 3.8 21.1 - - + -
154B PHE* 3.5 57.9 - + + -
160B PHE* 3.6 11.6 - + + -
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Residues in contact with ARG 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 PHE 3.0 12.8 + - - +
86B GLU* 3.5 10.1 - - - +
87B PHE 3.2 0.2 - - - -
88B PHE* 1.3 77.3 - - - +
90B LYS* 1.3 61.0 + - + +
92B LEU* 3.5 6.1 - - - +
93B ILE* 2.8 64.8 + - + +
106B VAL* 2.9 33.2 + - + +
107B PRO 3.1 20.1 + - - -
108B HIS* 3.5 20.0 - - - +
109B LEU* 4.1 24.0 - - + +
134B TRP* 4.2 9.0 - - + -
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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 GLU 3.3 13.9 + - - +
87B PHE* 3.3 24.2 + - + +
89B ARG* 1.3 78.7 - - + +
91B CME 1.3 56.0 + - - +
93B ILE* 3.6 6.4 - - - +
94B LYS* 2.8 36.5 + - - +
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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