Contacts of the helix formed by residues 81 - 90 (chain C) in PDB entry 1OHV
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 HIS 81 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C PHE 6.0 2.2 + - - -
77C ILE* 3.2 51.3 - - + +
78C GLY 4.1 3.7 + - - +
79C TYR 3.1 4.6 + - - -
80C SER* 1.3 76.1 - - - +
82C PRO* 1.3 71.6 - - + +
83C ALA* 3.1 42.4 + - + +
84C LEU* 2.9 31.9 + - + +
85C VAL* 3.0 10.6 + - - +
370C ILE* 3.8 28.1 - - + +
374C GLU* 6.1 0.2 - - - +
451C VAL* 4.8 7.9 - - + +
98D ILE* 4.4 2.0 - - - +
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Residues in contact with PRO 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 4.1 34.3 - - + +
53C ARG* 6.0 0.9 - - - +
80C SER 3.2 5.8 - - - +
81C HIS* 1.3 98.3 - - + +
83C ALA* 1.3 60.2 + - - +
85C VAL* 3.4 13.2 - - + +
86C LYS* 3.1 23.0 + - - +
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C HIS* 3.1 24.9 + - + +
82C PRO* 1.3 79.1 - - - +
84C LEU* 1.3 63.0 + - + +
86C LYS* 3.6 8.1 + - - +
87C LEU* 3.4 23.6 + - - +
366C GLU* 3.8 30.3 - - + +
370C ILE* 4.0 8.1 - - + -
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Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C PRO* 5.9 0.9 - - + -
77C ILE* 4.3 11.7 - - + -
78C GLY 5.4 2.9 - - - +
81C HIS* 2.9 26.9 + - + +
83C ALA* 1.3 74.1 - - - +
85C VAL* 1.3 68.4 + - - +
86C LYS 3.2 0.2 - - - -
87C LEU* 3.3 19.9 + - + +
88C VAL* 3.3 17.0 + - - +
332C MET* 4.7 10.5 - - + -
363C LEU* 3.9 28.4 - - + +
366C GLU* 4.0 19.1 - - + -
367C VAL* 4.2 18.8 - - + +
98D ILE* 3.7 34.0 - - + +
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ARG* 5.9 1.1 - - - +
80C SER* 4.0 13.9 - - - +
81C HIS 3.0 15.9 + - - +
82C PRO* 3.4 14.1 - - + +
84C LEU* 1.3 76.0 - - - +
86C LYS* 1.3 62.3 + - - +
88C VAL* 3.2 6.2 + - - +
89C GLN* 3.1 46.7 + - + +
94D VAL* 4.1 19.6 - - + +
98D ILE* 3.6 17.3 - - + -
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Residues in contact with LYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PRO 3.1 14.0 + - - +
83C ALA* 3.7 8.5 - - - +
84C LEU 3.2 0.2 - - - -
85C VAL* 1.3 79.4 - - - +
87C LEU* 1.3 63.2 + - + +
89C GLN* 3.1 21.3 + - - +
90C GLN* 2.8 32.2 + - - +
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ALA 3.4 12.7 + - - +
84C LEU* 3.3 10.7 + - + +
86C LYS* 1.3 78.6 - - + +
88C VAL* 1.3 63.1 + - - +
90C GLN* 3.2 11.2 + - + -
93C ASN* 2.8 40.0 + - - +
97C PHE* 5.0 1.1 - - - -
362C LEU* 3.6 38.1 - - + +
363C LEU* 4.1 22.4 - - + -
366C GLU* 3.6 30.3 - - + +
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C LEU 3.3 3.3 + - - +
85C VAL 3.2 8.1 + - - +
87C LEU* 1.3 76.9 - - - +
89C GLN* 1.3 61.1 + - - +
90C GLN 3.4 5.2 + - - +
93C ASN* 5.4 0.3 - - - +
94C VAL* 5.7 1.2 + - - +
97C PHE* 3.9 28.7 - - + -
363C LEU* 4.8 2.5 - - + -
88D VAL* 4.5 26.3 - - + +
93D ASN 5.6 0.2 - - - -
94D VAL* 4.2 29.8 - - + +
97D PHE* 4.1 19.7 - - + -
98D ILE* 3.4 33.7 - - + -
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Residues in contact with GLN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C VAL* 3.1 32.1 + - + +
86C LYS* 3.1 21.5 + - - +
88C VAL* 1.3 76.8 - - - +
90C GLN* 1.3 69.1 + - - +
91C PRO* 3.3 10.4 - - - +
91D PRO* 6.4 0.4 - - - +
94D VAL* 4.8 13.3 - - + +
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Residues in contact with GLN 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C LYS* 2.8 35.6 + - - +
87C LEU* 3.2 14.9 + - + +
88C VAL 4.1 4.0 - - - +
89C GLN* 1.3 85.1 + - - +
91C PRO* 1.3 72.4 - - - +
92C GLN* 3.2 27.0 + - - +
93C ASN* 3.0 30.5 + - - +
94C VAL* 3.9 3.9 + - - +
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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