Contacts of the helix formed by residues 110 - 118 (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 ASN 110 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C THR* 5.2 5.6 + - - -
108C PRO* 3.6 21.8 - - - +
109C GLU* 1.3 76.9 - - + +
111C PHE* 1.3 68.2 + - - +
112C VAL 3.4 2.5 - - - -
113C GLU* 3.3 13.3 + - + -
114C LYS* 2.9 45.0 + - + +
358C PRO* 5.7 2.8 - - - +
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Residues in contact with PHE 111 (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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103C LEU* 3.7 40.6 - - + -
107C PRO* 3.9 19.7 - - + -
108C PRO* 3.0 25.9 + - + +
109C GLU 3.2 2.0 + - - -
110C ASN* 1.3 82.6 - - - +
112C VAL* 1.3 64.3 + - + +
114C LYS* 4.0 2.7 - - + +
115C LEU* 3.1 48.1 + - + +
132C THR* 4.2 13.0 - - + -
358C PRO* 5.4 2.7 - - + -
361C ASN* 3.8 25.6 - - - -
34D LEU* 4.0 30.3 - - + -
38D GLN* 4.4 9.9 - - - -
46D PHE* 4.3 3.1 - - + -
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Residues in contact with VAL 112 (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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109C GLU 4.7 1.6 + - - -
110C ASN 3.4 0.2 - - - -
111C PHE* 1.3 75.7 - - + +
113C GLU* 1.3 59.1 + - - +
115C LEU* 3.2 9.7 + - + +
116C ARG* 2.9 62.1 + - + +
120C LEU* 5.3 0.2 - - + -
30D LEU* 4.4 12.3 - - + +
33D GLN* 4.1 11.2 - - + +
34D LEU* 3.9 38.6 - - + +
37D ILE* 4.4 19.5 - - + -
46D PHE* 4.4 11.2 - - + -
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Residues in contact with GLU 113 (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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109C GLU 5.4 1.0 + - - +
110C ASN* 3.3 16.3 + - + +
112C VAL* 1.3 77.1 - - - +
114C LYS* 1.3 58.3 + - - +
116C ARG* 3.1 21.8 + - - +
117C GLU* 2.9 35.3 + - - +
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Residues in contact with LYS 114 (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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110C ASN* 2.9 39.0 + - - +
111C PHE* 4.0 3.8 - - + +
113C GLU* 1.3 76.2 - - - +
115C LEU* 1.3 55.6 + - - +
117C GLU* 2.8 32.7 + - - +
118C SER* 2.7 32.2 + - - -
358C PRO 5.3 0.7 - - - +
361C ASN* 3.8 31.0 - - + +
362C LEU* 3.8 29.6 - - - +
365C ALA* 3.7 20.2 - - + +
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Residues in contact with LEU 115 (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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111C PHE* 3.1 47.4 + - + +
112C VAL* 3.2 12.3 + - + +
114C LYS* 1.3 74.8 - - - +
116C ARG* 1.3 64.3 + - - +
118C SER* 3.1 11.5 + - - +
119C LEU* 3.2 16.2 + - + -
120C LEU* 3.0 37.6 + - + -
130C LEU* 4.1 25.8 - - + -
132C THR* 4.2 7.6 - - + -
361C ASN* 4.0 21.3 - - - +
34D LEU* 4.7 9.4 - - + -
37D ILE* 5.1 7.9 - - + -
38D GLN* 5.6 2.9 - - - +
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Residues in contact with ARG 116 (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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112C VAL* 2.9 40.2 + - - +
113C GLU* 3.3 24.7 - - - +
115C LEU* 1.3 75.0 - - - +
117C GLU* 1.3 61.2 + - - +
118C SER 3.4 0.5 + - - -
120C LEU* 4.0 20.2 - - + +
121C SER* 3.6 20.1 + - - -
33D GLN* 3.3 37.6 + - - +
37D ILE* 5.4 4.4 - - - +
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Residues in contact with GLU 117 (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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113C GLU* 2.9 21.6 + - - +
114C LYS* 2.8 46.2 + - - +
116C ARG* 1.3 76.2 - - - +
118C SER* 1.3 57.2 + - - +
121C SER* 3.8 8.9 + - - -
365C ALA* 3.8 27.2 - - + +
368C ILE* 4.3 5.9 - - - +
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Residues in contact with SER 118 (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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114C LYS 2.7 20.5 + - - -
115C LEU* 3.1 11.1 + - - +
117C GLU* 1.3 78.7 - - - +
119C LEU* 1.3 75.2 + - - +
120C LEU 3.3 1.8 - - - -
121C SER* 2.7 25.5 + - - -
122C VAL 3.8 0.9 + - - -
361C ASN* 4.4 8.4 + - - +
364C LEU* 4.0 15.5 - - - +
365C ALA* 3.8 24.2 - - - +
368C ILE* 3.5 16.1 - - - +
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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