Contacts of the helix formed by residues 110 - 118 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C GLU* 6.2 0.2 - - - -
96D THR* 5.2 5.9 + - - -
108D PRO* 3.6 23.8 - - - +
109D GLU* 1.3 77.9 - - + +
111D PHE* 1.3 68.7 + - - +
112D VAL 3.4 2.5 - - - -
113D GLU* 3.3 13.4 + - + -
114D LYS* 2.8 44.8 + - + +
358D PRO* 5.8 2.4 - - - +
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Residues in contact with PHE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 4.0 28.7 - - + -
38C GLN* 4.3 11.2 - - - -
46C PHE* 4.3 3.4 - - + -
103D LEU* 3.8 35.9 - - + -
107D PRO* 4.0 20.2 - - + -
108D PRO* 3.0 26.3 + - + +
109D GLU 3.2 2.0 + - - -
110D ASN* 1.3 82.3 - - - +
112D VAL* 1.3 62.9 + - + +
114D LYS* 4.1 2.7 - - + +
115D LEU* 3.2 48.3 + - + +
132D THR* 4.2 17.7 - - + -
358D PRO* 5.4 2.9 - - + -
361D ASN* 3.8 25.3 + - - -
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Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU* 4.3 11.7 - - + +
33C GLN* 4.1 12.3 - - + +
34C LEU* 3.9 39.0 - - + +
37C ILE* 4.4 19.3 - - + -
46C PHE* 4.4 11.7 - - + -
109D GLU 4.7 1.2 + - - -
111D PHE* 1.3 76.5 - - + +
113D GLU* 1.3 59.1 + - - +
115D LEU* 3.2 9.8 + - + +
116D ARG* 2.8 61.3 + - - +
120D LEU* 5.3 0.4 - - + -
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Residues in contact with GLU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D GLU 5.4 0.6 + - - +
110D ASN* 3.3 16.4 + - + +
112D VAL* 1.3 78.6 - - - +
114D LYS* 1.3 57.9 + - - +
116D ARG* 3.1 20.6 + - - +
117D GLU* 3.0 34.9 + - - +
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Residues in contact with LYS 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ASN* 2.8 37.8 + - - +
111D PHE* 4.1 3.6 - - + +
113D GLU* 1.3 76.4 - - - +
115D LEU* 1.3 52.1 + - + +
117D GLU* 2.9 31.2 + - + +
118D SER* 2.7 34.3 + - - -
358D PRO 5.2 0.9 - - - +
361D ASN* 3.7 31.6 - - + +
362D LEU* 3.8 29.4 + - - +
365D ALA* 3.7 21.2 - - + +
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 4.9 7.9 - - + -
37C ILE* 5.1 6.7 - - + -
38C GLN* 5.6 3.1 - - - +
111D PHE* 3.2 48.8 + - + +
112D VAL* 3.2 11.4 + - + +
114D LYS* 1.3 74.3 - - - +
116D ARG* 1.3 65.2 + - - +
118D SER* 3.1 11.3 + - - +
119D LEU* 3.3 16.2 + - + -
120D LEU* 3.0 40.0 + - + -
130D LEU* 4.1 25.1 - - + -
132D THR* 4.2 7.9 - - + -
361D ASN* 3.9 22.0 - - - +
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Residues in contact with ARG 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLN* 3.3 39.2 + - - +
37C ILE* 5.4 3.4 - - - +
112D VAL* 2.8 47.9 + - - +
113D GLU* 3.1 23.6 + - - +
115D LEU* 1.3 77.5 - - - +
117D GLU* 1.3 60.1 + - - +
118D SER 3.5 0.5 + - - -
120D LEU* 4.0 21.6 - - + +
121D SER* 3.6 19.8 + - - -
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Residues in contact with GLU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D GLU* 3.0 21.6 + - - +
114D LYS* 2.9 44.7 + - - +
116D ARG* 1.3 75.8 - - - +
118D SER* 1.3 58.3 + - - +
121D SER* 3.8 8.7 + - - -
365D ALA* 3.8 27.2 - - + +
368D ILE* 4.3 6.4 - - - +
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Residues in contact with SER 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LYS 2.7 20.8 + - - -
115D LEU* 3.1 12.8 + - - +
117D GLU* 1.3 77.0 - - - +
119D LEU* 1.3 76.2 + - - +
120D LEU 3.3 1.3 - - - -
121D SER* 2.6 26.0 + - - -
122D VAL 3.7 0.9 + - - -
361D ASN* 4.3 8.1 + - - +
364D LEU* 4.0 15.5 - - - +
365D ALA* 3.8 23.3 - - - +
368D ILE* 3.5 16.4 - - - +
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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