Contacts of the helix formed by residues 104 - 111 (chain D) in PDB entry 1OVM
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 GLY 104 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549C CYS 5.7 4.6 + - - -
102D ALA 3.8 0.2 + - - -
103D PRO* 1.3 76.1 - - - +
105D THR* 1.3 67.4 + - - -
106D ALA* 3.2 3.6 - - - -
107D ALA* 3.0 11.9 + - - +
108D GLN* 3.0 19.6 + - - +
168D PRO* 4.6 0.2 - - - -
169D ALA* 4.7 4.4 - - - +
170D ASP* 3.2 22.2 - - - -
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Residues in contact with THR 105 (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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103D PRO 3.7 1.2 + - - -
104D GLY* 1.3 70.5 - - - -
106D ALA* 1.3 58.6 + - - +
108D GLN* 3.3 10.4 + - - +
109D GLN* 3.0 32.4 + - - +
140D LEU 4.8 2.5 - - - +
141D THR* 5.3 8.1 - - + -
142D GLU 5.8 0.2 - - - +
168D PRO* 3.9 12.3 - - + -
170D ASP* 2.9 19.2 + - - +
171D VAL* 3.8 28.9 - - + -
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Residues in contact with ALA 106 (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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104D GLY 3.2 1.0 - - - -
105D THR* 1.3 83.3 + - - +
107D ALA* 1.3 65.0 + - - +
109D GLN* 3.2 8.6 + - - +
110D ARG* 3.0 42.7 + - - +
170D ASP* 4.9 0.6 + - - +
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Residues in contact with ALA 107 (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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103D PRO* 4.6 0.9 - - + -
104D GLY* 3.0 18.9 + - - +
106D ALA* 1.3 78.4 - - - +
108D GLN* 1.3 62.3 + - - +
110D ARG* 3.3 24.0 + - - +
111D GLY 3.4 8.7 + - - -
112D GLU* 3.5 29.9 + - - +
114D LEU* 4.0 16.6 - - + -
123D PHE* 4.3 2.3 - - - -
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Residues in contact with GLN 108 (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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109A GLN* 5.0 0.2 - - - +
75D PHE* 5.8 0.2 - - - -
102D ALA* 3.9 7.3 - - - +
103D PRO* 2.8 30.2 + - + +
104D GLY 3.0 12.6 + - - +
105D THR* 3.6 10.5 - - - +
107D ALA* 1.3 75.1 - - - +
109D GLN* 1.3 65.7 + - - +
111D GLY* 3.0 14.7 + - - -
121D GLY 4.6 1.0 - - - +
123D PHE* 3.4 53.2 - - + +
124D ARG* 4.6 6.6 + - - -
166D MET* 3.2 36.0 - - - +
168D PRO* 4.3 4.4 - - - +
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Residues in contact with GLN 109 (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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109A GLN* 2.8 61.2 - - - +
110A ARG* 3.7 15.2 - - - +
111A GLY* 3.8 13.1 + - - -
120A ASP 5.9 0.4 + - - -
121A GLY* 5.2 4.9 + - - -
105D THR* 3.0 14.7 + - - +
106D ALA* 3.2 11.4 + - - +
108D GLN* 1.3 75.5 - - - +
110D ARG* 1.3 58.2 + - + +
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Residues in contact with ARG 110 (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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109A GLN* 3.7 11.3 - - - +
106D ALA* 3.0 35.2 + - - +
107D ALA* 3.5 22.5 - - - +
108D GLN 3.1 0.2 - - - -
109D GLN* 1.3 78.4 - - - +
111D GLY* 1.3 63.6 + - - +
112D GLU* 3.1 42.4 + - + +
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Residues in contact with GLY 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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109A GLN* 4.0 13.7 + - - -
107D ALA 3.4 1.8 + - - -
108D GLN 3.0 13.9 + - - -
109D GLN 3.1 0.6 - - - -
110D ARG* 1.3 79.0 - - - +
112D GLU* 1.3 63.8 + - - +
113D LEU* 5.2 2.4 - - - +
121D GLY* 3.5 34.5 - - - -
123D PHE* 4.0 2.0 - - - -
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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