Contacts of the helix formed by residues 104 - 111 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ALA 3.8 0.2 + - - -
103A PRO* 1.3 76.5 - - - +
105A THR* 1.3 65.7 + - - -
106A ALA* 3.2 3.6 - - - -
107A ALA* 3.1 11.0 + - - +
108A GLN* 3.1 19.4 + - - +
168A PRO* 4.5 0.4 - - - -
169A ALA* 4.6 3.8 - - - +
170A ASP* 3.2 24.0 - - - -
549B CYS 5.8 3.5 + - - -
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PRO 3.6 1.7 + - - -
104A GLY* 1.3 71.4 - - - -
106A ALA* 1.3 64.6 + - - +
108A GLN* 3.3 10.8 + - - +
109A GLN* 3.0 27.1 + - - +
140A LEU 4.9 2.2 - - - +
141A THR* 5.3 8.1 - - + -
142A GLU 5.8 0.2 - - - +
168A PRO* 3.9 12.3 - - + -
170A ASP* 3.0 24.8 + - - +
171A VAL* 3.9 21.8 - - + -
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Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A GLY* 3.2 1.2 - - - -
105A THR* 1.3 83.4 + - - +
107A ALA* 1.3 63.4 + - - +
109A GLN* 3.2 8.9 + - - +
110A ARG* 3.0 44.6 + - - +
170A ASP* 5.0 0.4 + - - -
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PRO* 4.7 0.7 - - + -
104A GLY* 3.1 18.1 + - - +
106A ALA* 1.3 79.0 - - - +
108A GLN* 1.3 61.3 + - - +
110A ARG* 3.4 17.4 + - - +
111A GLY* 3.4 14.2 + - - -
112A GLU* 3.5 31.2 + - - +
114A LEU* 4.0 15.9 - - + -
123A PHE* 4.3 3.5 - - - -
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Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PHE* 5.3 0.4 - - - -
102A ALA* 3.8 8.5 - - - +
103A PRO* 2.9 31.2 + - + +
104A GLY 3.1 15.3 + - - +
105A THR* 3.6 9.9 - - - +
106A ALA 3.2 0.2 - - - -
107A ALA* 1.3 75.9 - - - +
109A GLN* 1.3 65.8 + - - +
111A GLY* 3.1 13.7 + - - -
121A GLY 4.4 0.9 - - - +
123A PHE* 3.4 50.8 - - + +
124A ARG* 4.5 7.1 + - - -
139A VAL* 5.5 0.2 - - - +
166A MET* 3.1 35.4 - - - +
168A PRO* 4.3 3.8 - - - +
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Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A THR 3.0 15.1 + - - +
106A ALA* 3.6 11.0 - - - +
108A GLN* 1.3 75.9 - - - +
110A ARG* 1.3 58.3 + - + +
108D GLN 5.0 0.2 - - - +
109D GLN* 2.8 61.6 - - - +
110D ARG* 3.7 14.9 - - - +
111D GLY* 3.8 14.1 + - - -
120D ASP 5.9 0.2 + - - -
121D GLY* 5.0 5.7 + - - -
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Residues in contact with ARG 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ALA* 3.0 35.9 + - - +
107A ALA* 3.6 22.3 - - - +
108A GLN 3.1 0.2 - - - -
109A GLN* 1.3 79.3 - - + +
111A GLY* 1.3 62.8 + - - +
112A GLU* 3.1 43.1 + - + +
109D GLN* 3.7 10.6 - - - +
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Residues in contact with GLY 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ALA 3.4 1.4 + - - -
108A GLN 3.1 13.1 + - - -
109A GLN 3.1 1.4 - - - -
110A ARG* 1.3 79.8 - - - +
112A GLU* 1.3 65.5 + - - +
113A LEU* 4.0 2.9 + - - +
121A GLY* 3.5 34.3 - - - -
123A PHE* 3.9 1.8 - - - -
109D GLN* 4.1 13.6 + - - -
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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