Contacts of the helix formed by residues 170 - 177 (chain A) in PDB entry 2OM2
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 THR 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A CYS* 4.4 2.0 - - - -
154A TYR* 4.4 0.3 + - - -
161A ARG* 4.1 19.4 + - - +
168A ILE 4.2 6.1 - - - +
169A PRO* 1.3 76.5 - - - +
171A GLN* 1.3 64.8 + - - +
172A GLN* 3.5 8.6 + - - +
173A ASP* 3.2 27.7 + - - -
174A VAL* 3.0 22.7 + - - +
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Residues in contact with GLN 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.5 44.9 - - + +
59A ALA 5.4 0.2 + - - -
60A GLY* 4.3 2.2 - - - -
61A TYR* 3.5 39.9 + - + +
66A CYS* 4.5 8.7 - - - -
170A THR* 1.3 74.4 - - - +
172A GLN* 1.3 58.6 + - - +
174A VAL* 3.2 8.5 + - - +
175A LEU* 2.9 26.7 + - - +
329A THR* 5.6 0.2 + - - -
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Residues in contact with GLN 172 (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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154A TYR* 3.4 26.4 - - + +
170A THR* 3.2 7.2 + - - +
171A GLN* 1.3 79.8 - - - +
173A ASP* 1.3 62.1 + - - +
175A LEU* 3.2 22.7 + - - +
176A ARG* 3.0 27.9 + - + +
327A THR* 2.9 28.5 + - - +
329A THR* 4.6 8.1 + - - +
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Residues in contact with ASP 173 (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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73A VAL* 4.7 1.3 - - + -
154A TYR* 2.5 38.5 + - - -
155A TYR* 2.7 29.7 + - + -
161A ARG* 2.6 37.7 + - - -
162A ILE* 4.4 2.7 - - - -
167A TYR* 2.8 24.4 + - - +
169A PRO* 4.1 4.0 - - + -
170A THR* 3.2 27.3 + - - +
172A GLN* 1.3 77.1 - - - +
174A VAL* 1.3 61.8 + - - +
176A ARG 3.1 5.0 + - - -
177A THR* 3.2 3.3 + - - +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS* 3.6 4.7 + - + +
61A TYR* 3.7 29.6 - - + +
66A CYS* 4.0 26.2 - - + -
69A TYR* 3.6 48.2 - - + -
169A PRO* 4.4 4.7 - - + -
170A THR 3.0 14.8 + - - +
171A GLN* 3.5 7.9 - - - +
173A ASP* 1.3 75.7 - - - +
175A LEU* 1.3 61.9 + - - +
177A THR* 2.6 32.0 + - - -
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Residues in contact with LEU 175 (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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48A THR* 4.1 19.2 + - + +
51A LYS* 2.8 54.4 + - + +
52A GLN* 3.5 45.1 - - + +
55A ILE* 4.0 12.5 - - + +
61A TYR* 5.9 0.7 - - - -
171A GLN 2.9 12.8 + - - +
172A GLN* 3.3 26.0 - - - +
174A VAL* 1.3 76.4 - - - +
176A ARG* 1.3 57.8 + - + +
177A THR 3.8 0.5 - - - +
327A THR* 3.5 23.1 - - + +
329A THR* 4.2 2.9 - - - +
355A GDP 4.9 1.4 + - - -
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Residues in contact with ARG 176 (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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150A ASP 3.0 26.1 + - - -
151A SER* 2.9 28.1 + - - +
154A TYR* 3.7 46.3 - - + +
155A TYR* 3.1 22.9 + - + +
172A GLN* 3.0 21.5 + - - +
173A ASP 3.1 4.4 + - - +
175A LEU* 1.3 74.3 - - + +
177A THR* 1.3 66.2 + - - +
178A ARG* 3.7 2.4 + - - +
327A THR* 3.9 23.2 + - - +
355A GDP 3.0 59.5 + - - -
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Residues in contact with THR 177 (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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51A LYS* 2.8 26.9 + - - +
69A TYR* 3.6 18.3 - - + -
72A VAL* 3.5 33.0 - - + -
73A VAL* 3.7 14.1 - - + +
76A ASN* 3.5 3.8 - - - -
155A TYR* 3.3 15.5 - - + +
173A ASP 3.4 9.2 - - - +
174A VAL* 2.6 24.7 + - - +
175A LEU 3.8 0.3 - - - +
176A ARG* 1.3 80.9 - - - +
178A ARG* 1.3 60.2 + - - +
179A VAL* 4.2 3.7 - - - +
355A GDP 5.7 1.6 + - - -
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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