Contacts of the helix formed by residues 190 - 194 (chain A) in PDB entry 2OT7
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 GLU 190 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A HIS* 3.3 2.8 + - - -
189A THR* 1.3 76.7 - - - +
191A ASP* 1.3 58.6 + - - +
193A ASP* 2.7 25.9 + - - +
194A LEU 3.4 31.4 + - - +
196A SER* 3.6 5.2 - - - -
239A ARG* 2.9 12.2 + - - -
241A LYS* 5.4 2.6 + - - +
270A THR* 3.8 11.2 - - - +
271A PHE 5.9 0.2 - - - +
276A HIS* 2.9 10.0 - - + -
290A ASN* 2.9 32.4 + - - +
500A OGA 3.6 3.1 - - - -
501A NI 2.1 41.4 - - - +
9C MLZ 3.2 18.9 + - - -
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Residues in contact with ASP 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A VAL* 3.9 18.3 - - + +
189A THR 4.0 0.4 + - - -
190A GLU* 1.3 73.8 + - - +
192A MET* 1.3 68.0 + - - +
193A ASP 3.1 1.2 + - - -
194A LEU* 3.2 20.4 + - - +
239A ARG* 4.1 11.1 + - - +
241A LYS* 4.4 11.5 + - - +
290A ASN* 4.9 3.2 + - - +
312A MET* 6.0 0.2 - - - +
313A VAL* 3.5 49.9 + - + +
8C ARG 5.0 0.2 - - - +
9C MLZ 4.0 18.0 - - - +
10C SER 5.0 0.2 + - - -
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Residues in contact with MET 192 (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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190A GLU 3.2 0.8 + - - -
191A ASP* 1.3 72.9 - - - +
193A ASP* 1.3 62.3 + - - +
194A LEU* 3.3 4.0 - - + -
239A ARG* 4.1 5.6 - - - +
296A TRP* 2.9 28.9 + - + -
300A GLY* 3.5 33.9 - - - +
303A ALA* 4.0 11.2 - - + -
305A LEU* 3.9 28.1 - - + +
313A VAL* 4.1 9.3 + - + +
314A LYS* 4.0 8.7 - - + +
315A ILE* 3.5 59.5 - - + +
317A MET* 3.9 14.6 - - + -
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Residues in contact with ASP 193 (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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189A THR* 2.7 26.4 + - - -
190A GLU 2.7 20.2 + - - +
192A MET* 1.3 72.6 - - - +
194A LEU* 1.3 59.8 + - - +
239A ARG* 2.9 22.6 + - - +
272A PRO* 3.1 25.5 - - - +
273A TYR* 3.7 34.8 - - + +
296A TRP* 3.3 6.2 - - - -
299A TYR* 4.3 16.6 - - + +
303A ALA* 3.7 15.0 - - - -
304A VAL 4.6 0.7 + - - -
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Residues in contact with LEU 194 (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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157A LEU* 3.9 23.3 - - + -
171A VAL* 3.8 20.9 - - + -
190A GLU* 3.4 20.4 + - + +
191A ASP 3.2 18.8 + - - +
192A MET* 3.3 1.2 - - + -
193A ASP* 1.3 81.6 - - - +
195A TYR* 1.3 69.6 + - - +
270A THR* 4.6 0.2 + - - -
271A PHE 4.1 3.1 - - - +
272A PRO* 3.8 9.0 - - - +
273A TYR 4.7 0.3 + - - -
290A ASN* 3.8 21.1 - - + -
291A PHE 3.6 14.4 - - - +
292A ALA* 4.0 3.1 - - + -
296A TRP* 3.2 45.3 - - + +
315A ILE* 4.2 9.6 - - + -
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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