Contacts of the helix formed by residues 194 - 198 (chain A) in PDB entry 2OXD
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 SER 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A ASP* 2.7 24.9 + - - -
158A LYS* 3.0 35.2 + - - -
178A LEU* 5.5 0.2 - - - +
193A ALA* 1.3 76.0 - - - +
195A ARG* 1.3 67.5 - - - +
196A TYR* 3.4 2.0 - - - -
197A PHE* 3.0 25.7 + - - +
198A LYS* 3.2 11.0 + - - +
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Residues in contact with ARG 195 (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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194A SER* 1.3 71.1 - - - +
196A TYR* 1.3 77.9 + - + +
197A PHE 3.0 5.4 + - - -
198A LYS* 3.1 34.0 + - + +
235A GLY 3.7 15.5 - - - -
236A HIS 3.6 14.6 + - - -
237A ASP* 3.7 25.7 - - - +
238A ASN* 2.9 29.0 + - - +
241A GLN* 3.5 24.1 - - + +
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Residues in contact with TYR 196 (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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194A SER* 3.4 1.9 - - - -
195A ARG* 1.3 92.2 + - + +
197A PHE* 1.3 80.9 + + + +
198A LYS 3.6 0.2 - - - -
220A CYS* 3.6 18.4 - - - +
231A PRO* 3.6 32.7 - - + +
233A PHE* 3.4 25.3 + - - +
234A TYR* 3.3 28.1 + + - -
235A GLY 3.1 24.5 + - - -
236A HIS* 5.5 0.9 + - - -
241A GLN* 3.7 22.9 + - - +
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Residues in contact with PHE 197 (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 VAL 3.5 23.8 - - - +
158A LYS* 3.7 19.7 - - + -
159A PRO* 3.5 30.3 - - + -
160A HIS* 5.2 6.5 - + - -
193A ALA* 4.2 6.8 - - + +
194A SER* 3.0 22.2 + - - +
196A TYR* 1.3 104.5 - + + +
198A LYS* 1.3 63.5 + - - +
199A GLY 3.6 1.7 + - - -
213A LEU* 4.6 0.5 - - - +
216A TRP* 3.9 3.7 - - - -
217A SER* 2.7 36.5 + - - -
220A CYS* 3.8 23.6 - - + -
221A MET* 4.2 15.5 - - - -
231A PRO* 4.9 11.9 - - + -
232A PHE 6.2 0.4 - - - -
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Residues in contact with LYS 198 (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 VAL 3.6 15.5 + - - +
191A ARG* 4.1 6.7 - - - +
192A VAL 2.8 34.5 + - - +
193A ALA* 4.0 3.9 + - + -
194A SER 3.2 11.7 + - - +
195A ARG* 3.1 37.1 + - + +
197A PHE* 1.3 77.2 - - - +
199A GLY* 1.3 64.1 + - - +
200A PRO 4.0 0.2 - - - -
202A LEU* 3.9 15.3 - - + -
203A LEU* 4.0 35.7 - - + +
216A TRP* 3.4 11.5 + - - -
238A ASN* 4.1 24.0 - - - +
241A GLN* 4.6 1.7 + - - +
245A ILE* 4.3 4.2 - - - +
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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