Contacts of the helix formed by residues 191 - 197 (chain A) in PDB entry 1KNY
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 VAL 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A LEU* 4.0 12.8 - - + -
171A MET* 4.2 17.3 - - - -
174A ALA* 3.8 13.9 - - + -
175A MET* 3.8 25.4 - - + -
185A TYR* 3.5 26.6 - - + -
187A THR 3.0 20.6 - - - +
188A SER* 3.3 21.1 - - - +
189A ALA 3.3 0.8 - - - -
190A SER* 1.3 73.7 + - - +
192A LEU* 1.3 68.9 + - + +
194A GLU* 3.9 0.2 - - - -
195A ALA* 2.9 24.6 + - - +
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Residues in contact with LEU 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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170A ALA* 3.8 15.5 - - + +
171A MET* 3.4 35.2 - - + -
174A ALA* 4.8 1.8 - - + -
188A SER 5.0 0.2 + - - -
189A ALA 4.8 3.5 + - - +
190A SER 3.4 0.2 - - - -
191A VAL* 1.3 78.4 - - - +
193A THR* 1.3 62.3 + - + +
195A ALA* 3.8 1.6 - - - +
196A VAL* 3.1 27.9 + - - +
205A TYR* 3.8 20.4 - - - +
209A CYS* 3.9 12.4 - - - -
212A VAL* 3.8 26.0 - - + -
213A MET* 3.8 27.1 - - + +
160B THR* 4.4 8.3 - - - +
161B PHE* 5.5 3.8 - - + -
164B SER* 3.9 8.7 - - - +
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Residues in contact with THR 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 ALA 4.1 2.8 + - - -
190A SER* 2.8 25.5 + - - -
192A LEU* 1.3 75.2 - - - +
194A GLU* 1.3 58.9 + - - +
196A VAL* 3.4 16.0 - - + +
197A LYS* 3.1 31.8 - - - +
213A MET* 3.9 13.9 - - + -
158B PRO* 5.2 5.9 - - + +
160B THR* 3.7 28.4 + - + +
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Residues in contact with GLU 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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183A ILE* 5.6 1.3 - - + +
184A CYS 4.4 1.7 - - - +
185A TYR* 3.1 29.3 - - + +
186A THR* 2.7 50.2 + - - +
190A SER* 2.7 33.7 + - - +
193A THR* 1.3 75.4 - - - +
195A ALA* 1.3 65.0 + - - +
196A VAL 3.3 0.2 - - - -
197A LYS* 3.4 16.6 + - - +
198A GLN* 3.3 22.3 - - - +
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Residues in contact with ALA 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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174A ALA* 3.4 29.8 - - + -
177A ILE* 4.2 7.4 - - + +
185A TYR* 3.8 15.0 - - - +
191A VAL 2.9 18.6 + - - +
192A LEU 3.8 3.4 - - - +
194A GLU* 1.3 73.4 - - - +
196A VAL* 1.3 58.2 + - - +
197A LYS 2.8 10.7 + - - -
198A GLN* 3.3 13.2 + - - +
201A LEU* 3.5 14.9 - - - +
205A TYR* 3.8 13.6 - - + +
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Residues in contact with VAL 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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192A LEU 3.1 12.0 + - - +
193A THR* 3.4 23.3 - - + +
195A ALA* 1.3 76.6 - - - +
197A LYS* 1.3 62.3 + - + +
198A GLN 4.9 0.2 - - - +
201A LEU* 4.0 16.9 - - + +
205A TYR* 4.5 2.9 - - + -
206A ASP* 3.4 36.1 - - + +
209A CYS* 4.1 24.7 - - + -
210A GLN* 4.2 0.2 - - - +
213A MET* 4.1 12.6 - - + -
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Residues in contact with LYS 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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193A THR* 3.1 26.9 + - - +
194A GLU* 3.4 13.8 + - - +
195A ALA 2.8 1.2 + - - -
196A VAL* 1.3 84.4 - - + +
198A GLN* 1.3 74.5 + - - +
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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