Contacts of the helix formed by residues 187 - 196 (chain B) in PDB entry 1KOJ
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 ASP 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A ASP* 3.5 11.3 - - - +
342A GLN* 2.8 32.6 + - + +
383A GLY 5.1 0.2 - - - +
411A THR* 4.4 8.3 + - - -
420A HIS* 4.8 1.5 - - - -
421A HIS* 5.0 2.1 + - - +
424A LEU* 3.8 29.8 - - + +
185B ASN* 3.1 31.5 + - + +
186B ILE* 1.3 78.2 - - - +
188B GLY* 1.3 68.1 + - - +
189B THR* 3.0 23.6 + - - -
190B HIS* 3.2 11.6 + - - +
191B ILE* 4.4 1.2 + - - +
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Residues in contact with GLY 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A THR* 5.5 1.4 + - - -
413A HIS* 4.4 10.3 - - - -
415A ILE* 3.9 15.7 - - - +
420A HIS* 3.7 22.1 - - - +
421A HIS* 5.1 1.8 - - - +
186B ILE 2.9 8.2 + - - -
187B ASP* 1.3 74.1 + - - +
189B THR* 1.3 62.2 + - - +
190B HIS 3.2 0.4 + - - -
191B ILE* 3.5 3.8 + - - +
192B ALA* 3.0 28.1 + - - +
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Residues in contact with THR 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A ASP* 5.3 1.0 + - - -
342A GLN* 4.2 12.1 - - + -
343A TYR* 3.3 52.0 - - + +
411A THR* 4.4 5.9 + - - -
412A GLN* 5.0 1.0 + - - +
413A HIS* 3.3 25.7 - - - +
187B ASP* 3.0 22.0 + - - -
188B GLY* 1.3 75.7 - - - +
190B HIS* 1.3 64.3 + - - +
193B LYS* 3.0 26.8 + - + +
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Residues in contact with HIS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A GLN* 4.0 35.7 + - + +
182B PHE 3.2 21.2 + - - -
183B VAL* 4.3 4.3 - - + -
184B SER* 3.1 42.2 + - - -
185B ASN* 3.2 24.1 + - + +
187B ASP 3.2 12.3 + - - +
189B THR* 1.3 81.3 - - - +
191B ILE* 1.3 60.3 + - - +
193B LYS* 4.2 2.2 - - - +
194B THR* 2.9 29.2 + - - -
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Residues in contact with ILE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A ILE* 3.6 20.9 - - + -
420A HIS* 4.1 5.6 - - - +
152B ILE* 6.3 0.2 - - + -
154B ILE* 4.2 12.1 - - + -
183B VAL* 3.9 19.4 - - + +
187B ASP 4.4 0.6 + - - +
188B GLY* 3.5 12.0 + - - +
190B HIS* 1.3 75.6 - - - +
192B ALA* 1.3 65.4 + - - +
194B THR* 3.3 0.7 + - - -
195B LEU* 2.9 49.9 + - + +
220B ASN* 3.3 53.8 + - + +
223B THR* 4.4 5.8 - - + -
224B ALA* 4.2 10.8 - - + +
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A HIS* 4.2 23.6 - - + +
415A ILE* 4.2 20.2 - - + -
188B GLY 3.0 15.3 + - - +
189B THR 4.1 2.5 - - - +
191B ILE* 1.3 83.0 - - - +
193B LYS* 1.3 65.5 + - - +
195B LEU* 3.5 7.2 + - - +
196B ALA* 3.1 25.1 + - - +
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Residues in contact with LYS 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LYS* 5.4 10.1 - - + -
343A TYR* 3.3 30.1 - - + +
413A HIS* 3.2 27.3 + - - +
181B TRP* 4.9 0.7 - - - -
189B THR* 3.0 27.4 + - + +
190B HIS* 4.2 3.1 - - - +
192B ALA* 1.3 81.0 + - - +
194B THR* 1.3 61.1 + - - +
196B ALA* 3.7 17.0 - - - +
197B CYS* 3.5 21.5 - - - -
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Residues in contact with THR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ILE* 4.4 4.3 - - + -
181B TRP* 3.6 38.3 - - + -
182B PHE 5.0 1.7 + - - -
183B VAL* 3.5 25.5 - - + +
190B HIS* 2.9 22.4 + - - -
191B ILE 3.3 4.2 + - - -
192B ALA 3.2 0.4 - - - -
193B LYS* 1.3 77.5 - - - +
195B LEU* 1.3 67.8 - - + +
197B CYS* 3.1 13.9 + - - +
198B LEU* 3.2 31.3 - - + +
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Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B VAL* 5.9 0.9 - - + -
191B ILE* 2.9 45.3 + - + +
192B ALA* 3.9 6.5 - - - +
194B THR* 1.3 81.9 - - + +
196B ALA* 1.3 62.3 + - - +
198B LEU* 3.0 29.8 + - + +
205B PHE* 4.3 24.9 - - + -
223B THR* 4.6 13.2 - - + +
224B ALA* 4.8 1.6 - - - -
227B TRP* 3.7 57.0 + - + +
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ALA 3.1 19.0 + - - +
193B LYS* 3.7 22.4 - - - +
194B THR 3.2 0.6 - - - -
195B LEU* 1.3 75.9 - - - +
197B CYS* 1.3 61.2 + - - +
198B LEU 3.5 1.8 + - - +
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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