Contacts of the helix formed by residues 187 - 196 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A ASN* 3.1 25.1 + - + +
186A ILE* 1.3 78.1 - - - +
188A GLY* 1.3 62.7 + - - +
189A THR* 2.8 28.9 + - - -
190A HIS* 2.9 20.4 + - - +
191A ILE* 4.3 0.9 + - - +
341B ASP* 3.5 10.1 - - - +
342B GLN* 2.8 32.3 + - + +
411B THR* 4.4 7.6 + - - -
420B HIS 5.0 0.9 - - - -
421B HIS* 4.9 3.0 + - - -
424B LEU* 3.9 30.4 - - + +
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Residues in contact with GLY 188 (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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186A ILE 2.9 8.6 + - - -
187A ASP* 1.3 73.0 + - - +
189A THR* 1.3 61.9 + - - +
190A HIS 3.2 0.2 - - - -
191A ILE* 3.6 4.7 + - - +
192A ALA* 3.0 27.6 + - - +
411B THR* 5.5 0.4 + - - -
413B HIS* 4.3 10.5 - - - -
415B ILE* 3.7 22.8 - - - +
420B HIS* 3.7 16.0 - - - +
421B HIS* 5.1 1.6 + - - +
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Residues in contact with THR 189 (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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187A ASP* 2.8 25.3 + - - -
188A GLY* 1.3 74.7 - - - +
190A HIS* 1.3 64.0 + - - +
192A ALA* 3.9 0.2 - - - +
193A LYS* 3.0 35.3 + - - +
341B ASP* 5.3 1.9 + - - -
342B GLN* 4.0 11.9 - - + -
343B TYR* 3.5 50.7 - - + +
411B THR* 4.3 7.3 + - - -
412B GLN* 4.9 1.0 + - - +
413B HIS* 3.2 24.3 + - - +
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Residues in contact with HIS 190 (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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182A PHE 3.4 19.9 + - - -
183A VAL* 4.3 3.6 - - + -
184A SER* 3.1 42.2 + - - -
185A ASN* 3.2 23.5 + - + +
187A ASP 2.9 13.8 + - - +
189A THR* 1.3 82.4 - - - +
191A ILE* 1.3 62.7 + - - +
193A LYS* 3.5 11.3 - - + +
194A THR* 3.0 28.7 + - - -
342B GLN* 3.8 37.3 + - + +
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Residues in contact with ILE 191 (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 ILE* 4.5 7.4 - - + -
183A VAL* 3.9 18.1 - - + +
187A ASP 4.3 0.6 + - - -
188A GLY* 3.6 4.6 + - - +
190A HIS* 1.3 78.7 - - - +
192A ALA* 1.3 61.0 + - - +
194A THR* 3.1 1.9 + - - -
195A LEU* 2.9 52.9 + - + +
205A PHE* 5.8 0.4 - - + -
220A ASN* 3.2 52.9 + - + +
223A THR* 4.2 9.2 - - + -
224A ALA* 3.9 18.4 - - + +
415B ILE* 3.6 27.1 - - + -
420B HIS* 4.3 2.2 - - - +
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Residues in contact with ALA 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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188A GLY 3.0 19.9 + - - +
189A THR 3.9 2.5 - - - +
191A ILE* 1.3 80.4 - - - +
193A LYS* 1.3 61.3 + - - +
195A LEU* 3.5 4.8 + - - +
196A ALA* 3.2 25.1 + - - +
413B HIS* 3.9 29.6 - - + +
415B ILE* 4.3 13.7 - - + -
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Residues in contact with LYS 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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181A TRP* 5.4 0.3 - - - -
189A THR* 3.0 27.8 + - + +
190A HIS* 3.5 15.9 - - + +
192A ALA* 1.3 75.9 - - - +
194A THR* 1.3 66.7 + - - +
196A ALA* 4.0 8.0 + - - +
197A CYS* 3.4 22.2 - - - -
168B GLU* 4.6 11.3 + - - -
171B LYS* 4.5 13.4 - - - +
342B GLN* 5.6 4.1 - - + +
343B TYR* 3.8 38.5 - - - +
345B HIS* 5.6 3.2 + - - -
413B HIS* 5.4 4.2 - - + +
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Residues in contact with THR 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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152A ILE* 4.3 7.2 - - + -
181A TRP* 4.0 39.0 - - + +
182A PHE 4.9 2.3 + - - -
183A VAL* 3.7 25.3 - - + +
190A HIS* 3.0 23.5 + - - -
191A ILE 3.1 4.0 + - - -
192A ALA 3.1 0.8 - - - -
193A LYS* 1.3 82.2 - - - +
195A LEU* 1.3 64.8 + - + +
196A ALA 3.4 0.5 + - - -
197A CYS* 3.5 5.9 + - - +
198A LEU* 3.1 33.0 - - + +
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Residues in contact with LEU 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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152A ILE* 5.8 0.2 - - + -
191A ILE* 2.9 45.9 + - + +
192A ALA* 4.2 3.6 - - - +
194A THR* 1.3 74.9 - - + +
196A ALA* 1.3 62.0 + - - +
197A CYS 3.0 6.5 + - - -
198A LEU* 3.2 20.3 + - + +
205A PHE* 3.5 38.1 - - + -
223A THR* 4.7 5.4 - - + +
224A ALA* 4.4 4.0 - - - -
227A TRP* 3.3 67.7 + - + +
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Residues in contact with ALA 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 ALA 3.2 17.4 + - - +
193A LYS* 4.1 10.5 - - - +
194A THR 3.2 0.6 - - - -
195A LEU* 1.3 76.5 - - - +
197A CYS* 1.3 61.5 + - - +
198A LEU 3.5 1.9 - - - +
227A TRP* 5.5 0.7 - - - +
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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