Contacts of the helix formed by residues 188 - 197 (chain C) in PDB entry 1JIQ
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 188 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186C ASN* 3.0 25.1 + - + +
187C ILE* 1.3 79.4 - - - +
189C GLY* 1.3 61.6 + - - +
190C THR* 3.1 23.0 + - - -
191C HIS* 2.9 27.0 + - - +
192C ILE 4.3 0.5 + - - -
221C ASN* 5.3 0.2 - - - +
342D ASP* 3.5 10.6 - - - +
343D GLN* 2.9 30.1 + - + +
412D THR* 4.3 8.5 + - - -
421D HIS* 4.8 0.8 + - - -
422D HIS* 5.0 1.6 + - - -
425D LEU* 3.6 32.3 - - + +
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Residues in contact with GLY 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C ILE 2.9 8.2 + - - -
188C ASP* 1.3 71.9 + - - +
190C THR* 1.3 64.6 + - - +
191C HIS 3.0 0.6 + - - -
192C ILE* 3.4 4.7 + - - +
193C ALA* 2.9 28.6 + - - +
412D THR* 5.4 0.8 + - - -
414D HIS* 4.3 8.5 - - - -
416D ILE* 3.7 12.6 - - - +
421D HIS* 3.6 26.9 - - - +
422D HIS* 5.1 1.2 + - - +
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Residues in contact with THR 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C ASP* 3.0 22.8 + - - -
189C GLY* 1.3 76.4 - - - +
191C HIS* 1.3 63.4 + - - +
194C LYS* 3.0 30.6 + - + +
342D ASP* 5.4 1.9 + - - -
343D GLN* 4.2 12.1 - - + -
344D TYR* 3.4 50.4 - - + -
412D THR* 4.5 4.9 + - - -
413D GLN* 4.8 1.2 - - - +
414D HIS* 3.3 27.0 + - - +
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Residues in contact with HIS 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ASP* 5.8 0.2 - - - -
183C TYR* 3.4 20.5 + - + -
184C VAL* 4.4 4.5 - - + -
185C SER* 3.2 29.9 + - - -
186C ASN* 3.2 34.4 + - + +
188C ASP 2.9 14.5 + - - +
190C THR* 1.3 84.1 - - - +
192C ILE* 1.3 61.5 + - - +
194C LYS* 3.7 16.4 + - - +
195C THR* 2.7 30.6 + - - -
343D GLN* 4.0 31.5 + - + +
386D ASN* 4.9 1.1 - - - -
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Residues in contact with ILE 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ILE* 5.2 0.2 - - + -
155C ILE* 4.4 17.0 - - + -
184C VAL* 3.9 28.6 - - + +
188C ASP 4.3 0.4 + - - -
189C GLY* 3.6 3.8 - - - +
191C HIS* 1.3 77.3 - - - +
193C ALA* 1.3 64.0 + - - +
195C THR* 3.1 5.3 + - + -
196C LEU* 2.8 60.5 + - + +
206C PHE* 5.0 2.7 - - + -
221C ASN* 3.7 29.1 + - - +
224C THR* 4.0 10.8 - - + -
225C ALA* 4.5 2.5 - - + -
416D ILE* 3.6 26.0 - - + -
421D HIS* 3.9 6.5 - - + -
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Residues in contact with ALA 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C GLY 2.9 19.1 + - - +
190C THR 4.1 0.2 - - - +
192C ILE* 1.3 79.8 - - - +
194C LYS* 1.3 61.7 + - - +
196C LEU* 3.4 6.4 + - - +
197C ALA* 3.1 24.6 + - - +
414D HIS* 3.9 31.9 - - + +
416D ILE* 4.2 16.2 - - + -
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Residues in contact with LYS 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C THR* 3.0 41.9 + - + +
191C HIS* 3.7 24.9 + - - +
193C ALA* 1.3 77.5 - - - +
195C THR* 1.3 66.2 + - - +
197C ALA* 3.9 9.9 + - - +
198C GLN* 3.2 27.6 - - - +
169D GLU* 5.6 3.8 + - - -
172D LYS* 5.9 2.9 - - + -
343D GLN* 4.3 11.8 - - - +
344D TYR* 4.0 24.5 - - + +
346D HIS* 6.1 1.5 + - - -
414D HIS* 5.2 4.4 - - + +
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Residues in contact with THR 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ILE* 4.4 4.3 - - + -
182C TRP* 4.0 33.5 - - + -
183C TYR 4.8 1.9 + - - -
184C VAL* 3.7 26.2 - - + +
191C HIS* 2.7 27.7 + - - -
192C ILE* 3.1 6.9 + - + -
194C LYS* 1.3 80.5 + - - +
196C LEU* 1.3 65.2 - - + +
198C GLN* 3.0 19.1 + - - +
199C LEU* 3.4 27.5 - - + +
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Residues in contact with LEU 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ILE* 2.8 46.8 + - + +
193C ALA* 4.0 5.4 - - - +
195C THR* 1.3 73.8 - - + +
197C ALA* 1.3 60.6 + - - +
198C GLN 3.0 0.2 - - - -
199C LEU* 3.1 23.1 + - + +
206C PHE* 3.7 35.7 - - + -
224C THR* 4.3 9.9 - - + +
225C ALA* 4.2 8.5 - - - -
228C TRP* 3.6 64.4 + - + +
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Residues in contact with ALA 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C ALA 3.1 17.2 + - - +
194C LYS* 3.9 11.4 - - - +
195C THR 3.1 0.8 - - - -
196C LEU* 1.3 75.9 - - - +
198C GLN* 1.3 62.2 + - + +
199C LEU 3.4 2.1 + - - +
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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