Contacts of the helix formed by residues 187 - 196 (chain D) in PDB entry 1JLH
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341C ASP* 3.5 11.2 - - - +
342C GLN* 2.9 26.1 + - + +
411C THR* 4.3 5.9 + - - -
420C HIS* 4.8 0.8 - - - -
421C HIS* 5.1 2.3 + - - +
424C LEU* 3.7 29.4 - - + +
185D ASN* 2.9 31.9 + - + +
186D ILE* 1.3 78.1 - - - +
188D GLY* 1.3 68.9 + - - +
189D THR* 3.0 32.8 + - - +
190D HIS* 3.0 12.1 + - - +
191D ILE 4.3 0.5 + - - -
220D ASN* 5.1 0.2 - - - +
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Residues in contact with GLY 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411C THR* 5.6 0.6 + - - -
413C HIS* 4.4 8.1 - - - -
415C ILE* 3.7 10.9 - - - +
420C HIS* 3.6 33.4 - - - +
421C HIS* 5.8 0.4 - - - +
186D ILE 2.9 4.8 + - - -
187D ASP* 1.3 71.6 + - - +
189D THR* 1.3 64.3 + - - +
190D HIS 3.1 0.4 + - - -
191D ILE* 3.4 3.8 - - - +
192D ALA* 2.9 28.5 + - - +
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Residues in contact with THR 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C ASP* 5.3 2.9 - - - +
342C GLN* 3.2 25.8 - - - +
343C TYR* 3.9 25.1 + - + -
411C THR* 4.1 13.9 - - - +
412C GLN* 4.9 2.5 - - + +
413C HIS* 3.4 33.3 + - + +
187D ASP* 3.0 20.2 + - - +
188D GLY* 1.3 77.1 - - - +
190D HIS* 1.3 66.1 + - - +
193D LYS* 2.9 32.0 + - - +
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Residues in contact with HIS 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C GLN* 4.0 33.3 + - + -
385C ASN* 4.9 1.6 - - - -
182D TYR 3.3 21.2 + - - -
183D VAL* 4.3 5.2 - - + -
184D SER* 3.2 30.6 + - - -
185D ASN* 3.1 31.6 + - + +
187D ASP 3.0 13.4 + - - +
189D THR* 1.3 86.1 + - - +
191D ILE* 1.3 63.1 + - - +
193D LYS* 3.6 14.8 + - - +
194D THR* 2.9 29.7 + - - -
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Residues in contact with ILE 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C ILE* 3.5 21.3 - - + -
420C HIS* 4.1 6.1 - - - +
152D ILE* 5.4 0.7 - - + -
154D ILE* 4.6 6.7 - - + -
183D VAL* 4.0 25.9 - - + +
187D ASP 4.3 0.4 + - - -
188D GLY* 3.4 11.2 - - - +
190D HIS* 1.3 78.8 - - - +
192D ALA* 1.3 62.0 + - - +
194D THR* 3.2 3.0 + - - -
195D LEU* 2.9 67.6 + - + +
205D PHE* 5.1 1.1 - - + -
220D ASN* 3.7 36.1 + - + +
223D THR* 4.1 10.8 - - + -
224D ALA* 4.5 6.7 - - + -
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Residues in contact with ALA 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C HIS* 3.9 29.4 - - + +
415C ILE* 4.3 15.7 - - + -
188D GLY 2.9 20.3 + - - +
189D THR 3.8 2.2 - - - +
191D ILE* 1.3 80.0 - - - +
193D LYS* 1.3 62.5 + - - +
195D LEU* 3.4 6.3 + - - +
196D ALA* 3.2 23.4 + - - +
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Residues in contact with LYS 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C GLU* 5.9 1.0 + - - -
171C LYS* 5.8 4.0 - - + -
342C GLN* 4.2 25.7 - - - +
343C TYR* 3.8 39.0 - - + +
345C HIS* 6.5 0.9 - - - -
413C HIS* 5.0 5.5 - - + +
189D THR* 2.9 29.8 + - - +
190D HIS* 3.6 16.9 + - - +
192D ALA* 1.3 73.4 - - - +
194D THR* 1.3 66.2 + - - +
196D ALA* 3.8 9.5 + - - +
197D GLN* 3.1 28.7 + - - +
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Residues in contact with THR 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ILE* 4.5 4.5 - - + -
181D TRP* 4.0 32.0 - - + -
182D TYR 5.0 1.4 + - - -
183D VAL* 3.7 24.8 - - + +
190D HIS* 2.9 27.8 + - - -
191D ILE 3.2 4.2 + - - -
192D ALA 3.1 0.6 - - - -
193D LYS* 1.3 80.6 + - - +
195D LEU* 1.3 62.5 - - + +
197D GLN* 3.0 26.6 + - - +
198D LEU* 3.4 24.4 - - + +
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Residues in contact with LEU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D ILE* 2.9 51.4 + - + +
192D ALA* 3.9 5.6 - - - +
194D THR* 1.3 73.9 - - + +
196D ALA* 1.3 58.8 + - - +
197D GLN 2.9 10.0 + - - -
198D LEU* 3.0 29.1 + - + +
205D PHE* 3.9 27.6 - - + -
223D THR* 4.4 7.9 - - + -
224D ALA* 4.3 7.6 - - + -
227D TRP* 3.5 56.5 + - + +
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Residues in contact with ALA 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D ALA 3.2 15.8 + - - +
193D LYS* 3.9 11.7 - - - +
194D THR 3.2 1.4 - - - -
195D LEU* 1.3 75.7 - - - +
197D GLN* 1.3 61.0 + - + +
198D LEU 3.5 2.0 + - - +
227D TRP* 5.8 0.4 - - - +
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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