Contacts of the helix formed by residues 190 - 198 (chain D) in PDB entry 1HJV
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 190 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147D LYS* 4.1 15.5 + - + +
148D GLN* 6.4 0.2 - - - -
150D PHE* 5.7 0.4 - - - -
151D THR* 3.5 19.8 + - - +
189D TYR* 1.3 71.7 - - - +
191D ILE* 1.3 61.6 + - - +
192D ALA* 3.3 6.2 + - - +
193D LYS* 2.9 50.7 + - - +
194D ILE* 3.1 18.5 + - - +
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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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178D LEU* 3.9 19.7 - - + -
185D ILE* 4.5 0.9 - - + -
189D TYR* 3.3 16.9 + - + +
190D ASP* 1.3 74.0 - - - +
192D ALA* 1.3 55.4 + - - +
194D ILE* 4.0 6.3 - - + -
195D SER* 2.5 55.8 + - - +
201D ILE* 4.9 3.4 - - + -
244D MET* 3.5 36.1 - - + +
247D LEU* 4.0 31.6 - - + +
249D ALA* 3.2 31.6 - - + +
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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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190D ASP* 3.3 5.6 + - - +
191D ILE* 1.3 80.0 - - - +
193D LYS* 1.3 64.8 + - + +
195D SER* 4.0 6.1 - - - -
196D GLN* 3.6 16.4 + - - +
247D LEU 3.6 17.3 + - - +
248D GLY* 4.7 7.9 - - - -
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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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148D GLN* 5.8 3.1 - - - +
151D THR* 4.3 23.3 - - + -
190D ASP* 2.9 37.9 + - - +
192D ALA* 1.3 76.5 - - + +
194D ILE* 1.3 64.9 + - - +
195D SER 3.1 1.1 - - - -
196D GLN* 2.9 38.9 + - - +
197D HIS* 4.2 7.1 + - + -
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Residues in contact with ILE 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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150D PHE* 3.7 27.6 - - + -
151D THR* 3.7 41.3 - - + +
154D ILE* 4.1 20.0 - - + -
178D LEU* 4.1 22.0 - - + -
189D TYR* 4.5 8.3 - - + -
190D ASP 3.1 13.8 + - - +
191D ILE* 3.8 11.0 - - - +
193D LYS* 1.3 75.5 - - - +
195D SER* 1.3 66.6 + - - +
196D GLN 2.8 1.9 + - - -
197D HIS* 3.0 20.7 + - - +
198D LEU* 3.1 25.7 + - + +
201D ILE* 5.1 1.1 - - + -
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Residues in contact with SER 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* 2.5 47.5 + - - +
192D ALA* 4.0 8.1 - - - -
193D LYS 3.1 0.2 + - - -
194D ILE* 1.3 72.9 - - - +
196D GLN* 1.3 57.9 + - - +
198D LEU* 3.7 4.1 - - - +
201D ILE* 4.0 14.8 - - - +
248D GLY 4.9 0.4 - - - -
249D ALA* 3.3 11.2 - - - +
250D PRO* 3.6 22.7 - - - -
253D LYS* 2.9 32.5 + - - +
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Residues in contact with GLN 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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158D LYS* 4.9 4.5 + - - -
192D ALA 3.6 16.0 + - - +
193D LYS* 3.1 28.8 + - - +
194D ILE 2.8 1.6 + - - -
195D SER* 1.3 79.1 - - - +
197D HIS* 1.3 74.5 + - + +
198D LEU 4.1 0.2 - - - +
253D LYS* 2.8 20.7 + - - +
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Residues in contact with HIS 197 (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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151D THR* 5.0 3.8 - - + -
154D ILE* 3.8 19.7 - - + -
155D LYS* 3.4 43.7 + - + +
158D LYS* 3.1 54.5 + - + +
174D LEU* 4.4 5.7 - - - +
193D LYS* 4.3 13.9 + - + +
194D ILE* 3.0 6.0 + - - +
196D GLN* 1.3 90.4 + - + +
198D LEU* 1.3 60.9 + - - +
199D ASP 3.6 0.7 + - - -
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Residues in contact with LEU 198 (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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137D LEU* 5.3 0.4 - - + -
154D ILE* 3.9 28.0 - - + -
158D LYS* 4.9 0.2 - - - -
174D LEU* 3.6 19.3 - - + +
175D SER 3.8 19.1 - - - +
176D ALA* 3.9 16.2 - - + +
178D LEU* 5.0 0.7 - - + -
194D ILE* 3.1 33.0 + - + +
195D SER 4.6 2.2 - - - +
196D GLN 3.4 0.2 - - - -
197D HIS* 1.3 76.8 - - - +
199D ASP* 1.3 63.7 + - - +
200D PHE 3.3 9.8 + - - +
201D ILE* 3.7 32.3 - - + -
253D LYS* 3.2 26.9 + - - +
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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