Contacts of the helix formed by residues 195 - 210 (chain K) in PDB entry 1HVU
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 ILE 195 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193K LEU 3.5 1.6 + - - -
194K GLU* 1.3 71.7 - - - +
196K GLY* 1.3 62.5 + - - +
198K HIS* 3.2 9.0 - - - +
199K ARG* 3.1 22.7 + - - +
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Residues in contact with GLY 196 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194K GLU* 3.2 2.8 - - - +
195K ILE* 1.3 78.2 - - - +
197K GLN* 1.3 61.5 + - - +
198K HIS 3.1 1.2 + - - -
199K ARG* 3.2 16.4 + - - +
200K THR* 3.3 11.6 + - - -
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Residues in contact with GLN 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193K LEU* 4.0 15.6 - - + +
194K GLU* 2.9 20.1 + - + +
196K GLY* 1.3 68.7 - - - +
198K HIS* 1.3 65.5 + - - +
200K THR* 4.1 9.9 - - - -
201K LYS* 3.9 12.5 + - - +
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Residues in contact with HIS 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105K SER* 5.5 10.1 - - - -
191K SER* 5.1 11.0 - - - -
193K LEU* 4.1 15.3 - - + +
194K GLU 2.6 16.4 + - - +
195K ILE* 3.2 15.7 - - - +
196K GLY 3.0 0.2 - - - -
197K GLN* 1.3 72.0 - - - +
199K ARG* 1.3 68.2 + - - +
201K LYS* 2.9 25.4 + - - +
202K ILE* 3.1 6.0 + - - +
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Residues in contact with ARG 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195K ILE 3.1 8.4 + - - +
196K GLY* 3.2 10.5 + - - +
198K HIS* 1.3 79.7 - - - +
200K THR* 1.3 62.0 + - - +
202K ILE* 3.0 12.8 + - - +
203K GLU* 2.8 21.8 + - - +
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Residues in contact with THR 200 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196K GLY 3.3 9.5 + - - -
197K GLN* 4.1 11.9 - - - -
198K HIS 3.0 0.8 + - - -
199K ARG* 1.3 75.2 - - - +
201K LYS* 1.3 51.1 - - - +
203K GLU* 2.7 28.9 + - - +
204K GLU* 2.7 18.8 + - - +
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Residues in contact with LYS 201 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175K ASN* 5.9 7.2 - - + -
191K SER* 6.1 4.5 - - - -
197K GLN 3.9 8.2 + - - +
198K HIS* 2.9 12.5 + - - +
200K THR* 1.3 77.5 - - - +
202K ILE* 1.3 57.3 + - - +
204K GLU* 3.1 9.6 + - - +
205K LEU* 2.8 31.3 + - - +
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Residues in contact with ILE 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K THR* 5.7 9.4 - - - -
189K VAL* 5.8 8.7 - - + -
198K HIS 3.1 4.2 + - - +
199K ARG* 3.0 17.5 + - - +
201K LYS* 1.3 77.5 - - - +
203K GLU* 1.3 50.8 + - - +
205K LEU* 2.9 11.9 + - - +
206K ARG* 2.5 37.1 + - - +
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Residues in contact with GLU 203 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199K ARG 2.8 11.3 + - - +
200K THR* 2.7 19.1 + - - +
202K ILE* 1.3 71.6 - - - +
204K GLU* 1.3 55.0 + - - -
206K ARG* 3.2 10.5 - - - +
207K GLN* 2.9 27.2 + - - +
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Residues in contact with GLU 204 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171K PHE* 5.4 5.2 - - + +
200K THR 2.7 14.6 + - - +
201K LYS* 3.4 12.8 - - - +
203K GLU* 1.3 72.1 - - - +
205K LEU* 1.3 63.3 + - - +
207K GLN* 3.3 6.7 + - - +
208K HIS* 3.2 20.6 + - - +
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Residues in contact with LEU 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K PHE* 4.9 11.2 - - + -
189K VAL* 6.1 4.9 - - + -
201K LYS 2.8 12.7 + - - +
202K ILE* 3.1 14.6 - - - +
204K GLU* 1.3 77.2 - - - +
206K ARG* 1.3 54.8 + - - +
208K HIS* 3.3 10.0 - - - +
209K LEU* 3.1 27.1 + - - +
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Residues in contact with ARG 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202K ILE 2.5 19.5 + - - +
203K GLU* 3.2 14.4 - - - +
204K GLU 3.0 0.2 - - - -
205K LEU* 1.3 72.3 - - - +
207K GLN* 1.3 59.1 + - - +
209K LEU* 3.4 6.9 + - - +
210K LEU* 2.7 28.3 + - - +
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Residues in contact with GLN 207 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203K GLU 2.9 12.5 + - - +
204K GLU* 3.3 8.5 + - - +
206K ARG* 1.3 72.3 - - - +
208K HIS* 1.3 61.3 + - - +
210K LEU* 2.5 36.9 + - - +
211K ARG* 3.1 5.8 + - - +
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Residues in contact with HIS 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167K ILE* 4.5 20.0 - - + +
168K LEU* 6.0 0.4 - - - -
171K PHE* 5.0 11.0 - - + -
204K GLU 3.2 10.5 + - - +
205K LEU* 3.3 13.7 - - - +
207K GLN* 1.3 82.4 - - - +
209K LEU* 1.3 56.8 + - - +
211K ARG* 2.9 26.2 + - - +
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Residues in contact with LEU 209 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111K VAL* 6.6 0.2 - - - -
167K ILE* 6.3 2.7 - - - -
205K LEU 3.1 12.3 + - - +
206K ARG* 3.8 6.3 - - - +
207K GLN 3.1 0.6 - - - -
208K HIS* 1.3 74.1 - - - +
210K LEU* 1.3 57.7 + - - +
211K ARG* 3.0 14.5 + - - -
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Residues in contact with LEU 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206K ARG 2.7 15.6 + - - +
207K GLN* 2.5 25.6 + - - +
209K LEU* 1.3 71.7 - - - +
211K ARG* 1.3 55.8 + - - +
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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