Contacts of the helix formed by residues 195 - 208 (chain D) in PDB entry 6RI7
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 GLU 195 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193D ASP* 3.2 11.9 + - - +
194D LEU* 1.3 86.3 - - - +
196D GLN* 1.3 71.0 + - - +
197D GLU 3.0 1.3 - - - -
198D CYS* 3.1 19.5 + - - +
199D GLU* 3.0 38.3 + - - +
228D VAL* 5.1 8.8 - - - +
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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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193D ASP* 4.1 24.0 + - + +
195D GLU* 1.3 78.8 - - - +
197D GLU* 1.3 59.1 + - + +
199D GLU* 3.2 29.9 + - - +
200D GLN* 2.9 37.5 + - - +
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Residues in contact with GLU 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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192D MET* 4.3 20.8 - - + +
193D ASP 3.2 23.0 - - - +
194D LEU* 4.5 8.3 - - + -
195D GLU 3.0 0.4 - - - -
196D GLN* 1.3 76.6 - - + +
198D CYS* 1.3 68.5 + - - +
200D GLN* 4.8 9.6 - - - +
201D LEU* 2.9 36.5 + - - +
220D ARG* 2.7 37.4 + - - +
224D LEU* 4.0 18.6 - - + -
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Residues in contact with CYS 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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194D LEU 3.7 19.7 - - - -
195D GLU* 3.1 22.4 + - - +
197D GLU* 1.3 75.8 - - - +
199D GLU* 1.3 65.9 + - - +
202D ARG* 2.9 47.1 + - - +
221D ILE* 4.1 20.9 - - - -
224D LEU* 4.9 12.5 - - - +
225D GLU* 5.1 7.9 - - - -
228D VAL* 5.0 7.9 - - - -
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Residues in contact with GLU 199 (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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195D GLU* 3.0 29.4 + - - +
196D GLN* 3.2 36.1 + - - +
198D CYS* 1.3 76.8 - - + +
200D GLN* 1.3 63.4 + - - +
202D ARG* 3.8 4.9 - - - +
203D GLU* 3.0 24.8 + - - +
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Residues in contact with GLN 200 (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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196D GLN* 2.9 24.6 + - - +
197D GLU* 4.1 10.3 - - - +
199D GLU* 1.3 75.0 - - - +
201D LEU* 1.3 62.8 + - + +
203D GLU* 3.3 15.9 + - - +
204D GLU* 2.9 50.4 + - + +
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Residues in contact with LEU 201 (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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197D GLU* 2.9 28.4 + - - +
198D CYS 4.2 0.4 - - - +
200D GLN* 1.3 79.7 - - + +
202D ARG* 1.3 61.9 + - - +
204D GLU* 3.1 32.5 + - - +
205D LEU* 2.9 34.2 + - + +
217D LEU* 4.6 12.8 - - + +
220D ARG* 3.3 52.9 - - + +
221D ILE* 4.8 15.7 - - + +
224D LEU* 4.3 9.2 - - + -
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Residues in contact with ARG 202 (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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198D CYS* 2.9 34.7 + - - +
199D GLU* 3.8 4.3 - - - +
201D LEU* 1.3 76.3 - - - +
203D GLU* 1.3 62.5 + - - +
205D LEU* 3.3 11.4 + - + +
206D ASN* 2.9 23.4 + - - +
221D ILE* 4.1 25.6 - - + +
225D GLU* 3.0 31.5 + - - +
1275D LEU* 3.6 29.7 - - - +
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Residues in contact with GLU 203 (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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199D GLU 3.0 12.6 + - - +
200D GLN* 3.3 18.9 - - - +
201D LEU 3.2 0.2 - - - -
202D ARG* 1.3 78.2 - - - +
204D GLU* 1.3 57.4 + - + +
206D ASN* 3.2 7.9 + - + +
207D GLU* 2.9 46.9 + - + +
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Residues in contact with GLU 204 (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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200D GLN* 2.9 36.9 + - + +
201D LEU* 3.1 33.8 + - - +
203D GLU* 1.3 77.8 - - + +
205D LEU* 1.3 57.2 + - - +
207D GLU* 4.4 2.9 - - - +
208D THR* 2.7 45.4 + - + +
217D LEU* 3.3 21.0 - - + +
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Residues in contact with LEU 205 (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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201D LEU 2.9 17.5 + - - +
202D ARG* 3.7 11.0 - - + +
204D GLU* 1.3 76.4 - - - +
206D ASN* 1.3 64.4 + - - +
208D THR* 3.8 13.3 + - - +
214D ARG* 3.9 33.7 + - + +
217D LEU* 3.7 29.4 - - + -
218D THR* 4.4 12.3 - - - +
221D ILE* 4.3 26.5 - - + -
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Residues in contact with ASN 206 (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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202D ARG 2.9 13.8 + - - +
203D GLU* 3.2 12.0 + - - +
205D LEU* 1.3 79.4 - - - +
207D GLU* 1.3 73.2 + - + +
208D THR 4.2 1.4 - - - +
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Residues in contact with GLU 207 (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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203D GLU* 2.9 34.5 + - + +
204D GLU* 4.0 3.8 - - - +
206D ASN* 1.3 90.8 + - - +
208D THR* 1.3 73.2 + - + +
209D ASN* 3.9 10.0 + - - +
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Residues in contact with THR 208 (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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204D GLU* 2.7 39.5 + - + +
205D LEU* 3.8 16.1 + - - +
206D ASN 4.2 1.9 - - - +
207D GLU* 1.3 81.0 - - + +
209D ASN* 1.3 66.9 + - - +
210D SER* 4.7 4.1 + - - -
213D LYS* 5.1 15.3 - - - +
214D ARG* 3.9 12.1 + - - +
217D LEU* 5.0 7.2 - - + +
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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