Contacts of the helix formed by residues 317 - 327 (chain F) in PDB entry 6NR8
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 LYS 317 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213F ASP* 3.7 35.0 - - + +
214F HIS* 3.3 31.3 + - + +
294F GLN* 2.9 9.4 + - - +
315F ARG 4.6 1.2 + - - -
316F ALA* 1.3 73.4 - - - +
318F ARG* 1.3 61.0 + - - +
319F ARG* 3.2 17.0 - - + -
320F ASN* 3.0 35.2 + - - +
321F MET 3.3 5.4 + - - -
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Residues in contact with ARG 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222 SER* 2.8 49.5 + - - +
232 ALA* 3.7 23.9 - - + +
262 VAL* 4.1 12.9 - - - +
234F ASN* 3.3 20.2 - - - +
294F GLN* 3.3 41.9 + - - +
295F LYS* 4.1 19.0 - - - +
316F ALA 4.8 2.7 + - - +
317F LYS* 1.3 70.9 - - - +
319F ARG* 1.3 60.5 + - - +
321F MET* 3.3 14.7 + - - +
322F GLU* 2.9 22.7 - - - +
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Residues in contact with ARG 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192F GLU* 3.8 30.3 + - - +
193F ILE 4.5 11.5 + - - +
194F MET* 4.7 13.9 - - - +
195F GLU* 5.4 3.0 + - - -
213F ASP* 5.4 0.9 - - - -
317F LYS* 4.0 14.4 - - + -
318F ARG* 1.3 77.5 - - - +
320F ASN* 1.3 92.6 + - - +
321F MET 3.1 1.2 + - - -
322F GLU* 3.4 14.0 + - - +
323F ARG* 4.0 11.1 + - - +
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Residues in contact with ASN 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F GLU* 3.5 15.1 - - - +
194F MET* 3.7 6.4 - - - +
210F LEU* 5.5 3.2 - - - +
211F VAL 4.1 9.1 + - - +
212F LEU* 4.1 18.3 - - + +
213F ASP* 3.6 19.8 + - - -
294F GLN* 4.8 1.3 - - - +
317F LYS* 3.0 33.7 + - - +
319F ARG* 1.3 90.9 - - - +
321F MET* 1.3 63.3 + - - +
322F GLU 3.3 0.4 - - - -
323F ARG* 4.0 5.4 - - - +
324F LEU* 3.1 43.2 + - + +
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Residues in contact with MET 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222 SER* 3.5 25.4 - - - +
1202 GLU* 4.9 0.4 - - - +
1242 ILE* 3.8 18.3 - - + +
232F THR* 3.5 19.1 - - + +
233F CYS 4.6 0.2 - - - -
234F ASN* 3.6 29.6 - - + +
294F GLN* 3.4 32.5 - - + +
317F LYS 3.3 2.4 + - - -
318F ARG* 3.3 26.0 - - - +
319F ARG 3.1 1.0 - - - -
320F ASN* 1.3 79.3 - - - +
322F GLU* 1.3 63.4 + - - +
325F THR* 2.9 21.8 + - - -
332F ALA* 3.7 26.0 - - + -
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Residues in contact with GLU 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222 SER* 3.8 19.1 + - - -
1242 ILE* 5.5 13.3 - - + +
318F ARG 2.9 25.9 - - - +
319F ARG* 3.4 11.5 - - - +
320F ASN 3.3 0.2 - - - -
321F MET* 1.3 81.6 - - + +
323F ARG* 1.3 63.6 + - - +
325F THR* 3.1 16.8 + - - -
326F LEU* 3.1 22.7 + - + +
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Residues in contact with ARG 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F LEU 5.1 3.6 + - - -
189F PHE* 3.6 29.3 - - - +
190F MET* 4.7 4.0 - - - +
191F ILE* 4.8 5.9 - - - +
192F GLU* 3.3 55.5 + - - +
210F LEU* 3.8 14.0 - - + +
319F ARG 4.0 12.7 + - - +
320F ASN* 3.5 5.6 + - - +
322F GLU* 1.3 76.8 - - - +
324F LEU* 1.3 65.4 + - - +
326F LEU* 3.2 23.0 + - - +
327F ALA* 3.2 15.1 + - - +
371F SER* 3.3 31.1 + - - -
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Residues in contact with LEU 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F LEU* 3.7 33.4 - - + -
211F VAL 6.1 0.4 - - - +
212F LEU* 4.1 17.5 - - + +
230F ILE* 5.5 2.0 - - + -
232F THR* 3.9 18.6 - - + +
292F ILE* 3.7 32.1 - - + -
294F GLN* 5.6 0.2 - - - +
320F ASN* 3.1 27.8 + - + +
321F MET* 5.2 0.2 - - - -
323F ARG* 1.3 75.7 - - - +
325F THR* 1.3 50.8 + - - +
328F CYS* 3.2 23.3 + - + +
329F GLY 2.5 35.3 + - - +
363F ILE* 4.4 17.3 - - + -
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Residues in contact with THR 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1242 ILE* 5.1 14.4 - - + +
232F THR* 4.2 2.8 + - - +
321F MET 2.9 17.7 + - - -
322F GLU* 3.1 11.7 + - - -
324F LEU* 1.3 76.6 - - - +
326F LEU* 1.3 68.3 + - + +
329F GLY* 3.3 20.3 - - - -
330F GLY 3.0 27.1 + - - +
331F VAL* 4.5 13.5 - - + -
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Residues in contact with LEU 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189F PHE* 3.7 35.0 - - + -
322F GLU* 3.1 19.7 + - + +
323F ARG* 3.2 23.0 + - - +
325F THR* 1.3 85.2 - - + +
327F ALA* 1.3 62.0 + - + +
328F CYS 5.1 0.2 - - - -
368F ASN* 4.9 5.5 - - - +
370F ARG* 5.0 9.7 - - + +
371F SER* 5.2 2.5 - - - +
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Residues in contact with ALA 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F LEU* 3.7 26.5 - - + -
323F ARG 3.2 5.2 + - - +
326F LEU* 1.3 81.3 - - - +
328F CYS* 1.3 66.3 + - - +
366F CYS* 3.8 8.5 - - - -
367F ASN* 4.0 0.5 - - - +
368F ASN* 3.1 45.0 + - - +
370F ARG* 4.7 2.9 - - + -
371F SER* 4.2 20.6 - - - +
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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