Contacts of the strand formed by residues 359 - 366 (chain F) in PDB entry 6NRB
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 359 (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 2.8 21.9 - - - +
214F HIS* 4.9 9.7 + - - -
215F GLY 3.6 6.0 + - - +
216F ALA 2.7 41.0 + - - +
217F ARG* 4.7 2.6 + - - +
219F PRO* 3.5 23.1 - - + +
220F ASP* 4.2 4.3 - - - +
352F GLU* 2.9 40.4 - - + +
353F TYR 3.2 7.2 - - - +
354F THR* 3.1 19.7 - - - +
357F GLU 3.6 2.4 + - - -
358F GLU* 1.3 73.3 - - + +
360F PHE* 1.3 61.4 + - - +
361F THR 3.7 1.4 + - - -
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Residues in contact with PHE 360 (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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194F MET* 5.0 7.0 - - - -
195F GLU* 4.6 12.3 - - + -
196F MET* 3.4 32.8 - - + -
197F LYS* 4.0 24.9 - - + -
211F VAL* 3.6 17.5 - - + -
212F LEU 3.6 8.7 - - - -
213F ASP* 5.1 4.5 - - - -
353F TYR* 2.3 49.6 + - - +
355F LEU 4.4 0.2 - - - -
358F GLU* 3.1 63.5 - - + -
359F LYS* 1.3 65.3 - - - +
361F THR* 1.3 65.1 + - - +
362F PHE* 3.2 21.3 - - + -
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Residues in contact with THR 361 (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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211F VAL 3.3 0.5 - - - -
212F LEU* 2.3 66.1 + - + +
215F GLY* 3.4 17.8 + - - -
223F LYS 5.3 0.4 - - - +
311F VAL* 5.6 2.5 - - + -
313F LEU* 3.7 10.1 - - + -
350F VAL* 3.5 30.3 - - + -
351F TYR 3.0 13.0 - - - +
352F GLU* 3.3 25.5 - - + +
359F LYS 3.7 1.2 + - - -
360F PHE* 1.3 71.1 - - - +
362F PHE* 1.3 59.2 + - - +
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Residues in contact with PHE 362 (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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196F MET* 4.6 5.2 - - + -
207F ILE* 4.2 14.8 - - + -
210F LEU 3.7 4.9 - - - +
211F VAL* 3.4 39.0 - - + -
349F LEU 2.9 9.9 - - - +
350F VAL* 3.9 0.4 - - - -
351F TYR* 2.3 53.7 + + + +
353F TYR* 3.3 45.8 - + + -
360F PHE* 3.2 18.4 - - + -
361F THR* 1.3 70.0 - - - -
363F ILE* 1.3 59.8 + - - +
364F GLU* 3.3 28.3 + - - +
375F LEU* 4.7 14.8 - - + -
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Residues in contact with ILE 363 (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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209F GLY* 2.9 2.3 - - - -
210F LEU* 2.6 61.3 + - + +
212F LEU* 3.5 24.5 - - + -
228F ALA* 4.6 0.7 - - + -
230F ILE* 4.0 22.2 - - + -
290F VAL* 5.3 0.7 - - + -
292F ILE* 5.0 0.2 - - + -
324F LEU* 3.7 18.6 - - + -
328F CYS* 3.4 28.9 - - - -
347F ALA* 3.6 9.0 - - + -
349F LEU 3.2 2.2 - - - -
350F VAL* 3.4 28.3 - - + +
361F THR 3.6 2.6 + - - -
362F PHE* 1.3 71.8 - - - +
364F GLU* 1.3 56.4 + - - +
366F CYS* 3.2 1.4 - - - -
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Residues in contact with GLU 364 (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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206F LEU 5.0 0.5 - - - +
207F ILE* 3.1 30.1 - - + +
208F ARG* 4.0 8.3 + - + +
209F GLY* 3.6 14.6 - - - +
347F ALA* 3.2 2.6 - - - +
348F GLY 3.1 5.7 + - - -
349F LEU* 2.3 86.8 + - + +
362F PHE* 3.3 27.7 - - - +
363F ILE* 1.3 70.8 - - - +
365F LYS* 1.3 60.7 + - + +
366F CYS* 3.0 11.6 - - - -
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Residues in contact with LYS 365 (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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208F ARG* 4.0 19.9 - - + +
348F GLY* 3.2 37.3 + - - +
349F LEU* 3.2 32.9 - - + +
364F GLU* 1.3 81.8 - - + +
366F CYS* 1.3 64.5 + - - +
367F ASN* 3.3 13.3 + - - -
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Residues in contact with CYS 366 (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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208F ARG* 4.2 10.8 + - - +
209F GLY* 3.5 10.5 - - - -
210F LEU 4.3 1.3 - - - -
327F ALA* 3.0 26.7 - - + +
328F CYS* 3.4 27.4 - - - -
347F ALA* 3.6 11.4 - - - -
363F ILE 3.2 32.8 - - - -
364F GLU* 3.0 1.0 - - - +
365F LYS* 1.3 76.9 - - - +
367F ASN* 1.3 59.7 + - - +
369F PRO* 3.1 25.4 - - + +
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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