Contacts of the strand formed by residues 359 - 364 (chain P) 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 GLN 359 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352P LEU* 3.1 29.8 + - + +
353P SER* 2.9 17.6 + - - +
354P GLU* 3.7 29.5 - - + +
358P THR* 1.3 74.7 + - - +
360P VAL* 1.3 89.3 + - - +
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Residues in contact with VAL 360 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207P ILE* 5.0 2.5 - - + -
222P VAL* 4.2 2.0 - - + -
223P PHE 3.4 10.3 - - - +
224P LYS* 3.3 40.2 - - + +
225P LYS 3.8 7.4 - - - +
227P THR* 4.9 4.9 - - - -
352P LEU* 4.4 3.6 - - - -
353P SER 2.8 21.9 + - - +
355P VAL* 3.8 31.6 - - + +
358P THR* 3.2 14.5 + - + +
359P GLN* 1.3 89.4 - - - +
361P VAL* 1.3 64.0 + - - +
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Residues in contact with VAL 361 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222P VAL* 3.8 6.9 - - - +
223P PHE* 3.4 42.6 + - + +
227P THR* 3.5 21.4 + - + +
311P MET* 3.7 25.8 - - + -
313P VAL* 3.9 11.9 - - + -
350P VAL* 3.7 13.9 - - + -
351P TYR 3.7 11.4 - - - +
352P LEU* 3.8 20.8 - - + +
360P VAL* 1.3 76.4 - - - +
362P VAL* 1.3 65.4 + - - +
363P PHE* 4.6 5.4 - - + -
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Residues in contact with VAL 362 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218P LEU* 4.2 11.4 - - + -
219P HIS 3.8 9.2 - - - +
221P MET 3.5 5.6 - - - +
222P VAL* 3.7 22.9 - - + -
351P TYR* 2.9 72.5 + - + +
353P SER* 3.9 22.0 - - - +
355P VAL* 4.2 7.0 - - + -
361P VAL* 1.3 78.4 - - - +
363P PHE* 1.3 72.2 + - - +
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Residues in contact with PHE 363 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219P HIS 3.0 20.0 - - - +
220P GLY* 4.1 2.0 - - - -
221P MET* 2.6 39.7 + - + +
223P PHE* 3.5 39.5 - + - -
237P ALA* 4.2 10.5 - - + -
239P ILE* 4.7 10.5 - - + -
290P VAL* 3.7 33.7 - - + -
324P LEU* 5.4 3.1 - - + -
347P CYS* 4.6 7.0 - - + -
349P SER 3.3 8.5 - - - -
350P VAL* 3.6 31.0 - - + +
351P TYR* 3.5 6.7 - - - -
361P VAL* 4.6 8.3 - - + -
362P VAL* 1.3 81.8 - - - +
364P LYS* 1.3 60.8 + - - +
365P HIS* 3.8 18.4 - + + -
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Residues in contact with LYS 364 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219P HIS* 4.9 16.9 - - + +
220P GLY* 4.2 0.7 - - - -
347P CYS* 3.8 1.7 - - - +
348P ASP* 3.0 51.1 + - + +
349P SER* 2.8 31.2 + - - +
351P TYR* 4.5 10.5 - - + +
363P PHE* 1.3 79.2 - - - +
365P HIS* 1.3 70.4 + - - +
366P GLU* 3.6 39.6 - - - +
369P ASP* 3.4 1.0 - - - +
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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
------------------------------------------------------------
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