Contacts of the strand formed by residues 359 - 367 (chain I) 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 ASP 359 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200I ALA* 5.4 6.8 - - - +
201I HIS* 6.1 1.6 - - - -
220I VAL* 3.5 20.5 - - + +
354I GLU 3.5 0.9 - - - +
355I ARG* 3.3 2.0 - - - -
356I ILE* 2.9 37.7 + - - +
357I CYS* 3.2 18.8 - - - +
358I ASP* 1.3 85.9 - - - +
360I GLU* 1.3 62.2 + - - +
361I LEU* 3.4 20.9 + - + +
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Residues in contact with GLU 360 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218I CYS* 3.2 18.7 - - - -
220I VAL* 3.3 26.2 - - + +
227I LYS* 4.1 20.3 - - - +
228I ARG* 3.3 38.3 + - - +
353I GLN* 3.3 28.4 - - + +
354I GLU 3.6 9.6 - - - +
355I ARG* 3.7 24.2 + - + +
358I ASP 4.3 0.6 + - - -
359I ASP* 1.3 68.4 - - - +
361I LEU* 1.3 62.7 + - - +
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Residues in contact with LEU 361 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198I LEU* 4.6 7.9 - - + -
199I LYS 5.9 2.2 - - - +
216I LEU 3.6 17.5 - - - +
217I ASN* 3.8 22.9 - - - +
218I CYS* 3.8 14.1 - - - +
220I VAL* 6.1 0.4 - - + -
353I GLN* 3.6 4.9 - - - +
354I GLU 3.1 32.4 + - - +
356I ILE* 5.3 10.1 - - + +
359I ASP* 3.4 19.0 + - + +
360I GLU* 1.3 76.8 - - - +
362I ILE* 1.3 65.0 + - - +
363I LEU* 3.6 14.9 + - + +
376I ILE* 3.8 33.0 - - + -
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Residues in contact with ILE 362 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216I LEU* 3.2 39.1 + - + +
218I CYS* 3.7 14.5 - - + -
227I LYS* 3.8 17.7 - - - +
285I VAL* 4.8 10.8 - - + -
287I LEU* 3.8 15.3 - - + -
308I VAL* 3.8 37.7 - - + -
351I VAL* 4.0 15.7 - - + -
352I VAL 4.4 2.7 - - - -
353I GLN* 4.3 12.6 - - + +
360I GLU* 5.9 0.2 - - + -
361I LEU* 1.3 73.4 - - - +
363I LEU* 1.3 61.8 + - - +
364I ILE* 3.7 24.0 + - + +
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Residues in contact with LEU 363 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211I ILE* 3.8 28.5 - - + -
214I TYR 4.0 1.8 - - - -
215I ALA* 3.7 27.4 - - + -
351I VAL* 4.0 3.3 - - - +
352I VAL 3.4 30.3 + - - +
354I GLU* 3.3 39.9 - - + +
356I ILE* 6.3 1.8 - - + -
361I LEU* 4.4 15.7 - - + +
362I ILE* 1.3 73.4 - - - +
364I ILE* 1.3 62.3 + - - +
365I LYS* 3.2 32.1 + - - +
376I ILE* 4.3 9.2 - - + -
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Residues in contact with ILE 364 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212I SER 4.5 0.9 - - - -
213I GLY* 3.3 20.9 - - - -
214I TYR 3.0 17.7 + - - +
216I LEU* 5.4 0.9 - - + -
234I ILE* 3.8 40.2 - - + -
287I LEU* 5.3 4.0 - - + -
319I ILE* 4.0 25.1 - - + -
323I SER* 4.8 2.9 - - - -
348I ALA* 3.9 20.4 - - + -
350I GLU 4.8 2.0 - - - -
351I VAL* 3.9 7.6 - - + -
362I ILE* 3.9 26.0 - - + +
363I LEU* 1.3 67.6 - - - +
365I LYS* 1.3 62.3 + - - +
366I ASN 3.3 0.3 + - - -
367I THR* 3.7 25.1 - - + +
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Residues in contact with LYS 365 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211I ILE* 4.3 9.0 - - - -
212I SER* 3.3 23.6 - - - +
348I ALA* 3.5 13.9 - - - +
349I GLU* 3.2 26.3 - - - +
350I GLU* 3.6 17.1 + - + +
352I VAL* 3.6 18.2 - - + +
354I GLU* 3.4 21.6 + - - -
363I LEU* 3.2 39.6 + - + +
364I ILE* 1.3 69.6 - - - +
366I ASN* 1.3 73.4 + - - +
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Residues in contact with ASN 366 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212I SER* 3.2 22.3 + - - -
213I GLY* 3.8 9.8 - - - -
348I ALA* 3.7 4.2 - - - -
349I GLU* 3.7 26.9 + - + +
364I ILE 3.3 2.8 + - - -
365I LYS* 1.3 76.6 - - - +
367I THR* 1.3 69.4 + - - +
368I LYS* 3.4 21.4 + - - +
371I THR* 3.4 27.4 - - + +
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Residues in contact with THR 367 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213I GLY* 4.7 1.4 - - - -
214I TYR* 4.2 17.5 - - + +
319I ILE* 5.0 1.6 - - + +
322I ALA* 3.3 35.0 + - + +
323I SER* 3.9 3.8 - - - +
347I GLN 4.0 6.3 - - - -
364I ILE* 3.7 32.1 - - + +
365I LYS 3.7 0.2 - - - -
366I ASN* 1.3 75.0 - - - +
368I LYS* 1.3 59.7 + - - +
370I ARG 2.3 46.4 + - - +
371I THR* 3.4 10.3 + - - +
372I SER* 3.7 9.9 + - - -
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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