Contacts of the strand formed by residues 469 - 475 (chain A) in PDB entry 5F6K
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 PHE 469 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A ASP* 5.3 4.3 - - - -
317A ARG* 4.0 19.1 - - + -
318A ALA 3.3 16.4 - - - +
319A SER 3.9 11.4 - - - -
320A HIS* 3.3 18.4 - - - -
321A GLY* 3.2 18.8 - - - -
346A TRP* 3.3 6.0 - - - -
347A SER 2.7 43.1 + - - +
349A PRO* 3.7 27.6 - - + -
467A VAL* 3.7 25.4 - - + -
468A TYR* 1.3 76.8 - - - +
470A PRO* 1.3 74.7 - - + +
471A ALA* 3.3 1.0 + - - +
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Residues in contact with PRO 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A LEU* 5.9 0.6 - - - +
317A ARG* 3.5 1.7 - - - -
318A ALA* 2.9 38.0 + - + +
320A HIS 3.6 16.4 - - - +
329A PHE* 3.4 44.0 - - + -
345A GLY 3.8 2.0 - - - +
346A TRP* 3.8 9.2 - - + -
468A TYR 4.2 0.4 - - - +
469A PHE* 1.3 83.3 - - + +
471A ALA* 1.3 58.2 + - - +
472A ILE* 5.7 0.2 - - - -
482A ILE* 4.3 4.0 - - + -
484A PHE* 3.9 15.9 - - + -
500A MET* 3.7 24.9 - - + -
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Residues in contact with ALA 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A MET* 4.2 1.8 - - - -
316A VAL 3.5 8.3 - - - +
317A ARG* 4.1 5.4 - - + -
329A PHE* 4.4 1.8 - - - -
331A ILE* 4.8 2.3 - - - +
344A LEU* 3.8 2.3 - - - +
345A GLY 3.0 31.6 + - - +
347A SER* 3.6 31.4 - - - +
357A LEU* 3.5 20.5 - - + +
469A PHE 3.7 2.0 - - - +
470A PRO* 1.3 75.4 - - - +
472A ILE* 1.3 67.1 + - - +
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Residues in contact with ILE 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A LEU* 4.0 23.3 - - + -
298A LEU* 4.7 0.5 - - - +
307A VAL* 3.9 21.1 - - + -
314A SER 3.9 0.7 - - - +
315A MET* 3.2 3.9 - - - -
316A VAL* 2.8 46.5 + - + +
331A ILE* 3.7 27.4 - - + -
344A LEU* 3.7 15.9 - - + -
357A LEU* 5.3 0.2 - - - -
470A PRO 5.7 0.2 - - - -
471A ALA* 1.3 77.8 - - - +
473A SER* 1.3 62.6 + - - +
474A LEU* 3.8 23.3 - - + -
480A VAL* 3.8 14.6 - - + -
482A ILE* 4.1 18.2 - - + +
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Residues in contact with SER 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A TYR* 3.8 11.2 - - - -
314A SER 3.2 11.4 - - - -
315A MET* 4.2 7.4 - - - -
342A ALA* 3.8 0.5 - - - +
343A ARG* 2.6 53.9 + - - +
344A LEU* 4.1 0.3 - - - +
356A PRO* 4.2 2.7 - - - -
357A LEU* 3.1 31.4 + - - +
472A ILE* 1.3 75.2 - - - +
474A LEU* 1.3 70.1 + - - +
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Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A LEU* 4.5 4.9 - - + -
307A VAL* 3.5 36.8 - - + +
308A VAL 3.8 2.0 - - - -
309A GLY* 3.4 38.5 - - - +
310A GLU 5.0 0.5 + - - -
311A LYS 4.2 0.2 - - - +
312A GLY 3.8 3.5 - - - +
313A TYR* 3.3 21.6 - - - -
314A SER* 3.1 14.2 + - - +
341A ALA 3.7 1.1 - - - -
342A ALA* 3.7 19.5 - - + -
472A ILE* 3.8 16.8 - - + +
473A SER* 1.3 86.0 - - - +
475A TYR* 1.3 61.5 + - - +
476A LYS 4.0 1.1 + - - -
478A CYS* 3.7 18.8 - - - +
480A VAL* 4.1 11.9 - - + -
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Residues in contact with TYR 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LYS 3.7 13.2 - - - -
312A GLY* 4.3 8.1 - - - -
313A TYR* 3.5 46.4 - + + +
339A ASP* 3.3 24.0 - - + -
340A THR* 3.5 2.9 - - - -
341A ALA* 2.8 42.4 + - + +
474A LEU* 1.3 71.1 - - - +
476A LYS* 1.3 98.6 + - + +
478A CYS* 4.1 0.3 - - - -
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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