Contacts of the strand formed by residues 487 - 491 (chain A) in PDB entry 1HNY
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 487 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A ARG 5.3 0.2 - - - -
322A LYS* 3.4 33.2 - - + -
323A MET* 3.4 31.4 - - + -
326A GLY* 4.3 15.5 - - - -
390A GLN* 4.5 5.6 - - + -
394A MET* 4.6 0.4 - - + -
427A ILE* 4.2 10.1 - - + -
428A VAL 3.1 14.1 - - - +
429A PHE* 3.6 26.7 - + + -
451A ASP* 4.5 1.0 - - - +
453A ILE* 3.5 62.9 - - + +
479A ILE* 4.1 3.0 - - - +
485A ASP* 2.9 19.8 + - + +
486A PRO* 1.3 82.0 - - + +
488A ILE* 1.3 68.8 - - - +
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Residues in contact with ILE 488 (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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426A PHE 4.2 0.2 - - - +
427A ILE* 3.3 5.1 - - - +
428A VAL* 2.8 33.6 + - + +
451A ASP* 3.4 30.7 - - + +
453A ILE* 4.2 1.1 - - - -
465A ILE* 4.8 15.5 - - + -
467A ILE* 4.0 18.2 - - + -
477A PHE* 3.9 35.2 - - + -
478A SER 3.9 11.9 - - - +
479A ILE* 3.6 31.0 - - + -
485A ASP 5.7 0.7 - - - +
487A PHE* 1.3 80.3 - - - +
489A ALA* 1.3 66.5 - - - +
490A ILE* 4.4 3.4 - - + -
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Residues in contact with ALA 489 (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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394A MET* 3.8 29.2 - - - -
397A PHE* 4.1 6.5 - - + -
426A PHE 3.5 6.7 - - - +
427A ILE* 3.9 12.3 - - + -
451A ASP* 3.0 7.7 + - - +
452A VAL* 2.8 37.7 + - + +
453A ILE* 3.7 12.5 - - + +
488A ILE* 1.3 75.4 - - - +
490A ILE* 1.3 66.1 + - - +
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Residues in contact with ILE 490 (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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397A PHE* 3.5 2.7 - - - -
425A GLY* 3.2 0.9 - - - -
426A PHE* 3.0 41.6 + - + +
442A THR* 5.1 1.1 - - + -
444A LEU* 3.6 27.6 - - + -
449A TYR* 3.8 19.3 - - + -
450A CYS 3.6 14.6 - - - +
451A ASP* 3.9 3.8 - - - -
467A ILE* 3.8 45.5 - - + -
469A VAL* 4.0 13.5 - - + -
477A PHE* 4.4 12.1 - - + -
488A ILE* 4.4 3.8 - - + -
489A ALA* 1.3 79.7 - - - +
491A HIS* 1.3 67.6 + - - +
494A SER* 3.9 3.1 - - - -
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Residues in contact with HIS 491 (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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393A ASN 4.6 1.2 + - - -
396A ILE* 4.4 16.7 - - + +
397A PHE* 3.8 33.3 + + + -
400A VAL* 3.8 20.6 - - + +
401A VAL* 4.7 1.3 - - + -
424A ARG 3.2 16.2 - - - +
425A GLY* 4.0 4.0 - - - -
444A LEU* 5.3 0.9 - - - -
449A TYR* 3.3 17.3 - - - -
452A VAL* 3.7 27.1 - - + +
490A ILE* 1.3 76.9 - - - +
492A ALA* 1.3 66.9 + - - +
493A GLU* 3.1 43.4 + - + +
494A SER* 2.9 32.1 + - - -
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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