Contacts of the strand formed by residues 488 - 494 (chain A) in PDB entry 2QR8
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 TYR 488 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A ILE* 3.8 21.3 - - + -
453A ILE 3.3 13.5 - - - +
454A ASP* 3.8 32.8 + - + -
455A LYS* 4.2 0.4 - - - -
484A ASP* 3.5 6.1 - - - +
485A ASP* 2.8 35.6 + - - +
487A LYS* 1.3 114.3 + - + +
489A VAL* 1.3 61.3 + - - +
490A TYR* 3.6 26.4 - - + -
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Residues in contact with VAL 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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451A LYS 3.6 0.5 - - - +
452A ILE* 3.4 4.9 - - - +
453A ILE* 3.0 35.5 + - + +
455A LYS* 3.6 17.5 - - + +
460A PRO* 3.9 20.2 - - + -
464A ILE* 3.4 31.9 - - + -
482A VAL* 4.1 3.4 - - + -
483A TYR 3.4 8.1 - - - +
484A ASP* 3.3 28.0 - - + +
488A TYR* 1.3 73.8 - - - +
490A TYR* 1.3 63.8 + - - +
491A VAL* 3.8 13.2 - - + -
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Residues in contact with TYR 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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418A PHE* 3.6 44.0 - + + -
419A THR* 5.8 1.6 - - + -
424A VAL* 6.2 0.2 - - + -
450A VAL* 3.8 9.4 - - + -
451A LYS 3.6 4.7 - - - -
452A ILE* 3.9 30.6 - - + +
482A VAL* 3.3 6.8 - - - +
483A TYR* 2.7 53.1 + - + +
485A ASP* 3.5 29.7 + - + -
488A TYR* 3.6 30.5 - - + +
489A VAL* 1.3 76.0 - - - +
491A VAL* 1.3 61.7 + - - +
492A VAL* 3.8 1.9 + - - -
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Residues in contact with VAL 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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449A ALA 3.7 0.5 - - - +
450A VAL* 3.5 1.7 - - - +
451A LYS* 2.9 42.1 + - + +
453A ILE* 3.8 19.7 - - + -
463A GLU* 5.5 4.0 - - - +
464A ILE* 4.0 16.4 - - + -
467A LEU* 4.1 18.2 - - + -
479A LEU* 3.3 28.7 - - + -
481A ASP 3.9 2.5 - - - -
482A VAL* 4.8 2.9 - - + +
489A VAL* 3.8 20.9 - - + -
490A TYR* 1.3 71.9 - - - +
492A VAL* 1.3 59.1 + - - +
493A THR* 3.8 9.7 + - + +
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Residues in contact with VAL 492 (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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418A PHE* 3.7 32.3 - - + -
422A TYR* 3.9 21.8 - - + +
439A CYS* 4.4 2.2 - - - -
448A PHE* 3.7 24.5 - - + -
449A ALA 3.3 10.1 - - - +
450A VAL* 4.1 8.3 - - + -
479A LEU* 3.6 2.3 - - - +
480A LYS* 2.8 28.7 + - + -
481A ASP* 2.9 32.4 + - + +
483A TYR* 4.6 1.1 - - + -
490A TYR 4.5 3.8 - - - +
491A VAL* 1.3 73.5 - - - +
493A THR* 1.3 63.4 + - - +
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Residues in contact with THR 493 (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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448A PHE* 3.5 9.0 - - - +
449A ALA* 2.9 35.9 + - - +
451A LYS* 6.4 0.7 - - + -
467A LEU* 4.9 7.4 - - + -
477A ILE* 3.3 32.1 - - + +
478A THR 3.3 17.0 - - - +
479A LEU* 4.2 15.9 - - + -
480A LYS* 4.0 7.0 - - - +
491A VAL* 3.8 12.6 + - + +
492A VAL* 1.3 78.9 - - - +
494A GLU* 1.3 67.3 + - - +
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Residues in contact with GLU 494 (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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448A PHE* 4.2 9.6 - - + -
449A ALA* 4.3 1.6 - - - +
477A ILE* 3.8 3.4 - - + +
478A THR* 2.8 47.1 + - - +
480A LYS* 4.0 16.8 + - - +
493A THR* 1.3 85.4 + - - +
495A LEU* 1.3 61.2 + - - +
496A MET* 3.1 34.9 + - + +
548A VAL* 3.9 10.5 - - + +
558A ARG* 3.1 35.4 + - - -
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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