Contacts of the strand formed by residues 444 - 449 (chain A) in PDB entry 5HQG
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 LYS 444 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A TYR* 2.6 27.1 + - - +
417A LEU* 5.7 6.3 - - + -
438A ILE 3.6 0.7 - - - +
439A ALA* 3.5 9.9 - - - -
442A THR* 3.2 28.0 - - - +
443A LYS* 1.3 82.7 - - - +
445A ILE* 1.3 61.8 + - - +
446A LYS* 3.5 33.2 - - - +
466A GLU* 2.4 35.7 + - + +
467A MET 3.2 6.1 - - - +
468A THR* 4.3 16.2 + - + +
473A ILE* 3.7 1.8 - - - +
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Residues in contact with ILE 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ALA* 4.3 12.6 - - + -
438A ILE 3.3 8.5 - - - +
439A ALA* 4.2 6.5 - - + -
444A LYS* 1.3 71.4 - - - +
446A LYS* 1.3 62.9 + - - +
447A VAL* 4.7 0.2 - - + -
466A GLU* 3.3 5.4 - - - +
467A MET* 2.7 62.4 + - + +
469A CYS* 5.8 1.3 - - + +
473A ILE* 3.5 20.9 - - + -
476A ILE* 4.4 9.2 - - + -
486A LEU* 4.2 16.4 - - + -
488A SER* 3.6 20.0 - - - +
498A TRP* 3.6 39.9 - - + +
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Residues in contact with LYS 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A SER 4.7 2.4 + - - -
413A TYR* 3.0 43.7 + - + +
414A ALA 4.4 9.9 - - - -
417A LEU* 5.8 1.2 - - - +
437A ALA* 3.4 2.0 - - - -
438A ILE* 2.9 37.1 + - + +
444A LYS* 3.5 25.6 - - + +
445A ILE* 1.3 76.1 - - - +
447A VAL* 1.3 62.4 + - - +
448A TYR* 3.6 34.6 + - + +
463A PRO* 4.1 11.1 - - + +
465A ASN 3.7 3.4 - - - -
466A GLU* 3.4 28.0 + - + +
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Residues in contact with VAL 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A TYR* 3.9 28.5 - - + -
436A PHE 3.5 9.4 - - - +
437A ALA* 4.3 13.2 - - + -
445A ILE* 4.7 0.4 - - + -
446A LYS* 1.3 76.2 - - - +
448A TYR* 1.3 57.3 + - - +
463A PRO* 3.1 5.4 - - - +
464A GLU* 2.6 35.7 + - + -
465A ASN 2.9 15.4 + - - +
467A MET* 3.6 30.3 - - + -
478A TRP* 4.3 17.7 - - + -
486A LEU* 4.7 0.9 - - + -
500A GLY 3.8 13.0 - - - +
501A PHE* 4.7 4.3 - - + -
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Residues in contact with TYR 448 (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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411A LEU* 3.9 25.3 - - + +
412A SER 4.1 14.6 + - - -
413A TYR* 5.2 1.5 - + - -
435A TYR* 3.2 11.1 - - - -
436A PHE* 2.9 67.3 + + + -
438A ILE* 4.1 15.7 - - + -
446A LYS* 3.6 43.9 + - + +
447A VAL* 1.3 74.8 - - - +
449A GLU* 1.3 60.0 + - - +
450A TYR 3.6 0.2 + - - -
453A VAL* 3.8 10.3 - - + -
461A HIS* 4.1 14.9 + - + -
462A TYR 4.4 4.0 - - - -
463A PRO* 3.7 33.9 - - + +
464A GLU* 4.2 2.7 - - - +
725A ILE* 5.3 1.6 - - + +
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Residues in contact with GLU 449 (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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434A ASP* 4.3 5.2 - - + +
435A TYR* 3.5 38.6 + - + -
448A TYR* 1.3 70.7 - - - +
450A TYR* 1.3 68.3 + - - +
451A ASP* 4.4 8.9 - - + +
452A THR* 3.0 38.9 + - - +
453A VAL* 3.1 15.4 + - - +
464A GLU* 4.4 14.4 - - + +
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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