Contacts of the strand formed by residues 453 - 459 (chain B) in PDB entry 6HYI
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 VAL 453 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383B GLU 4.1 0.2 - - - +
384B GLU* 3.2 6.8 - - - +
385B PHE* 2.8 39.5 + - + +
391B ILE* 4.3 10.3 - - + -
404B ILE* 4.5 5.6 - - + -
406B GLU 3.2 9.6 - - - +
408B THR 3.3 35.0 - - - +
409B VAL* 4.0 9.6 - - + -
449B ALA* 3.7 13.9 - - + -
451B THR 3.4 11.7 - - - +
452B HIS* 1.3 77.2 - - - +
454B ILE* 1.3 67.4 + - - +
455B THR* 3.6 25.8 - - + -
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Residues in contact with ILE 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B SER* 5.2 6.1 - - - +
383B GLU 3.8 2.9 - - - +
384B GLU* 4.0 22.9 - - + +
404B ILE* 3.7 1.2 - - - -
405B MET* 2.7 47.7 + - + -
406B GLU* 2.9 44.3 + - + +
452B HIS* 3.7 23.3 - - + +
453B VAL* 1.3 77.1 - - - +
455B THR* 1.3 66.6 + - - +
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Residues in contact with THR 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B SER* 3.3 10.0 + - - -
383B GLU* 2.8 48.4 + - - +
385B PHE* 3.8 15.1 - - + -
391B ILE* 4.6 5.2 - - + -
402B TYR* 3.5 35.4 - - + -
403B ILE 3.3 10.1 - - - +
404B ILE* 4.6 7.2 - - + -
405B MET* 4.1 6.1 - - - +
432B ILE* 5.5 0.2 - - + -
453B VAL* 3.6 20.9 - - + -
454B ILE* 1.3 79.0 - - - +
456B ALA* 1.3 60.8 - - - +
457B LYS* 4.7 0.2 - - - +
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Residues in contact with ALA 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B TYR* 4.0 24.0 - - + -
358B PHE* 4.7 4.0 - - + -
380B LEU* 4.1 20.9 - - + -
381B SER 3.3 5.2 - - - +
382B SER* 4.6 0.2 - - - +
401B LEU 3.8 0.7 - - - +
402B TYR* 3.3 4.0 - - - -
403B ILE* 2.8 45.5 + - + +
405B MET* 3.9 12.6 - - + +
455B THR* 1.3 74.1 - - - +
457B LYS* 1.3 59.8 + - - +
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Residues in contact with LYS 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B ALA 3.6 1.7 - - - +
380B LEU* 3.4 8.8 - - - +
381B SER* 2.7 46.7 + - - +
382B SER 5.5 0.4 - - - +
383B GLU* 2.6 39.5 + - + +
400B TRP* 3.2 56.0 - - + +
401B LEU 3.4 4.5 - - - +
402B TYR* 3.6 27.2 + - + +
455B THR* 4.7 2.5 - - - +
456B ALA* 1.3 75.8 - - - +
458B LEU* 1.3 59.1 + - - +
459B ASN 4.5 0.2 + - - -
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Residues in contact with LEU 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B LEU* 4.1 14.6 - - + -
379B ALA* 3.5 34.5 - - + +
380B LEU* 4.0 9.2 - - + -
400B TRP* 3.6 6.1 - - - -
401B LEU* 2.8 49.9 + - + +
457B LYS* 1.3 73.2 - - - +
459B ASN* 1.3 68.6 + - - +
462B HIS* 3.8 15.0 - - + -
463B PHE* 4.2 21.3 - - + -
466B CYS* 4.0 8.5 - - + -
467B LEU* 3.7 31.4 - - + -
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Residues in contact with ASN 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B ALA 4.7 2.2 + - - -
399B GLU* 3.1 36.0 + - - +
400B TRP* 3.3 32.6 - - + -
437B PHE* 4.7 0.4 - - - -
457B LYS 4.5 0.2 + - - -
458B LEU* 1.3 82.7 - - - +
460B ARG* 1.3 68.6 + - - +
461B ARG* 2.9 52.8 + - + +
462B HIS* 2.9 22.6 + - + +
463B PHE 3.5 5.9 + - - -
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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