Contacts of the helix formed by residues 450 - 461 (chain B) in PDB entry 5KYT
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 ALA 450 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387B ARG* 5.4 2.5 - - - +
435B VAL* 3.8 31.0 - - + +
436B ASP* 4.1 8.7 - - + +
441B LEU* 3.8 12.3 - - + -
448B GLN 4.1 1.2 + - - -
449B VAL* 1.3 79.4 - - - +
451B PRO* 1.3 62.7 - - + +
452B ALA 4.3 1.3 - - - +
453B GLU* 2.7 44.2 + - + +
454B LEU 3.7 2.3 + - - -
510B LYS* 5.3 0.4 - - - +
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Residues in contact with PRO 451 (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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436B ASP* 3.4 14.6 - - - +
440B SER* 3.1 39.3 - - - +
441B LEU* 4.4 0.2 - - - -
442B ILE* 4.0 10.7 - - + -
449B VAL 3.5 6.3 - - - +
450B ALA* 1.3 83.8 - - + +
452B ALA* 1.3 58.0 + - - +
453B GLU 3.1 0.5 + - - -
454B LEU* 3.2 3.1 + - + +
455B GLU* 2.8 42.4 + - - +
469B VAL* 3.3 39.3 - - + +
470B ALA* 4.9 1.8 - - - -
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Residues in contact with ALA 452 (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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318B PRO* 5.2 14.6 - - + -
435B VAL 3.5 19.7 - - - +
436B ASP* 3.1 18.4 + - + +
450B ALA* 3.0 1.8 - - + -
451B PRO* 1.3 79.9 - - - +
453B GLU* 1.3 62.6 + - - +
455B GLU* 3.7 13.2 - - - +
456B SER* 3.1 22.3 + - - -
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Residues in contact with GLU 453 (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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387B ARG* 5.2 7.8 + - - -
449B VAL* 5.5 0.7 - - + -
450B ALA* 2.7 22.6 + - + +
452B ALA* 1.3 79.1 - - - +
454B LEU* 1.3 63.8 + - + +
456B SER* 3.1 16.3 + - - -
457B ILE* 3.2 25.5 + - + +
506B VAL* 5.8 0.7 - - - +
510B LYS* 3.4 41.8 + - + +
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Residues in contact with LEU 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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442B ILE* 5.5 0.2 - - + -
449B VAL* 4.0 20.9 - - + -
450B ALA 3.7 1.3 + - - +
451B PRO 3.2 3.4 + - - +
453B GLU* 1.3 76.7 - - + +
455B GLU* 1.3 68.9 + - - +
457B ILE* 3.1 8.3 + - + +
458B LEU* 2.9 28.5 + - + +
469B VAL* 3.9 24.7 - - + -
481B PRO* 3.6 27.4 - - + -
502B VAL* 3.8 22.7 - - + -
506B VAL* 4.1 14.6 - - + -
510B LYS* 3.2 31.9 - - + +
512B LEU* 4.3 8.3 - - + -
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Residues in contact with GLU 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B PRO* 2.8 29.8 + - - +
452B ALA* 3.7 13.8 - - - +
454B LEU* 1.3 77.1 - - - +
456B SER* 1.3 61.4 + - - +
458B LEU* 3.4 5.8 + - - +
459B LEU* 3.0 35.9 + - + +
467B ALA* 3.8 15.4 - - - +
468B GLY* 3.6 2.4 - - - -
469B VAL* 2.7 48.3 + - + +
530B LEU* 3.7 24.3 - - - +
535B ILE* 5.0 1.4 - - - +
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Residues in contact with SER 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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320B SER* 3.4 20.0 + - - -
322B GLU* 3.2 24.6 + - - +
452B ALA 3.1 14.4 + - - -
453B GLU* 3.1 11.4 + - - -
455B GLU* 1.3 77.1 - - - +
457B ILE* 1.3 61.4 + - - +
459B LEU* 3.5 12.0 + - - +
460B GLN* 3.3 19.8 + - - +
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Residues in contact with ILE 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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453B GLU* 3.2 27.5 + - + +
454B LEU* 3.1 16.0 + - + +
456B SER* 1.3 75.6 - - - +
458B LEU* 1.3 67.6 + - - +
460B GLN* 3.1 21.6 + - + +
461B HIS 3.7 2.3 + - - -
501B TYR* 3.7 24.1 - - + -
502B VAL* 4.9 9.9 - - + -
505B GLN* 4.1 21.8 - - + +
506B VAL* 3.2 35.0 - - + -
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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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454B LEU* 2.9 22.5 + - + +
455B GLU* 3.8 3.6 - - - +
457B ILE* 1.3 76.0 - - - +
459B LEU* 1.3 64.2 + - - +
461B HIS* 2.9 22.0 + - - +
464B ILE* 3.5 26.1 - - + +
467B ALA* 3.9 20.6 - - + -
469B VAL* 3.9 13.2 - - + -
483B ALA* 3.7 29.4 - - + -
485B VAL* 4.7 3.6 - - + -
498B ILE* 3.6 30.7 - - + -
501B TYR* 4.8 4.5 - - + -
502B VAL* 3.9 19.7 - - + -
512B LEU* 4.8 4.9 - - + -
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Residues in contact with LEU 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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320B SER* 5.3 5.2 - - - +
323B VAL* 5.2 18.2 - - + -
455B GLU* 3.0 31.9 + - + +
456B SER* 3.7 9.6 - - - +
458B LEU* 1.3 75.7 - - - +
460B GLN* 1.3 61.5 + - - +
461B HIS 3.2 9.2 + - - +
464B ILE* 4.0 8.8 - - - +
465B PHE 3.7 9.9 - - - +
466B ASP* 3.7 39.5 - - - +
467B ALA* 4.2 6.7 - - + +
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Residues in contact with GLN 460 (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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322B GLU* 6.2 4.9 - - + -
456B SER 3.3 10.0 + - - +
457B ILE* 3.1 16.7 + - - +
458B LEU 3.1 1.0 - - - -
459B LEU* 1.3 77.8 - - - +
461B HIS* 1.3 60.6 + - - +
462B PRO* 3.5 5.4 - - - +
501B TYR* 5.2 5.2 - - + -
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Residues in contact with HIS 461 (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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457B ILE 3.7 1.8 + - - -
458B LEU 2.9 14.6 + - - +
459B LEU 3.3 11.1 - - - +
460B GLN* 1.3 77.3 - - - +
462B PRO* 1.3 97.1 - - + +
463B ASN* 3.0 35.7 + - - -
464B ILE* 3.3 23.8 + - + +
493B MET* 3.4 25.1 - - + +
501B TYR* 3.7 49.0 - + + +
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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