Contacts of the helix formed by residues 481 - 496 (chain B) in PDB entry 4KZI
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 ASP 481 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480B GLY* 1.3 70.3 - - - -
482B TRP* 1.3 64.2 + - - +
484B ASP* 2.9 30.5 + - + +
485B SER* 3.1 13.6 + - - +
568B GLN* 5.0 4.9 - - - +
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Residues in contact with TRP 482 (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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406B PHE* 3.7 29.8 - + - -
410B LEU* 4.8 3.4 - - + -
444B LEU* 4.5 17.3 - - + -
447B PHE* 4.4 16.4 - + - -
448B ILE* 3.8 26.4 - - + +
479B PHE* 3.4 34.7 + + - +
480B GLY 2.9 1.2 + - - -
481B ASP* 1.3 78.3 - - - +
483B ILE* 1.3 55.3 + - - +
485B SER* 3.1 2.3 + - - -
486B ILE* 2.8 49.3 + - + +
565B LEU* 3.0 23.5 + - + +
568B GLN* 3.5 37.7 + - + +
569B GLY* 3.4 28.7 - - - -
572B ARG* 4.6 5.6 - - + -
573B ILE* 6.1 0.4 - - + -
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Residues in contact with ILE 483 (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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451B LEU* 4.6 5.2 - - + -
462B LEU* 4.0 35.9 - - + -
464B PHE* 5.5 0.4 - - + -
472B ARG* 4.5 13.5 - - + +
475B CYS* 4.2 12.8 - - + -
476B ALA* 4.4 19.1 - - + -
479B PHE* 3.9 38.8 - - + +
480B GLY 3.2 14.1 + - - +
481B ASP 3.1 1.2 + - - -
482B TRP* 1.3 73.2 - - - +
484B ASP* 1.3 74.8 + - - +
486B ILE* 3.2 15.0 + - + +
487B LEU* 2.8 31.5 + - + +
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Residues in contact with ASP 484 (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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472B ARG* 3.1 40.9 + - - -
480B GLY 5.5 0.2 - - - -
481B ASP* 2.9 22.2 + - - +
483B ILE* 1.3 81.7 - - - +
485B SER* 1.3 58.7 + - - +
487B LEU* 3.1 8.0 + - - +
488B ALA* 2.9 26.7 + - - +
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Residues in contact with SER 485 (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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481B ASP* 3.1 7.4 + - - +
482B TRP 3.1 5.2 + - - -
484B ASP* 1.3 74.6 - - - +
486B ILE* 1.3 66.8 + - - +
488B ALA* 3.4 8.4 + - - +
489B PHE* 3.0 22.7 + - - +
565B LEU* 3.5 24.1 - - - +
568B GLN* 3.0 28.5 + - - -
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Residues in contact with ILE 486 (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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447B PHE* 5.2 1.3 - - + -
448B ILE* 4.3 25.8 - - + +
451B LEU* 4.4 25.1 - - + -
452B ALA* 4.4 12.5 - - + +
462B LEU* 5.1 4.3 - - + -
479B PHE* 4.7 2.9 - - + -
482B TRP* 2.8 60.6 + - + +
483B ILE* 3.6 26.2 - - + +
484B ASP 3.2 0.2 - - - -
485B SER* 1.3 76.4 - - - +
487B LEU* 1.3 57.5 + - + +
489B PHE* 3.2 6.1 + - - +
490B SER* 2.8 26.5 + - - -
565B LEU* 4.3 5.4 - - + -
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Residues in contact with LEU 487 (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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455B SER* 5.1 2.0 - - - -
457B PRO* 3.9 34.0 - - + +
460B GLY* 4.9 5.6 - - - -
461B LYS 5.0 4.3 - - - +
462B LEU* 4.0 29.4 - - + -
472B ARG* 3.6 44.2 - - + +
483B ILE* 2.8 23.6 + - + +
484B ASP* 3.5 6.3 - - - +
486B ILE* 1.3 75.4 - - + +
488B ALA* 1.3 65.1 + - - +
490B SER* 3.1 8.1 + - - -
491B ARG* 2.9 24.8 + - - +
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Residues in contact with ALA 488 (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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484B ASP 2.9 12.6 + - - +
485B SER* 3.6 12.3 - - - +
487B LEU* 1.3 75.1 - - - +
489B PHE* 1.3 62.0 + - - +
491B ARG* 3.3 10.7 + - - +
492B SER* 3.0 23.5 + - - -
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Residues in contact with PHE 489 (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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448B ILE* 4.5 3.8 - - + -
449B LEU* 4.0 22.9 - - + -
452B ALA* 3.7 21.8 - - + -
485B SER 3.0 14.5 + - - +
486B ILE 3.4 8.1 - - - +
488B ALA* 1.3 73.3 - - - +
490B SER* 1.3 60.7 + - - +
492B SER* 3.2 5.7 + - - -
493B LEU* 2.7 33.8 + - + +
558B LYS* 3.9 35.7 - - + -
561B GLU* 3.8 31.6 - - + -
562B LEU* 3.8 28.7 - - + -
565B LEU* 3.5 23.1 - - + -
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Residues in contact with SER 490 (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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452B ALA* 2.5 41.7 + - - -
455B SER* 4.3 2.5 + - - -
457B PRO* 3.3 14.2 - - - +
486B ILE* 2.8 14.3 + - - -
487B LEU* 3.1 14.8 + - - -
489B PHE* 1.3 77.4 - - - +
491B ARG* 1.3 57.9 + - - +
493B LEU* 3.2 2.5 + - - +
494B HIS* 2.8 46.9 + - - -
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Residues in contact with ARG 491 (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 PRO* 3.7 18.3 - - + +
487B LEU 2.9 12.5 + - - +
488B ALA* 3.6 11.4 - - - +
490B SER* 1.3 76.4 - - - +
492B SER* 1.3 64.4 + - - +
494B HIS* 3.3 4.6 + - - +
495B SER* 3.1 28.6 + - - +
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Residues in contact with SER 492 (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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488B ALA 3.0 16.5 + - - -
489B PHE* 3.6 5.6 - - - -
491B ARG* 1.3 80.7 - - - +
493B LEU* 1.3 61.9 + - - +
495B SER* 3.3 16.8 + - - -
496B LEU* 3.6 12.6 + - - +
558B LYS* 2.3 34.4 + - - -
561B GLU* 4.6 1.5 + - - -
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Residues in contact with LEU 493 (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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449B LEU* 4.3 19.7 - - + -
452B ALA* 4.3 5.2 - - + -
453B TYR* 3.8 49.4 - - + +
489B PHE* 2.7 31.5 + - + +
490B SER* 3.5 5.4 - - - +
492B SER* 1.3 72.9 - - - +
494B HIS* 1.3 63.7 + - + +
496B LEU* 3.2 16.5 + - + +
497B LEU 3.8 2.8 + - - -
498B VAL* 3.7 29.3 + - + +
503B PHE* 4.4 3.4 - - + -
506B LEU* 5.3 5.2 - - + -
558B LYS* 3.7 23.0 - - + +
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Residues in contact with HIS 494 (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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452B ALA 3.2 9.0 - - - -
453B TYR* 3.3 27.4 + + - -
455B SER 3.0 26.0 + - - -
456B LYS* 5.3 4.0 + - + +
457B PRO* 3.5 14.5 - - + +
490B SER* 2.8 44.5 + - - +
491B ARG* 3.7 6.5 - - - +
493B LEU* 1.3 75.4 - - + +
495B SER* 1.3 61.2 + - - +
497B LEU* 3.0 25.0 + - - +
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Residues in contact with SER 495 (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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491B ARG* 3.1 18.8 + - - +
492B SER* 3.6 11.8 - - - -
493B LEU 3.3 0.6 - - - -
494B HIS* 1.3 75.8 - - - +
496B LEU* 1.3 67.0 + - - +
497B LEU* 3.4 13.2 + - - +
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Residues in contact with LEU 496 (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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492B SER* 3.6 8.0 + - - +
493B LEU* 3.2 11.3 + - + +
494B HIS 3.1 1.0 - - - -
495B SER* 1.3 83.5 - - - +
497B LEU* 1.3 74.4 + - - +
498B VAL* 3.6 17.2 - - + -
551B CYS* 5.8 4.8 - - - +
554B ARG* 4.0 57.2 + - + +
555B LEU* 4.5 7.2 - - + +
558B LYS* 4.0 34.5 - - + -
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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