Contacts of the helix formed by residues 585 - 596 (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 PRO 585 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404B GLN* 6.1 1.6 - - - +
407B TYR* 3.5 32.1 - - + -
408B ASP* 5.9 1.1 - - - +
411B SER* 3.4 25.8 - - - +
414B LEU* 6.5 0.2 - - + -
583B PRO 3.7 1.7 - - - +
584B PRO* 1.3 86.8 - - + +
586B PRO* 1.3 72.4 - - + +
587B ILE* 3.3 3.1 - - + +
588B ILE* 3.1 16.3 + - + +
589B ASP* 2.9 24.8 + - - +
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Residues in contact with PRO 586 (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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584B PRO 3.5 2.9 - - - +
585B PRO* 1.3 86.7 - - + +
587B ILE* 1.3 61.7 + - + +
589B ASP* 3.4 8.4 + - + +
590B LYS* 2.8 29.8 + - - +
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Residues in contact with ILE 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B LEU* 4.0 31.4 - - + -
418B ARG* 4.9 13.5 - - - +
585B PRO* 3.3 2.8 - - + +
586B PRO* 1.3 77.6 - - + +
588B ILE* 1.3 65.4 + - - +
590B LYS* 3.3 7.8 + - + +
591B ILE* 3.0 35.0 + - + +
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Residues in contact with ILE 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B TYR* 4.5 17.5 - - + +
410B LEU* 4.3 17.5 - - + -
411B SER* 3.9 8.7 - - - +
414B LEU* 4.0 24.0 - - + -
443B PHE* 4.0 26.9 - - + -
444B LEU* 6.3 0.4 - - + -
573B ILE* 4.3 26.2 - - + -
584B PRO* 4.8 1.8 - - + -
585B PRO* 3.1 31.9 + - + +
587B ILE* 1.3 73.5 - - - +
589B ASP* 1.3 63.8 + - - +
591B ILE* 3.1 10.1 + - + +
592B PHE* 2.8 26.3 + - - +
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Residues in contact with ASP 589 (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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573B ILE* 6.2 0.4 - - - -
577B LYS* 2.6 37.8 + - - +
584B PRO* 3.5 22.3 - - + +
585B PRO 2.9 13.0 + - - +
586B PRO* 3.5 12.6 - - + +
588B ILE* 1.3 77.6 - - - +
590B LYS* 1.3 58.1 + - - +
592B PHE* 3.3 5.5 + - - +
593B MET* 2.8 45.6 + - - +
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Residues in contact with LYS 590 (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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440B GLU* 3.8 17.5 + - - +
586B PRO 2.8 16.7 + - - +
587B ILE* 3.7 8.3 - - + +
588B ILE 3.1 0.4 - - - -
589B ASP* 1.3 77.0 - - - +
591B ILE* 1.3 53.3 + - - +
593B MET* 3.2 5.0 + - - -
594B ASP* 2.6 73.8 + - - +
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Residues in contact with ILE 591 (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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414B LEU* 4.2 18.4 - - + -
440B GLU* 3.6 49.1 - - + +
443B PHE* 4.1 34.8 - - + -
444B LEU* 5.2 12.3 - - + +
587B ILE* 3.0 27.9 + - + +
588B ILE* 3.1 10.5 + - + +
590B LYS* 1.3 75.7 - - + +
592B PHE* 1.3 57.4 + - - +
594B ASP 3.8 0.2 - - - -
595B THR* 2.5 42.7 + - + +
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Residues in contact with PHE 592 (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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574A PHE* 4.1 11.4 - + - -
598A PHE* 4.6 5.2 - + - -
444B LEU* 6.3 0.2 - - - -
570B LEU* 3.4 42.0 - - + -
573B ILE* 3.5 29.6 - - + -
574B PHE* 3.6 29.8 - + + -
577B LYS* 3.6 28.7 - - + -
588B ILE 2.8 11.9 + - - +
589B ASP* 3.5 8.5 - - - +
591B ILE* 1.3 80.1 - - - +
593B MET* 1.3 77.4 + - + +
594B ASP 3.3 0.2 + - - -
595B THR* 3.3 6.3 + - - -
596B LEU* 3.2 48.1 + - + +
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Residues in contact with MET 593 (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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598A PHE* 3.5 33.0 - - + -
577B LYS* 3.5 28.5 - - - +
589B ASP* 2.8 34.1 + - - +
590B LYS* 3.8 5.6 - - - +
592B PHE* 1.3 90.3 - - + +
594B ASP* 1.3 65.7 + - - +
596B LEU* 3.3 23.7 + - - +
598B PHE 5.3 1.2 - - - +
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Residues in contact with ASP 594 (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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440B GLU* 2.4 33.3 - - + +
590B LYS* 2.6 52.0 + - - +
591B ILE 4.1 0.4 - - - +
593B MET* 1.3 76.2 - - - +
595B THR* 1.3 62.1 + - + +
596B LEU 3.2 5.6 + - - +
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Residues in contact with THR 595 (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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578A LEU* 5.3 0.2 - - - +
440B GLU* 3.8 26.7 - - + +
441B SER* 3.9 22.4 - - - +
444B LEU* 5.6 0.5 - - - +
570B LEU* 3.9 21.4 - - - +
591B ILE* 2.5 29.3 + - + +
592B PHE* 3.3 8.1 + - - -
594B ASP* 1.3 77.2 - - - +
596B LEU* 1.3 63.7 + - - +
597B PRO* 3.0 16.1 - - - +
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Residues in contact with LEU 596 (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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574A PHE* 4.0 22.7 - - + -
578A LEU* 4.4 13.5 - - + -
598A PHE* 6.1 0.9 - - + -
570B LEU* 4.5 14.8 - - + -
592B PHE* 3.2 44.9 - - + +
593B MET* 3.6 17.9 - - - +
594B ASP 3.2 7.0 - - - +
595B THR* 1.3 80.1 - - - +
597B PRO* 1.3 57.2 - - + +
598B PHE* 2.8 53.7 + - + +
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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