Contacts of the helix formed by residues 585 - 599 (chain B) in PDB entry 2K7L
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 585 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487A GLU* 4.3 7.5 + - - +
583B ASP* 2.6 17.2 + - + +
584B TPO 1.3 70.1 - - - -
586B GLU* 1.3 57.2 + - - +
587B ASP 3.5 1.3 - - - +
588B ASP* 2.8 47.7 - - - +
589B HIS* 3.0 25.5 + - - +
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Residues in contact with GLU 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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475A LYS* 6.2 0.3 - - - -
486A SER* 4.9 20.0 + - - +
487A GLU* 4.7 11.2 - - + -
490A VAL* 5.2 2.1 - - - +
584B TPO 3.1 30.3 + - + +
585B ASP* 1.3 75.9 - - - +
587B ASP* 1.3 71.1 + - + +
589B HIS* 2.6 35.6 + - - +
590B LEU* 3.6 6.1 - - - +
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Residues in contact with ASP 587 (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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475A LYS* 4.5 8.5 - - - -
584B TPO 4.5 2.1 + - - +
586B GLU* 1.3 88.5 - - + +
588B ASP* 1.3 67.2 + - - +
589B HIS 3.3 1.1 - - - -
590B LEU* 3.0 45.8 + - - +
591B ILE* 3.3 24.2 + - + +
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Residues in contact with ASP 588 (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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585B ASP* 2.8 47.9 - - - +
586B GLU 3.4 0.2 - - - -
587B ASP* 1.3 81.3 - - - +
589B HIS* 1.3 60.0 + - - +
591B ILE* 3.7 10.6 + - - +
592B TYR* 3.8 8.8 + - - +
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Residues in contact with HIS 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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486A SER 4.8 0.2 + - - -
487A GLU* 3.3 48.4 + - + +
490A VAL* 4.6 15.6 - - + +
585B ASP* 3.0 24.0 + - - +
586B GLU* 2.6 32.7 + - - -
588B ASP* 1.3 72.4 + - - +
590B LEU* 1.3 78.4 + - + +
591B ILE 3.1 2.2 - - - -
592B TYR* 2.9 31.4 + - + -
593B LEU* 2.9 15.8 + - - +
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Residues in contact with LEU 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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470A THR* 4.3 0.9 + - - -
471A LYS* 3.0 42.6 - - + +
474A LEU* 3.0 44.9 - - + -
475A LYS* 4.1 8.3 - - - -
490A VAL* 4.4 2.5 - - + -
586B GLU 3.6 5.8 - - - +
587B ASP* 3.0 49.5 + - - +
589B HIS* 1.3 85.7 - - + +
591B ILE* 1.3 55.6 + - + +
593B LEU* 2.5 25.2 - - - +
594B GLU* 3.5 7.8 - - - +
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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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471A LYS* 5.4 2.0 - - + -
587B ASP* 3.3 26.1 + - + +
588B ASP* 4.1 6.5 - - - +
589B HIS 3.1 0.4 - - - -
590B LEU* 1.3 80.1 - - + +
592B TYR* 1.3 63.5 + - - +
594B GLU* 3.0 52.3 - - - +
595B GLU* 3.6 3.8 + - - +
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Residues in contact with TYR 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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494A ALA* 5.5 2.0 - - + -
588B ASP* 3.8 4.7 + - - +
589B HIS* 2.9 31.2 + - + +
591B ILE* 1.3 79.4 - - - +
593B LEU* 1.3 87.5 + - + +
595B GLU* 2.7 38.3 - - - +
596B ILE* 3.7 19.3 + - + +
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Residues in contact with LEU 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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470A THR* 3.2 30.1 - - + -
474A LEU* 5.3 0.7 - - + -
490A VAL* 3.4 28.5 - - + +
493A LEU* 5.7 0.2 - - + -
494A ALA* 3.3 39.5 - - + +
497A LEU* 4.7 1.1 - - + -
589B HIS 2.9 5.8 + - - +
590B LEU* 2.5 40.8 - - + +
592B TYR* 1.3 92.2 - - + +
594B GLU* 1.3 68.9 + - - +
595B GLU 3.1 1.1 - - - -
596B ILE* 2.7 27.9 + - + +
597B LEU* 3.5 2.9 + - - +
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Residues in contact with GLU 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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470A THR* 3.3 25.4 - - - +
471A LYS* 3.0 25.4 + - - +
513A PHE* 4.4 4.0 - - + -
590B LEU 3.5 7.2 - - - +
591B ILE* 3.0 41.3 + - - +
592B TYR 3.1 0.4 - - - -
593B LEU* 1.3 84.8 - - - +
595B GLU* 1.3 61.6 - - + +
597B LEU* 3.7 12.3 - - - +
598B VAL 4.0 0.2 + - - -
599B ARG* 3.2 51.1 + - + +
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Residues in contact with GLU 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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591B ILE 4.2 4.4 - - - +
592B TYR* 2.7 36.0 - - - +
594B GLU* 1.3 79.7 - - + +
596B ILE* 1.3 71.7 + - + +
597B LEU 2.8 6.6 + - - -
598B VAL 3.5 0.2 + - - -
599B ARG* 2.7 33.9 + - + +
600B VAL* 2.9 39.5 + - - +
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Residues in contact with ILE 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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494A ALA* 3.3 27.6 - - + +
498A LYS* 2.9 41.2 - - - +
592B TYR* 4.3 23.6 - - + +
593B LEU* 2.7 38.4 - - + +
595B GLU* 1.3 88.0 - - + +
597B LEU* 1.3 71.5 + - + +
600B VAL* 4.5 10.7 - - - +
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Residues in contact with LEU 597 (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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468A MET* 4.8 0.2 - - + -
470A THR* 4.1 0.9 - - + -
497A LEU* 2.9 61.5 - - + +
498A LYS* 3.0 20.6 - - - +
500A LEU* 5.1 0.4 - - + -
502A PRO* 5.0 3.6 - - + -
513A PHE* 3.0 52.0 - - + -
593B LEU 4.0 6.5 - - - +
594B GLU 3.7 7.6 - - - +
595B GLU 2.8 1.6 + - - -
596B ILE* 1.3 90.4 - - + +
598B VAL* 1.3 86.4 + - + +
600B VAL* 5.3 2.2 - - - +
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Residues in contact with VAL 598 (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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498A LYS* 5.3 1.3 - - - -
501A ASN* 5.6 1.6 - - - -
502A PRO* 4.1 23.8 - - + +
503A GLU 6.1 0.4 - - - -
504A ARG* 5.0 16.8 - - + +
513A PHE* 3.2 46.2 - - + -
594B GLU 4.0 0.2 + - - -
597B LEU* 1.3 103.2 - - + +
599B ARG* 1.3 61.9 + - + +
600B VAL* 3.8 4.5 - - - -
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Residues in contact with ARG 599 (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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471A LYS* 5.4 2.2 - - - +
504A ARG* 6.2 0.2 - - + -
511A MET* 3.4 43.6 - - - +
513A PHE* 3.8 25.4 - - + -
594B GLU* 3.2 47.9 + - + +
595B GLU* 2.7 30.1 + - + +
598B VAL* 1.3 84.7 - - - +
600B VAL* 1.3 62.5 + - - +
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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