Contacts of the helix formed by residues 591 - 605 (chain B) in PDB entry 5JO3
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 LYS 591 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589B GLN* 2.9 36.1 + - - +
590B MET* 1.3 74.3 - - - +
592B HIS* 1.3 66.4 + - - +
593B GLU* 4.6 6.3 - - + +
594B VAL* 3.1 27.9 + - + +
595B LEU* 3.0 21.5 + - - +
702B SER* 5.9 3.4 - - - +
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Residues in contact with HIS 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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543B LEU 4.4 1.8 + - - -
544B ALA* 3.2 29.2 + - - -
546B ALA 4.8 4.2 + - - -
548B VAL* 4.6 9.4 - - + -
576B ILE* 4.3 25.9 - - + +
585B VAL* 6.0 4.5 - - - +
590B MET 3.7 3.2 + - - -
591B LYS* 1.3 72.3 - - - +
593B GLU* 1.3 77.1 + - - +
595B LEU* 3.3 8.8 + - - +
596B CYS* 2.9 55.6 + - - -
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Residues in contact with GLU 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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540B LEU* 4.0 5.4 - - + +
544B ALA* 4.5 15.1 - - + +
591B LYS* 3.3 6.0 - - + +
592B HIS* 1.3 101.9 + - - +
594B VAL* 1.3 60.4 + - + +
596B CYS* 3.6 7.3 + - - +
597B ARG* 2.9 44.7 + - - +
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Residues in contact with VAL 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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590B MET* 6.3 0.2 - - - -
591B LYS* 3.1 32.0 + - + +
593B GLU* 1.3 76.7 - - + +
595B LEU* 1.3 60.7 + - - +
597B ARG* 3.2 7.2 + - - +
598B TRP* 2.8 28.8 + - - +
697B GLY* 3.6 19.3 - - - +
698B ASN 3.7 2.0 - - - -
699B GLN 3.5 40.6 - - - +
700B ILE* 3.9 7.0 - - + -
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Residues in contact with LEU 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B ILE* 4.3 21.1 - - + -
579B PHE* 3.9 43.7 - - + -
585B VAL* 3.8 31.2 - - + -
590B MET* 4.3 11.0 - - + -
591B LYS 3.0 13.3 + - - +
592B HIS* 3.7 12.1 - - - +
594B VAL* 1.3 78.0 - - - +
596B CYS* 1.3 62.2 + - - +
598B TRP* 3.3 3.6 + - + +
599B ILE* 2.9 41.5 + - + +
700B ILE* 3.7 20.3 - - + +
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Residues in contact with CYS 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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540B LEU* 3.6 19.7 - - + -
543B LEU* 3.7 16.3 - - + +
544B ALA* 3.8 16.2 - - + -
576B ILE* 3.7 21.1 - - - -
592B HIS* 2.9 49.1 + - - +
593B GLU* 3.8 3.1 - - - +
595B LEU* 1.3 77.0 - - - +
597B ARG* 1.3 62.7 + - - +
599B ILE* 3.3 4.3 + - - +
600B LEU* 3.1 27.2 + - - +
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Residues in contact with ARG 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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540B LEU* 3.5 36.5 - - + +
593B GLU* 2.9 38.1 + - - +
594B VAL* 3.2 5.8 + - - +
596B CYS* 1.3 75.6 - - - +
598B TRP* 1.3 59.1 + - - +
600B LEU* 3.2 5.7 + - + +
601B SER* 2.9 29.9 + - - +
696B PRO 4.4 1.8 - - - -
697B GLY* 2.8 48.4 + - - +
698B ASN* 3.1 24.3 - - - +
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Residues in contact with TRP 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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579B PHE* 3.6 26.5 - + - -
594B VAL 2.8 17.4 + - - +
595B LEU* 3.7 6.1 - - + +
597B ARG* 1.3 77.6 - - - +
599B ILE* 1.3 87.2 + - + +
601B SER* 3.1 2.1 + - - -
602B VAL* 2.9 43.5 + - + +
648B ILE* 4.0 21.8 - - + -
651B LEU* 3.8 30.3 - - + -
652B SER* 3.8 12.6 - - - -
689B CYS* 5.2 0.6 + - - -
692B ILE* 3.5 26.8 - - + +
693B LEU* 3.6 18.4 - - + +
698B ASN* 3.3 34.9 + - - +
700B ILE* 3.7 24.7 - - + -
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Residues in contact with ILE 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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543B LEU* 4.8 1.1 - - + -
572B ALA* 4.0 30.3 - - + +
575B THR* 3.8 31.0 - - + +
576B ILE* 3.5 35.0 - - + +
595B LEU* 2.9 35.5 + - + +
596B CYS* 3.7 5.4 - - - +
597B ARG 3.3 0.2 - - - -
598B TRP* 1.3 93.2 - - + +
600B LEU* 1.3 58.1 + - + +
602B VAL* 3.3 5.1 + - - +
603B LYS* 2.9 28.5 + - + +
615B TRP* 4.5 12.1 - - + -
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Residues in contact with LEU 600 (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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539B GLU* 3.6 35.9 - - + +
540B LEU* 3.5 43.5 - - + +
543B LEU* 3.7 22.0 - - + -
569B LEU* 6.5 0.2 - - - -
572B ALA* 4.6 2.5 - - + -
596B CYS 3.1 18.2 + - - +
597B ARG* 3.7 4.7 - - + +
599B ILE* 1.3 76.1 - - - +
601B SER* 1.3 56.3 + - - +
603B LYS* 3.4 24.4 + - - +
604B LYS* 2.9 30.4 + - - +
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Residues in contact with SER 601 (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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597B ARG* 2.9 13.0 + - - +
598B TRP 3.6 3.1 - - - -
600B LEU* 1.3 74.5 - - - +
602B VAL* 1.3 64.8 + - - +
604B LYS* 3.4 6.3 + - - +
605B ASN* 2.7 38.1 + - - +
692B ILE* 3.7 16.2 - - - -
698B ASN* 2.6 33.1 + - - -
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Residues in contact with VAL 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B TRP* 2.9 54.8 + - + +
599B ILE* 3.6 9.0 - - - +
601B SER* 1.3 75.1 - - - +
603B LYS* 1.3 64.3 + - - +
605B ASN 3.1 10.0 + - - -
606B TYR* 3.2 25.3 - - + -
615B TRP* 3.9 11.9 - - + -
651B LEU* 3.5 32.5 - - + +
652B SER* 4.4 5.4 - - - +
655B LEU* 3.5 8.3 - - + +
692B ILE* 4.0 18.2 - - + -
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Residues in contact with LYS 603 (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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539B GLU* 3.5 26.7 + - - -
568B ASP* 3.1 42.2 + - + +
569B LEU* 4.2 1.0 - - - +
571B THR* 4.3 0.2 + - - -
572B ALA* 3.8 12.2 - - - +
599B ILE 2.9 15.4 + - - +
600B LEU* 3.7 22.9 - - - +
602B VAL* 1.3 78.6 - - - +
604B LYS* 1.3 61.3 + - - +
605B ASN 3.3 0.7 + - - -
606B TYR* 3.3 17.5 + - - +
608B LYS* 5.8 6.5 - - - +
615B TRP* 3.5 54.9 - - + +
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Residues in contact with LYS 604 (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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600B LEU 2.9 20.8 + - - +
601B SER* 3.7 8.7 - - - +
602B VAL 3.3 0.2 - - - -
603B LYS* 1.3 74.1 - - - +
605B ASN* 1.3 66.4 + - - +
606B TYR 3.2 13.7 - - - +
608B LYS* 5.9 7.9 - - - +
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Residues in contact with ASN 605 (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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601B SER* 2.7 30.5 + - - +
602B VAL 3.1 5.0 + - - -
604B LYS* 1.3 87.0 - - - +
606B TYR* 1.3 59.9 + - - +
607B ARG* 5.7 0.2 - - - -
655B LEU* 3.8 17.2 - - + -
656B ASP* 2.8 32.2 + - - +
688B GLN* 4.2 15.1 - - - +
691B MET* 4.3 10.2 - - - +
692B ILE* 3.7 18.2 - - + +
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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