Contacts of the helix formed by residues 597 - 614 (chain B) in PDB entry 3HZJ
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 GLY 597 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B TYR 5.5 2.0 - - - -
594B ASP* 3.0 31.6 + - - +
595B THR 3.5 0.4 - - - -
596B GLY* 1.3 81.5 - - - +
598B ASP* 1.3 63.6 + - - -
599B GLY 3.2 4.2 + - - -
600B GLN 3.6 2.8 + - - -
601B GLU* 3.4 22.9 + - - +
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Residues in contact with ASP 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B TYR* 4.3 11.8 + - + -
597B GLY* 1.3 69.9 - - - -
599B GLY* 1.3 62.1 + - - +
601B GLU* 4.3 5.2 - - - +
602B SER* 3.5 21.1 + - - -
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Residues in contact with GLY 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B TYR* 3.4 46.7 + - - -
592B PHE* 3.9 7.4 - - - -
597B GLY 3.2 0.6 - - - -
598B ASP* 1.3 77.7 - - - +
600B GLN* 1.3 63.7 + - - +
602B SER* 3.3 4.0 + - - -
603B LEU* 3.1 22.5 + - - +
631B LEU* 3.8 4.3 - - - +
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Residues in contact with GLN 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B ILE* 3.9 36.6 + - + +
583B HIS* 5.3 5.8 + - - +
587B PRO* 6.0 1.6 - - - +
591B TYR 4.3 1.4 + - - -
592B PHE* 3.0 35.9 + - + +
593B LYS 4.3 2.8 + - - -
594B ASP 3.2 28.2 + - - +
595B THR* 3.4 25.1 - - - +
597B GLY 3.6 4.4 + - - +
599B GLY* 1.3 74.8 - - - +
601B GLU* 1.3 58.3 + - - +
603B LEU* 3.5 6.5 + - + +
604B TYR* 2.9 29.0 + - - +
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Residues in contact with GLU 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B GLY 6.0 0.9 - - - -
597B GLY 3.4 15.1 + - - +
598B ASP* 4.6 5.2 - - - +
599B GLY 3.3 0.6 - - - -
600B GLN* 1.3 78.0 - - - +
602B SER* 1.3 62.8 + - - +
604B TYR* 3.1 9.9 + - - +
605B LYS* 3.1 27.1 + - - +
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Residues in contact with SER 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B TYR* 4.6 1.0 + - - -
591B TYR* 4.8 2.7 - - - -
598B ASP 3.5 17.5 + - - -
599B GLY 3.3 4.5 + - - -
601B GLU* 1.3 79.5 - - - +
603B LEU* 1.3 60.8 + - - +
605B LYS* 3.6 6.3 + - - +
606B ILE* 3.2 26.0 + - - +
631B LEU* 4.0 16.4 - - - -
636B GLU* 4.0 22.4 - - - +
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Residues in contact with LEU 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B ILE* 4.3 17.3 - - + +
585B THR* 4.0 19.5 - - + -
592B PHE* 4.2 11.9 - - + -
599B GLY 3.1 15.9 + - - +
600B GLN* 3.7 5.8 - - + +
602B SER* 1.3 75.2 - - - +
604B TYR* 1.3 63.4 + - - +
606B ILE* 3.2 6.3 + - + +
607B CYS* 3.1 36.2 + - - -
624B SER* 3.8 5.4 - - - +
627B ALA* 3.3 37.7 - - + +
628B ALA* 3.5 31.6 - - + +
631B LEU* 3.7 11.1 - - + +
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Residues in contact with TYR 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B ILE* 4.6 3.7 - - + +
582B ILE* 3.4 22.6 - - + +
600B GLN 2.9 15.4 + - - +
601B GLU* 3.1 14.6 + - - +
603B LEU* 1.3 76.8 - - - +
605B LYS* 1.3 62.3 + - + +
607B CYS* 3.6 1.9 + - - +
608B LYS* 3.2 25.1 + - - +
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Residues in contact with LYS 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B TYR* 3.5 16.4 + - - +
568B ILE* 4.2 22.7 - - + +
601B GLU 3.1 14.3 + - - +
602B SER* 4.0 5.4 - - - +
603B LEU 3.3 0.4 - - - -
604B TYR* 1.3 78.3 - - + +
606B ILE* 1.3 65.7 + - - +
608B LYS* 4.1 4.8 - - - +
609B ALA* 3.2 25.5 + - - +
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Residues in contact with ILE 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B TYR* 3.9 12.8 - - - +
602B SER 3.2 16.8 + - - +
603B LEU* 3.2 18.9 + - + +
605B LYS* 1.3 79.1 - - - +
607B CYS* 1.3 63.5 + - - +
609B ALA* 3.8 2.9 - - - +
610B TYR* 3.3 20.0 + - + +
627B ALA* 4.2 20.2 - - + +
631B LEU* 4.3 15.5 - - + -
636B GLU* 3.7 27.8 - - - +
639B ALA* 3.8 17.7 - - + -
640B PHE* 3.9 26.0 - - + +
643B LEU* 4.9 7.4 - - + -
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Residues in contact with CYS 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B ILE* 3.7 25.8 - - + +
582B ILE* 5.1 1.8 - - - -
603B LEU* 3.1 31.3 + - - +
604B TYR 4.1 0.2 - - - +
606B ILE* 1.3 77.3 - - - +
608B LYS* 1.3 65.1 + - - +
610B TYR* 3.4 6.9 + - - +
611B SER* 3.2 15.9 + - - -
619B TYR* 3.6 36.3 - - + -
623B GLN 5.3 0.2 - - - -
624B SER* 4.1 23.6 - - - -
627B ALA* 4.3 6.5 - - - -
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Residues in contact with LYS 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B LEU 5.3 1.7 - - - +
568B ILE* 6.0 4.0 - - - +
570B LYS 5.9 2.7 - - - +
572B SER* 4.6 16.2 - - - +
578B ILE* 3.7 16.9 - - + +
604B TYR 3.2 18.5 + - - +
605B LYS* 4.1 5.8 - - - +
607B CYS* 1.3 77.2 - - - +
609B ALA* 1.3 57.9 + - - +
611B SER* 2.9 26.0 + - - -
612B VAL* 3.5 4.7 + - - +
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Residues in contact with ALA 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B TYR* 3.9 12.6 - - + -
567B LEU* 4.2 34.8 + - + +
568B ILE* 4.5 2.0 - - + +
605B LYS 3.2 17.2 + - - +
606B ILE 3.8 0.9 - - - +
608B LYS* 1.3 78.4 - - - +
610B TYR* 1.3 60.4 + - - +
612B VAL* 3.3 6.2 + - - +
613B TYR* 3.1 22.2 + - - +
640B PHE* 3.7 21.5 - - + -
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Residues in contact with TYR 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B ILE* 3.3 11.4 + - + +
607B CYS* 3.8 9.6 - - - +
608B LYS 3.3 0.6 - - - -
609B ALA* 1.3 77.9 - - - +
611B SER* 1.3 61.8 + - - +
612B VAL 3.2 0.5 + - - -
613B TYR* 4.2 14.8 - + + -
614B ASP* 2.9 50.9 + - + +
618B GLY* 3.4 21.2 - - - -
619B TYR* 4.5 0.9 - - + -
623B GLN* 3.5 23.1 - - - +
640B PHE* 4.0 6.0 - + + -
643B LEU* 5.4 4.0 - - + -
644B VAL* 4.4 29.4 - - + -
647B MSE 3.1 49.2 - - + +
653B ARG* 4.4 1.4 - - - +
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Residues in contact with SER 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B SER* 4.7 12.1 - - - -
574B GLN* 4.9 9.6 - - - -
578B ILE* 4.3 6.7 - - - -
607B CYS 3.2 11.5 + - - -
608B LYS* 2.9 18.5 + - - -
610B TYR* 1.3 76.4 - - - +
612B VAL* 1.3 56.3 - - - +
614B ASP 3.6 10.0 - - - +
618B GLY* 4.0 5.4 - - - -
619B TYR* 3.8 24.7 - - - +
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Residues in contact with VAL 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B LEU* 5.2 14.1 - - + +
570B LYS* 4.9 17.3 - - + -
571B ASP 5.6 2.9 - - - +
608B LYS 3.5 4.3 + - - +
609B ALA 3.3 7.0 + - - +
610B TYR 3.1 0.6 - - - -
611B SER* 1.3 77.9 - - - +
613B TYR* 1.3 68.6 + - - +
614B ASP 3.2 11.7 + - - +
615B GLU* 3.8 5.4 + - - +
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Residues in contact with TYR 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B ARG* 5.6 8.3 - - + -
567B LEU* 3.7 27.5 - - + +
609B ALA 3.1 14.0 + - - +
610B TYR* 3.5 20.6 + + + +
612B VAL* 1.3 79.1 - - - +
614B ASP* 1.3 61.9 + - + +
615B GLU* 3.3 5.2 + - - +
640B PHE* 4.4 13.5 - + + -
644B VAL* 3.8 31.1 - - + +
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Residues in contact with ASP 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B TYR* 2.9 47.7 + - + +
611B SER 3.6 6.1 - - - +
612B VAL 3.3 7.1 - - - +
613B TYR* 1.3 80.7 - - + +
615B GLU* 1.3 62.4 + - - +
616B ASP* 3.4 17.2 + - - +
617B ILE* 3.4 14.5 + - - +
618B GLY* 3.5 28.6 + - - +
647B MSE 4.6 0.7 - - - +
653B ARG* 4.3 11.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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