Contacts of the helix formed by residues 596 - 607 (chain B) in PDB entry 2HDX
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 SER 596 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585B GLY 3.4 14.8 - - - -
587B CYS* 3.7 7.4 - - - +
594B PHE* 3.2 4.9 + - - +
595B GLN* 1.3 81.8 - - - +
597B ILE* 1.3 64.4 + - - +
598B PHE* 3.0 31.7 + - - +
599B ASP* 2.9 27.3 + - - +
600B MET* 3.0 20.3 + - - +
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Residues in contact with ILE 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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522B LEU* 3.9 22.0 - - + -
527B TRP* 3.6 32.5 - - + -
554B VAL* 3.7 24.5 - - + -
564B CYS* 5.5 0.9 - - + -
579B LEU* 4.1 8.3 - - + -
581B LEU* 4.6 13.2 - - + +
585B GLY 4.3 2.8 + - - +
587B CYS* 3.6 15.8 - - + +
596B SER* 1.3 72.4 - - - +
598B PHE* 1.3 82.4 + - + +
600B MET* 3.5 20.3 - - + +
601B LEU* 2.9 30.1 + - + +
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Residues in contact with PHE 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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520B GLN* 4.4 11.7 - - + -
522B LEU* 3.8 17.5 - - + -
525B TYR* 3.1 52.5 - + - -
527B TRP* 4.1 16.4 - + - -
585B GLY 5.7 1.1 - - - -
596B SER* 3.0 26.0 - - - +
597B ILE* 1.3 84.5 - - + +
599B ASP* 1.3 62.1 + - - +
601B LEU* 3.3 8.8 + - - +
602B GLU* 2.9 36.0 + - + +
558F GLU 5.8 0.4 - - - -
559F THR* 6.2 0.2 - - + -
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Residues in contact with ASP 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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594B PHE* 4.2 11.9 - - + -
595B GLN* 3.4 24.4 - - - +
596B SER* 2.9 22.8 + - - +
598B PHE* 1.3 76.0 - - - +
600B MET* 1.3 58.1 + - - +
602B GLU* 2.9 11.5 + - - +
603B HIS* 2.7 36.9 + - - +
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Residues in contact with MET 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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566B LEU* 4.3 7.4 - - + -
579B LEU* 3.4 40.8 - - + -
587B CYS* 4.1 9.9 - - - -
589B VAL* 4.5 1.1 - - + -
594B PHE* 3.5 41.0 - - + -
596B SER 3.0 12.0 + - - +
597B ILE* 3.5 26.5 - - + +
599B ASP* 1.3 77.6 - - - +
601B LEU* 1.3 82.4 + - + +
603B HIS* 3.4 1.6 + - - +
604B PHE* 3.2 45.6 + - + -
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Residues in contact with LEU 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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527B TRP* 3.6 51.1 - - + +
552B PHE* 3.9 17.3 - - + -
554B VAL* 4.3 2.7 - - + -
566B LEU* 3.9 9.4 - - + -
597B ILE* 2.9 27.4 + - + +
598B PHE* 3.6 6.1 - - - +
600B MET* 1.3 95.2 - - + +
602B GLU* 1.3 61.7 + - - +
604B PHE 3.6 0.3 + - - -
605B ARG* 3.3 19.8 + - - +
621B LEU* 3.7 30.1 - - + +
531F MET* 4.3 18.3 - - + +
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Residues in contact with GLU 602 (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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598B PHE* 2.9 30.2 + - + +
599B ASP* 3.3 13.9 - - - +
601B LEU* 1.3 75.2 - - + +
603B HIS* 1.3 62.2 + - - +
605B ARG* 2.8 31.0 - - - +
606B VAL* 3.7 7.4 + - - +
531F MET* 5.7 2.1 - - + +
533F SER* 3.9 18.1 + - - -
536F LYS* 5.0 7.8 + - - -
558F GLU* 2.7 36.1 - - - +
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Residues in contact with HIS 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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592B LEU* 5.1 8.2 - - + +
594B PHE* 3.5 29.5 - + + -
599B ASP 2.7 19.7 + - - +
600B MET 3.6 2.0 - - - +
602B GLU* 1.3 73.7 - - - +
604B PHE* 1.3 83.0 + + - +
605B ARG 3.0 2.1 + - - -
606B VAL* 3.1 3.1 + - - +
607B HIS* 2.8 71.4 + + + -
608B PRO 5.6 0.9 - - - -
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Residues in contact with PHE 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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566B LEU* 4.5 7.0 - - + -
577B LEU* 4.4 20.6 - - + -
589B VAL* 4.6 4.5 - - + -
592B LEU* 3.7 25.8 - - + -
594B PHE* 4.3 5.2 - + - -
600B MET* 3.2 44.1 + - + +
601B LEU 3.9 1.1 - - - -
603B HIS* 1.3 90.3 - + - +
605B ARG* 1.3 61.5 + - - +
607B HIS 3.2 17.7 - - - +
609B ILE* 3.9 21.1 - - + -
610B PRO* 4.0 23.3 - - + -
620B VAL* 3.4 9.0 - - - +
621B LEU* 2.8 42.9 + - + -
816H LEU* 5.0 1.1 - - + -
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Residues in contact with ARG 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 LEU 3.3 11.4 + - - +
602B GLU* 2.8 24.0 + - - +
603B HIS 2.9 0.4 - - - -
604B PHE* 1.3 79.7 - - - +
606B VAL* 1.3 57.3 + - + +
620B VAL* 3.5 19.4 - - - +
621B LEU* 3.2 16.8 + - + -
622B VAL* 2.6 42.4 + - - +
529F HIS* 2.6 27.3 + - - +
531F MET* 3.5 26.9 + - - +
532F LEU* 3.6 28.2 - - + +
533F SER 6.0 1.1 - - - +
536F LYS* 4.4 16.6 - - + +
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Residues in contact with VAL 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B GLU 4.3 6.3 - - - +
603B HIS* 3.1 2.3 + - - +
605B ARG* 1.3 80.0 - - + +
607B HIS* 1.3 88.1 + - + +
608B PRO* 3.4 8.7 - - - +
620B VAL* 3.5 9.2 - - - +
536F LYS* 3.0 32.5 - - - +
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Residues in contact with HIS 607 (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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603B HIS* 2.8 53.0 + + + -
604B PHE* 3.2 26.0 - - - -
606B VAL* 1.3 90.3 - - + +
608B PRO* 1.3 72.4 - - + +
620B VAL* 4.1 0.7 - - - -
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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