Contacts of the helix formed by residues 596 - 607 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585C GLY 3.4 14.8 - - - -
587C CYS* 3.8 7.2 - - - +
594C PHE* 3.4 7.0 + - - +
595C GLN* 1.3 79.6 - - - +
597C ILE* 1.3 64.6 + - - +
598C PHE* 3.2 32.3 - - - +
599C ASP* 2.6 35.3 + - - +
600C MET* 3.1 10.6 + - - +
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Residues in contact with ILE 597 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522C LEU* 3.5 37.5 - - + -
527C TRP* 4.1 15.7 - - + -
554C VAL* 4.3 13.5 - - + -
564C CYS* 4.3 12.8 - - + -
579C LEU* 4.4 2.7 - - + -
581C LEU* 3.5 35.4 - - + -
585C GLY 4.3 1.4 + - - +
587C CYS* 3.9 9.3 - - + +
596C SER* 1.3 74.1 - - - +
598C PHE* 1.3 59.5 + - + +
600C MET* 3.3 20.9 + - + +
601C LEU* 2.8 46.2 + - + +
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Residues in contact with PHE 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520C GLN 5.5 2.2 - - - -
522C LEU* 3.8 14.1 - - + -
525C TYR* 3.4 47.3 - + - -
527C TRP* 3.4 30.3 - + - -
596C SER* 3.2 27.8 - - - +
597C ILE* 1.3 79.7 - - - +
599C ASP* 1.3 56.9 + - - +
601C LEU* 3.1 10.1 + - - +
602C GLU* 2.8 43.2 + - + +
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Residues in contact with ASP 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594C PHE* 4.3 7.9 - - + -
595C GLN* 3.3 23.0 - - - +
596C SER* 2.6 36.2 + - - +
598C PHE* 1.3 73.6 - - - +
600C MET* 1.3 60.4 + - - +
602C GLU* 3.1 17.1 + - - +
603C HIS* 2.8 33.4 + - - +
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Residues in contact with MET 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566C LEU* 4.4 8.5 - - + -
579C LEU* 3.7 29.8 - - + -
587C CYS* 4.3 4.9 - - - -
589C VAL* 3.9 11.7 - - + -
594C PHE* 3.4 45.4 - - + -
596C SER 3.1 8.7 + - - +
597C ILE* 3.6 34.3 - - + +
599C ASP* 1.3 78.9 - - - +
601C LEU* 1.3 76.8 + - + +
603C HIS* 3.5 1.7 + - - +
604C PHE* 3.1 42.6 + - + +
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Residues in contact with LEU 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527C TRP* 3.5 50.9 - - + +
552C PHE* 3.9 16.6 - - + -
554C VAL* 4.4 4.3 - - + -
566C LEU* 4.2 8.1 - - + -
597C ILE* 2.8 26.0 + - + +
598C PHE* 3.3 10.3 - - - +
600C MET* 1.3 90.0 - - + +
602C GLU* 1.3 66.6 + - + +
604C PHE* 3.2 11.8 + - - +
605C ARG* 3.3 18.0 + - - +
621C LEU* 3.5 26.0 - - + +
531E MET* 4.6 13.2 - - + -
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Residues in contact with GLU 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598C PHE* 2.8 35.0 + - + +
599C ASP* 3.6 16.7 - - - +
601C LEU* 1.3 72.2 - - + +
603C HIS* 1.3 65.0 + - - +
605C ARG* 2.9 31.0 + - - +
606C VAL* 3.5 10.8 + - - +
531E MET* 6.0 3.6 - - + -
536E LYS* 5.8 0.2 + - - -
558E GLU* 5.5 7.6 - - - +
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Residues in contact with HIS 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592C LEU* 5.1 8.0 - - + +
594C PHE* 3.7 30.4 - + + -
599C ASP 2.8 20.6 + - - +
600C MET 3.8 1.3 - - - +
602C GLU* 1.3 72.7 - - - +
604C PHE* 1.3 84.4 + + - +
606C VAL* 5.2 2.0 - - - -
607C HIS* 2.9 61.8 + + + +
610C PRO* 6.1 0.2 - - + -
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Residues in contact with PHE 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566C LEU* 4.7 3.4 - - + -
577C LEU* 4.3 17.0 - - + -
589C VAL* 4.9 2.7 - - + -
592C LEU* 3.8 24.2 - - + -
594C PHE* 4.5 2.2 - + - -
600C MET* 3.1 46.6 + - + +
601C LEU 3.7 2.5 - - - +
602C GLU 3.1 1.4 - - - -
603C HIS* 1.3 100.7 - + - +
605C ARG* 1.3 60.6 + - - +
607C HIS 3.3 18.5 - - - +
608C PRO 4.4 0.7 - - - -
609C ILE* 4.0 22.4 - - + +
610C PRO* 3.9 24.5 - - + -
620C VAL* 3.4 8.0 - - - +
621C LEU* 2.8 40.9 + - + -
816I LEU* 4.8 3.1 - - + -
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Residues in contact with ARG 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552C PHE* 3.8 11.4 - - - -
601C LEU 3.4 14.6 - - - +
602C GLU* 2.9 15.7 + - - +
604C PHE* 1.3 79.3 - - - +
606C VAL* 1.3 64.4 + - + +
620C VAL* 3.3 22.9 - - - +
621C LEU* 2.4 43.2 + - + +
622C VAL* 2.6 31.3 + - - +
623C SER* 4.3 0.2 - - - +
529E HIS 5.4 0.6 + - - -
531E MET* 2.6 67.1 + - - +
532E LEU* 5.5 2.0 - - - +
533E SER 6.0 0.4 - - - +
536E LYS* 5.4 9.4 - - - +
558E GLU* 6.1 0.7 - - - -
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Residues in contact with VAL 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602C GLU 3.5 12.7 + - - +
603C HIS* 4.1 1.8 - - - +
605C ARG* 1.3 82.2 - - + +
607C HIS* 1.3 84.4 + - + +
608C PRO* 4.0 5.0 - - - +
620C VAL* 4.3 3.1 - - - +
536E LYS* 4.1 23.6 - - - +
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Residues in contact with HIS 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603C HIS* 2.9 52.2 + + + +
604C PHE* 3.3 26.2 - - - +
606C VAL* 1.3 102.1 - - + +
608C PRO* 1.3 74.6 - - + +
620C VAL* 3.8 2.5 - - - -
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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