Contacts of the helix formed by residues 596 - 607 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585F GLY 3.6 11.7 - - - -
587F CYS* 3.5 8.6 - - - +
594F PHE* 3.1 11.2 - - - +
595F GLN* 1.3 80.3 - - - +
597F ILE* 1.3 64.2 + - - +
598F PHE* 3.3 10.1 + - - +
599F ASP* 2.9 30.2 + - - -
600F MET* 3.2 14.6 + - - +
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Residues in contact with ILE 597 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522F LEU* 3.5 38.6 - - + -
527F TRP* 3.8 26.2 - - + -
554F VAL* 4.5 19.1 - - + -
564F CYS* 4.6 6.1 - - + -
579F LEU* 4.7 2.0 - - + -
581F LEU* 3.6 33.0 - - + -
585F GLY 4.3 2.3 + - - +
587F CYS* 3.8 9.4 - - + +
596F SER* 1.3 74.1 - - - +
598F PHE* 1.3 59.2 + - - +
600F MET* 3.1 21.6 + - + +
601F LEU* 2.8 29.6 + - + +
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Residues in contact with PHE 598 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531D MET* 3.8 21.5 - - + -
558D GLU* 3.6 46.4 - - + -
559D THR* 5.3 4.9 - - + -
525F TYR* 4.6 14.6 - + + +
527F TRP* 3.9 26.3 - + + -
596F SER* 3.3 8.1 + - - +
597F ILE* 1.3 76.0 - - - +
599F ASP* 1.3 55.4 + - - +
601F LEU* 3.0 10.7 + - + +
602F GLU* 2.7 79.6 + - + +
605F ARG* 4.3 0.7 - - - -
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Residues in contact with ASP 599 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594F PHE* 4.3 6.9 - - + -
595F GLN* 3.4 30.4 - - - +
596F SER* 2.9 32.0 + - - +
597F ILE 3.3 0.2 - - - -
598F PHE* 1.3 75.6 - - - +
600F MET* 1.3 58.0 + - - +
602F GLU* 3.3 19.3 + - - +
603F HIS* 2.8 30.0 + - - +
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Residues in contact with MET 600 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566F LEU* 4.1 11.7 - - + -
579F LEU* 3.4 41.3 - - + -
587F CYS* 4.3 4.3 - - - -
589F VAL* 4.1 6.7 - - + -
594F PHE* 3.4 43.4 - - + -
596F SER 3.2 7.1 + - - +
597F ILE* 3.1 28.1 + - + +
599F ASP* 1.3 80.0 - - - +
601F LEU* 1.3 78.9 + - + +
603F HIS* 3.1 2.9 + - - +
604F PHE* 3.0 45.0 + - + +
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Residues in contact with LEU 601 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531D MET* 4.6 9.9 - - + +
527F TRP* 3.4 56.8 - - + +
552F PHE* 3.8 17.5 - - + -
554F VAL* 4.3 4.5 - - + -
566F LEU* 4.1 14.6 - - + -
597F ILE* 2.8 17.1 + - + +
598F PHE* 3.0 12.8 + - + +
600F MET* 1.3 84.9 - - + +
602F GLU* 1.3 61.6 + - - +
604F PHE 3.2 2.9 + - - -
605F ARG* 3.1 23.8 + - - +
621F LEU* 3.6 28.9 - - + +
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Residues in contact with GLU 602 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558D GLU* 4.4 3.1 - - - +
598F PHE* 2.7 55.8 + - + +
599F ASP* 3.6 22.8 - - - +
601F LEU* 1.3 72.1 - - - +
603F HIS* 1.3 62.3 + - - +
605F ARG* 3.0 46.3 + - - +
606F VAL* 3.7 12.6 + - - +
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Residues in contact with HIS 603 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592F LEU* 5.5 5.6 - - + -
594F PHE* 3.5 28.5 - + + -
599F ASP 2.8 16.8 + - - +
600F MET 3.1 4.9 + - - +
602F GLU* 1.3 79.1 - - - +
604F PHE* 1.3 78.2 + + - +
605F ARG 3.2 0.6 + - - -
606F VAL* 3.4 1.5 + - - -
607F HIS* 2.9 69.2 + + + -
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Residues in contact with PHE 604 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566F LEU* 4.6 2.7 - - + -
577F LEU* 4.5 15.3 - - + -
589F VAL* 5.1 3.4 - - + -
592F LEU* 3.9 24.0 - - + -
594F PHE* 4.4 5.4 - + - -
600F MET* 3.0 47.7 + - + +
601F LEU 3.7 1.1 - - - -
603F HIS* 1.3 92.5 - + - +
605F ARG* 1.3 62.2 + - - +
606F VAL 3.2 1.6 - - - -
607F HIS 3.3 19.4 - - - +
609F ILE* 3.8 24.0 - - + -
610F PRO* 3.8 25.8 - - + -
619F VAL 4.8 0.2 - - - +
620F VAL* 3.4 10.0 - - - +
621F LEU* 3.0 37.2 + - + -
816L LEU* 4.9 4.3 - - + -
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Residues in contact with ARG 605 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531D MET* 2.9 44.9 + - + +
532D LEU* 4.9 7.9 - - - +
533D SER* 3.4 19.7 - - - +
558D GLU* 2.8 28.1 + - - -
598F PHE* 4.3 0.4 - - - -
601F LEU 3.1 8.9 + - - +
602F GLU* 3.0 50.4 + - - +
603F HIS 3.2 0.4 - - - -
604F PHE* 1.3 78.6 - - - +
606F VAL* 1.3 64.3 + - + +
620F VAL* 3.9 14.4 - - - +
621F LEU* 3.4 25.9 - - + +
622F VAL 5.4 2.2 - - - +
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Residues in contact with VAL 606 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536D LYS* 5.5 13.7 - - - +
602F GLU 3.7 11.0 + - - +
603F HIS* 3.4 2.8 + - - +
605F ARG* 1.3 86.7 - - + +
607F HIS* 1.3 86.3 + - + +
608F PRO* 3.8 6.2 - - - +
620F VAL* 4.2 5.8 - - - +
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Residues in contact with HIS 607 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603F HIS* 2.9 56.0 + + + +
604F PHE* 3.3 24.1 - - - +
606F VAL* 1.3 94.2 - - + +
608F PRO* 1.3 74.2 - - + +
609F ILE 3.4 0.3 + - - -
620F VAL* 4.0 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