Contacts of the helix formed by residues 596 - 607 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585E GLY 3.2 13.0 - - - -
587E CYS* 3.7 6.5 - - - +
594E PHE* 3.2 10.4 - - - +
595E GLN* 1.3 80.5 - - - +
597E ILE* 1.3 63.0 + - - +
598E PHE* 3.4 22.8 + - - +
599E ASP* 3.1 28.8 + - - -
600E MET 3.2 15.2 + - - -
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Residues in contact with ILE 597 (chain E).
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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522E LEU* 4.0 29.6 - - + -
527E TRP* 4.1 11.2 - - + -
554E VAL* 3.9 20.4 - - + -
564E CYS* 5.1 0.4 - - + -
579E LEU* 3.7 23.3 - - + -
581E LEU* 4.3 17.9 - - + -
585E GLY 4.0 3.8 + - - -
587E CYS* 3.8 12.0 - - - +
596E SER* 1.3 75.0 - - - +
598E PHE* 1.3 83.3 + - + +
600E MET* 3.3 18.6 + - + +
601E LEU* 3.0 32.4 + - + +
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Residues in contact with PHE 598 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520E GLN 4.1 10.8 - - - -
522E LEU* 4.4 8.7 - - + -
525E TYR* 3.2 52.0 - + - -
527E TRP* 3.7 26.5 - + - -
596E SER* 3.6 19.1 - - - +
597E ILE* 1.3 85.7 - - + +
599E ASP* 1.3 67.4 + - - +
601E LEU* 3.3 7.1 + - - +
602E GLU* 3.0 34.4 + - + +
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Residues in contact with ASP 599 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594E PHE* 4.0 12.3 - - + -
595E GLN* 3.6 24.5 + - - +
596E SER* 3.1 23.8 + - - +
597E ILE 3.3 0.2 - - - -
598E PHE* 1.3 75.4 - - - +
600E MET* 1.3 60.4 + - - +
602E GLU* 3.3 14.2 + - - +
603E HIS* 2.8 32.2 + - - +
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Residues in contact with MET 600 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566E LEU* 4.6 7.9 - - + -
579E LEU* 3.4 42.4 - - + -
587E CYS* 4.2 4.0 - - - -
589E VAL* 4.0 11.9 - - + -
594E PHE* 3.5 42.7 - - + -
596E SER 3.2 7.5 + - - +
597E ILE* 3.3 26.0 - - + +
598E PHE 3.2 0.2 - - - -
599E ASP* 1.3 79.7 - - - +
601E LEU* 1.3 81.3 + - + +
603E HIS* 3.3 2.9 + - - +
604E PHE* 3.1 42.3 + - + +
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Residues in contact with LEU 601 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531B MET* 5.5 3.1 - - + -
527E TRP* 3.4 53.4 - - + +
552E PHE* 3.8 17.9 - - + -
554E VAL* 4.5 2.2 - - + -
566E LEU* 3.8 16.6 - - + -
597E ILE* 3.0 21.1 + - + +
598E PHE* 3.8 6.3 - - - +
600E MET* 1.3 88.1 - - + +
602E GLU* 1.3 58.5 + - + +
604E PHE 3.1 3.8 + - - -
605E ARG* 3.0 36.2 + - + +
621E LEU* 3.5 26.2 - - + +
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Residues in contact with GLU 602 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558B GLU* 5.0 2.3 - - - +
598E PHE* 3.0 23.9 + - + +
599E ASP* 3.9 14.4 - - - +
601E LEU* 1.3 72.9 - - + +
603E HIS* 1.3 65.8 + - - +
605E ARG* 3.3 44.6 + - - +
606E VAL* 3.6 13.0 + - - +
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Residues in contact with HIS 603 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592E LEU* 5.5 5.4 - - + -
594E PHE* 3.6 23.6 - + + -
599E ASP 2.8 18.1 + - - +
600E MET 3.6 4.7 - - - +
602E GLU* 1.3 77.4 - - - +
604E PHE* 1.3 79.0 + + - +
607E HIS* 2.8 75.4 + + + +
608E PRO 5.8 0.2 - - - -
610E PRO* 6.3 0.2 - - + -
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Residues in contact with PHE 604 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566E LEU* 4.6 4.5 - - + -
577E LEU* 4.3 20.0 - - + -
589E VAL* 5.1 2.7 - - + -
592E LEU* 3.9 23.8 - - + -
594E PHE* 4.4 5.4 - + - -
600E MET* 3.1 43.4 + - + +
601E LEU 3.1 2.0 + - - -
603E HIS* 1.3 99.4 - + - +
605E ARG* 1.3 58.9 + - - +
606E VAL 3.4 0.7 - - - -
607E HIS 3.3 17.0 - - - +
608E PRO 4.6 0.4 - - - -
609E ILE* 3.9 23.5 - - + +
610E PRO* 4.1 23.1 - - + -
620E VAL* 3.5 7.6 - - - -
621E LEU* 2.9 39.8 + - + -
816K LEU* 5.2 2.9 - - + -
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Residues in contact with ARG 605 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531B MET* 2.9 56.4 + - + +
532B LEU* 4.2 0.4 - - - +
533B SER* 3.4 21.0 - - - +
536B LYS* 5.8 1.4 + - - +
558B GLU* 2.7 33.9 + - - +
601E LEU* 3.0 18.2 + - - +
602E GLU* 3.5 40.7 + - - +
603E HIS 3.2 0.2 - - - -
604E PHE* 1.3 80.7 - - - +
606E VAL* 1.3 64.3 + - + +
620E VAL* 3.6 18.9 - - - +
621E LEU* 3.8 22.6 + - + +
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Residues in contact with VAL 606 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536B LYS* 4.7 17.5 - - - +
602E GLU 3.9 11.4 - - - +
603E HIS 3.5 0.8 + - - -
605E ARG* 1.3 86.1 - - + +
607E HIS* 1.3 87.1 + - + +
608E PRO* 4.0 4.9 - - - +
620E VAL* 4.1 6.3 - - - +
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Residues in contact with HIS 607 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603E HIS* 2.8 56.9 + + + +
604E PHE* 3.3 25.8 - - - +
606E VAL* 1.3 98.0 - - + +
608E PRO* 1.3 75.3 - - + +
620E VAL* 4.0 1.8 - - - -
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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