Contacts of the helix formed by residues 596 - 607 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585D GLY 3.3 13.2 - - - -
587D CYS* 3.9 7.2 - - - +
594D PHE* 3.3 8.5 - - - +
595D GLN* 1.3 80.9 - - - +
597D ILE* 1.3 64.5 + - - +
598D PHE* 3.5 8.9 + - - +
599D ASP* 3.0 28.6 + - - +
600D MET* 3.1 16.6 + - - +
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Residues in contact with ILE 597 (chain D).
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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522D LEU* 3.8 32.3 - - + -
527D TRP* 3.9 26.7 - - + -
554D VAL* 4.5 8.1 - - + -
564D CYS* 4.3 15.3 - - + -
579D LEU* 4.5 5.2 - - + -
581D LEU* 3.5 35.9 - - + -
585D GLY 4.1 1.8 + - - +
587D CYS* 4.1 8.9 - - + +
596D SER* 1.3 75.4 - - - +
598D PHE* 1.3 57.6 + - - +
600D MET* 3.1 24.1 + - + +
601D LEU* 2.9 27.7 + - + +
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Residues in contact with PHE 598 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525D TYR* 4.7 16.6 - + + +
527D TRP* 3.9 36.9 - + + -
596D SER* 3.2 8.3 + - - +
597D ILE* 1.3 76.7 - - - +
599D ASP* 1.3 62.1 + - - +
601D LEU* 3.0 15.0 + - + +
602D GLU* 2.8 68.0 + - + +
605D ARG* 4.8 10.8 - - - -
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Residues in contact with ASP 599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594D PHE* 4.4 7.7 - - + -
595D GLN* 3.5 26.4 - - - +
596D SER* 3.0 27.0 + - - +
598D PHE* 1.3 79.1 - - - +
600D MET* 1.3 64.1 + - - +
602D GLU* 3.2 19.3 + - - +
603D HIS* 2.9 25.6 + - - +
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Residues in contact with MET 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554D VAL* 5.1 0.2 - - + -
566D LEU* 4.3 11.7 - - + -
579D LEU* 3.6 36.8 - - + -
587D CYS* 4.2 4.7 - - - -
589D VAL* 4.1 9.4 - - + -
594D PHE* 3.5 41.4 - - + -
596D SER 3.1 10.6 + - - +
597D ILE* 3.1 22.6 + - + +
598D PHE 3.1 0.4 - - - -
599D ASP* 1.3 76.8 - - - +
601D LEU* 1.3 87.3 + - + +
603D HIS* 3.4 2.4 + - - +
604D PHE* 3.1 45.0 + - + +
621D LEU* 5.0 0.2 - - - -
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Residues in contact with LEU 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D TRP* 3.4 57.9 - - + +
552D PHE* 3.6 27.4 - - + -
554D VAL* 4.2 2.9 - - + -
566D LEU* 3.9 7.4 - - + -
597D ILE* 2.9 17.4 + - + +
598D PHE* 3.0 14.3 + - + +
600D MET* 1.3 95.9 - - + +
602D GLU* 1.3 62.5 + - - +
604D PHE 3.4 2.6 + - - -
605D ARG* 3.1 23.4 + - - +
621D LEU* 3.7 20.6 - - + +
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Residues in contact with GLU 602 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598D PHE* 2.8 56.5 + - + +
599D ASP* 3.7 20.4 - - - +
601D LEU* 1.3 71.5 - - - +
603D HIS* 1.3 63.8 + - - +
605D ARG* 3.1 48.7 + - - +
606D VAL* 3.4 12.5 + - - +
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Residues in contact with HIS 603 (chain D).
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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592D LEU* 5.1 8.9 - - + +
594D PHE* 3.7 25.9 - + + -
599D ASP 2.9 16.6 + - - +
600D MET 3.6 4.7 - - - +
601D LEU 3.2 0.2 - - - -
602D GLU* 1.3 77.7 - - - +
604D PHE* 1.3 74.1 + + - +
606D VAL* 3.1 4.1 + - - -
607D HIS* 2.7 82.9 + + + -
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Residues in contact with PHE 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566D LEU* 4.6 6.1 - - + -
577D LEU* 4.2 17.9 - - + -
589D VAL* 4.7 2.7 - - + -
592D LEU* 3.5 28.0 - - + -
594D PHE* 4.4 4.0 - + - -
600D MET* 3.1 43.6 + - + +
601D LEU 3.4 1.5 + - - -
603D HIS* 1.3 95.0 - + - +
605D ARG* 1.3 59.0 + - - +
606D VAL 3.3 0.2 - - - -
607D HIS 3.1 15.5 - - - +
608D PRO 4.5 0.7 - - - -
609D ILE* 3.9 20.0 - - + -
610D PRO* 3.9 24.9 - - + -
620D VAL* 3.4 10.2 - - - -
621D LEU* 2.8 39.6 + - + -
816J LEU* 4.7 7.0 - - + -
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Residues in contact with ARG 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598D PHE* 4.8 8.5 - - - -
601D LEU 3.1 11.7 + - - +
602D GLU* 3.1 49.7 + - - +
603D HIS 3.0 0.4 - - - -
604D PHE* 1.3 78.6 - - - +
606D VAL* 1.3 64.7 + - + +
620D VAL* 3.8 14.7 - - - +
621D LEU* 3.7 25.1 - - + +
622D VAL 5.5 4.0 - - - -
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Residues in contact with VAL 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602D GLU 3.4 10.1 + - - +
603D HIS 3.1 4.8 + - - +
605D ARG* 1.3 88.7 - - + +
607D HIS* 1.3 83.3 + - + +
608D PRO* 4.0 4.5 - - - +
620D VAL* 4.1 7.6 - - - +
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Residues in contact with HIS 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603D HIS* 2.7 60.5 + + + +
604D PHE* 3.1 25.5 - - - +
606D VAL* 1.3 94.6 - - + +
608D PRO* 1.3 75.3 - - + +
620D VAL* 3.9 2.0 - - - -
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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