Contacts of the helix formed by residues 601 - 612 (chain D) in PDB entry 2DB3
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 ILE 601 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566D MET* 3.8 29.6 - - + -
567D PRO* 3.3 27.4 - - + +
568D SER* 3.7 11.2 - - - +
569D LYS 3.6 6.3 - - - +
570D ILE* 3.6 43.3 - - + +
593D PHE* 4.4 6.5 - - + -
598D ASP* 3.2 19.2 + - + +
599D ARG 3.1 0.6 - - - -
600D ALA* 1.3 77.3 - - - +
602D ALA* 1.3 69.9 + - - +
603D ALA 3.4 1.6 - - - -
604D ASP* 3.2 9.8 + - + +
605D LEU* 3.0 23.0 + - + +
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Residues in contact with ALA 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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593D PHE* 4.1 23.1 - - + -
598D ASP 3.7 0.8 + - - -
599D ARG* 3.1 16.9 + - - +
601D ILE* 1.3 83.0 - - - +
603D ALA* 1.3 58.3 + - - +
605D LEU* 3.2 5.9 + - - +
606D VAL* 2.9 34.7 + - - +
620D LEU* 3.8 24.5 - - + +
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Residues in contact with ALA 603 (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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599D ARG 4.6 1.2 + - - -
600D ALA 4.8 4.4 + - - +
601D ILE 3.4 0.6 - - - -
602D ALA* 1.3 79.1 - - - +
604D ASP* 1.3 65.3 + - - +
606D VAL* 3.4 8.9 + - - +
607D LYS* 3.1 35.7 + - - +
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Residues in contact with ASP 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570D ILE* 3.7 38.3 + - + +
600D ALA 5.1 5.5 + - - +
601D ILE* 3.2 12.7 + - + +
603D ALA* 1.3 76.0 - - - +
605D LEU* 1.3 61.5 + - - +
607D LYS* 3.1 26.4 + - - +
608D ILE* 2.8 30.8 + - + +
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Residues in contact with LEU 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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469D ILE* 3.9 21.5 - - + -
566D MET* 4.2 16.8 - - + -
570D ILE* 3.8 12.7 - - + +
573D TYR* 3.6 45.5 - - + +
593D PHE* 4.6 5.6 - - + -
601D ILE* 3.0 15.9 + - + +
602D ALA 3.6 7.6 - - - +
604D ASP* 1.3 75.1 - - - +
606D VAL* 1.3 67.4 + - - +
608D ILE* 3.0 2.7 + - + -
609D LEU* 2.7 38.6 + - + +
620D LEU* 3.8 27.8 - - + -
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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 ALA 2.9 22.2 + - - +
603D ALA* 3.6 10.1 - - - +
604D ASP 3.3 0.2 - - - -
605D LEU* 1.3 74.8 - - - +
607D LYS* 1.3 59.9 + - - +
609D LEU* 3.1 10.4 + - - +
610D GLU* 2.8 49.5 + - - +
616D VAL* 4.1 17.7 - - + -
620D LEU* 3.9 31.4 - - + +
621D ARG* 4.3 15.9 - - + +
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Residues in contact with LYS 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 ALA* 3.1 22.3 + - - +
604D ASP* 3.1 31.5 + - - +
606D VAL* 1.3 81.4 - - - +
608D ILE* 1.3 59.8 + - + +
610D GLU* 3.9 9.5 - - - +
611D GLY* 2.9 25.6 + - - -
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Residues in contact with ILE 608 (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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459D GLY 3.7 19.5 - - - +
460D GLY* 4.7 3.4 - - - -
461D ALA* 3.9 21.2 + - + +
467D GLN* 4.0 5.2 - - - +
570D ILE* 4.0 23.3 - - + -
573D TYR* 3.8 28.3 - - + -
574D VAL* 3.7 20.2 - - + -
604D ASP* 2.8 16.9 + - + +
605D LEU* 3.0 8.3 + - + +
607D LYS* 1.3 73.6 - - + +
609D LEU* 1.3 59.8 + - - +
611D GLY* 3.4 1.7 + - - -
612D SER* 2.7 33.8 + - - -
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Residues in contact with LEU 609 (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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467D GLN* 3.6 30.5 - - + +
469D ILE* 4.1 10.8 - - + -
573D TYR* 4.4 5.4 - - - +
605D LEU* 2.7 27.6 + - + +
606D VAL* 3.4 5.8 - - - +
608D ILE* 1.3 75.4 - - - +
610D GLU* 1.3 65.0 + - - +
612D SER* 3.2 9.1 + - - -
614D GLN* 2.8 47.5 + - + -
615D THR 4.2 5.2 - - - +
616D VAL* 3.9 11.9 - - + -
617D PRO* 4.1 13.7 - - + -
620D LEU* 3.5 31.9 - - + -
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Residues in contact with GLU 610 (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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606D VAL* 2.8 31.5 + - + +
607D LYS* 4.0 9.6 - - - +
609D LEU* 1.3 74.1 - - - +
611D GLY* 1.3 60.5 + - - +
612D SER 3.3 0.9 + - - -
613D GLY* 3.4 10.1 + - - -
614D GLN 4.6 4.7 - - - +
616D VAL* 3.7 16.2 - - + -
621D ARG* 3.1 24.2 + - - -
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Residues in contact with GLY 611 (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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457D ILE* 4.3 24.1 - - - +
460D GLY* 6.1 2.7 - - - -
461D ALA 5.3 1.5 - - - +
607D LYS 2.9 18.8 + - - -
608D ILE* 3.4 3.8 + - - -
609D LEU 3.2 0.4 - - - -
610D GLU* 1.3 78.2 - - - +
612D SER* 1.3 57.2 + - - +
613D GLY 3.5 0.2 - - - -
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Residues in contact with SER 612 (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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461D ALA* 3.7 27.1 - - - +
463D SER* 3.9 24.9 - - - +
467D GLN* 3.2 25.7 + - - -
608D ILE 2.7 20.6 + - - -
609D LEU 3.5 3.6 + - - -
610D GLU 3.2 0.6 - - - -
611D GLY* 1.3 78.1 - - - +
613D GLY* 1.3 63.3 + - - +
614D GLN* 3.1 14.3 + - - +
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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