Contacts of the helix formed by residues 602 - 613 (chain D) in PDB entry 2ZXI
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 THR 602 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577D THR* 6.1 1.2 - - - +
579D GLU* 6.1 0.2 - - - +
600D GLY 4.0 9.4 - - - +
601D ILE* 1.3 77.9 - - - +
603D PRO* 1.3 74.0 - - + +
604D ALA* 3.0 11.3 + - - +
605D ALA* 2.9 31.9 + - - +
606D ILE* 3.2 14.4 + - - +
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Residues in contact with PRO 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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601D ILE 4.4 2.2 - - - +
602D THR* 1.3 87.8 - - - +
604D ALA* 1.3 58.2 + - - +
606D ILE* 3.5 12.6 + - + +
607D THR* 2.9 25.5 + - - -
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Residues in contact with ALA 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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575D GLY 5.3 3.6 - - - +
602D THR* 2.9 10.2 + - - +
603D PRO* 1.3 77.4 - - - +
605D ALA* 1.3 60.5 + - - +
607D THR* 2.8 25.5 + - - -
608D ALA* 2.8 13.8 + - - +
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Residues in contact with ALA 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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575D GLY 5.0 2.0 - - - -
576D LEU* 3.5 27.8 - - + +
577D THR* 5.9 0.2 - - - +
580D ALA* 4.7 10.1 - - + -
584D LEU* 5.3 2.2 - - + -
601D ILE* 3.7 18.8 - - + -
602D THR* 2.9 20.5 + - - +
604D ALA* 1.3 78.9 - - - +
606D ILE* 1.3 62.6 + - - +
608D ALA* 3.1 6.4 + - - +
609D LEU* 2.9 24.6 + - - +
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Residues in contact with ILE 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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559D LEU* 4.2 11.0 - - + -
592D VAL* 4.1 17.6 - - + +
595D ALA* 4.4 3.8 - - + +
596D SER* 3.7 37.5 - - - +
601D ILE* 3.1 36.6 - - + +
602D THR 3.2 8.6 + - - +
603D PRO* 3.7 13.2 - - + +
605D ALA* 1.3 77.5 - - - +
607D THR* 1.3 54.0 + - - +
609D LEU* 3.3 8.9 + - + +
610D LEU* 2.8 52.1 + - + +
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Residues in contact with THR 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 PRO 2.9 13.5 + - - -
604D ALA* 2.8 16.2 + - - -
606D ILE* 1.3 78.7 - - - +
608D ALA* 1.3 54.1 + - - +
610D LEU* 3.0 9.8 + - + +
611D VAL* 2.7 51.5 + - + +
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Residues in contact with ALA 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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573D ILE* 4.0 4.7 - - + +
574D PRO 3.6 17.1 - - - +
575D GLY* 3.3 28.5 - - - +
576D LEU* 4.1 8.1 - - + -
604D ALA 2.8 12.6 + - - +
605D ALA 3.4 7.6 - - - +
607D THR* 1.3 74.5 - - - +
609D LEU* 1.3 59.1 + - - +
611D VAL* 3.4 7.8 + - - +
612D TYR* 2.9 30.0 + - - +
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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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564D ILE* 3.6 26.7 - - + -
568D ILE* 3.9 17.3 - - + -
570D TYR* 4.3 12.1 - - + -
573D ILE* 3.8 28.0 - - + +
576D LEU* 5.5 4.7 - - + -
584D LEU* 5.1 6.5 - - + -
592D VAL* 4.3 12.8 - - + -
595D ALA* 4.3 14.8 - - + -
605D ALA 2.9 12.6 + - - +
606D ILE* 3.4 11.2 - - + +
608D ALA* 1.3 75.3 - - - +
610D LEU* 1.3 60.9 + - - +
612D TYR* 3.2 5.7 + - + +
613D LEU* 2.9 47.4 + - + +
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Residues in contact with LEU 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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558D LYS* 5.5 14.1 - - + +
559D LEU* 3.9 13.5 - - + -
562D THR* 3.9 33.0 - - + +
592D VAL* 4.2 15.5 - - + -
606D ILE* 2.8 38.4 + - + +
607D THR* 3.0 7.8 + - + +
609D LEU* 1.3 73.8 - - - +
611D VAL* 1.3 64.8 + - + +
613D LEU* 3.2 9.3 + - - +
615D LYS* 2.9 44.8 + - + +
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Residues in contact with VAL 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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607D THR* 2.7 39.4 + - + +
608D ALA* 3.5 7.9 - - - +
610D LEU* 1.3 73.7 - - + +
612D TYR* 1.3 60.3 + - - +
614D GLY* 2.9 20.4 + - - -
615D LYS 4.7 7.6 - - - +
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Residues in contact with TYR 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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568D ILE* 4.1 24.3 - - + +
569D ASP* 4.7 4.0 + - - +
572D LYS* 3.8 33.6 - - + +
573D ILE* 3.4 36.1 - - + -
574D PRO* 4.0 18.2 - - + -
608D ALA 2.9 16.9 + - - +
609D LEU* 3.2 5.1 + - - +
611D VAL* 1.3 79.3 - - - +
613D LEU* 1.3 63.3 + - + +
614D GLY 3.2 3.8 + - - -
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Residues in contact with LEU 613 (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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562D THR* 3.8 7.2 - - + -
563D LYS 3.5 21.1 - - - +
564D ILE* 4.2 6.3 - - + -
565D PRO* 3.7 29.2 - - + -
568D ILE* 4.3 15.5 - - + -
592D VAL* 3.7 26.9 - - + -
609D LEU* 2.9 24.9 + - + +
610D LEU* 3.2 6.9 + - - +
612D TYR* 1.3 81.5 - - + +
614D GLY* 1.3 61.4 + - - +
615D LYS* 3.7 20.6 + - + -
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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