Contacts of the strand formed by residues 587 - 599 (chain D) in PDB entry 3E20
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 VAL 587 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580D VAL* 3.5 25.4 - - + -
581D MET 3.4 4.0 - - - -
582D HIS* 3.2 31.9 - - + +
584D HIS 5.3 0.7 - - - +
585D THR 4.2 3.3 + - - +
586D ALA* 1.3 81.9 - - - +
588D GLU* 1.3 76.4 + - - +
648D GLN* 6.0 0.4 - - - -
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Residues in contact with GLU 588 (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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580D VAL* 3.6 5.3 - - - -
581D MET* 2.7 49.7 + - - +
586D ALA* 5.6 4.0 - - + +
587D VAL* 1.3 87.1 - - - +
589D GLU* 1.3 80.6 + - - +
590D VAL 3.5 0.3 + - - -
625D THR* 4.6 4.7 - - + -
626D GLN* 5.1 4.5 - - - +
627D THR* 3.7 26.0 + - - +
628D PRO 6.0 0.4 - - - -
629D VAL* 4.2 28.9 - - + +
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Residues in contact with GLU 589 (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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578D SER* 2.9 28.3 + - - -
579D CYS* 3.1 12.5 + - - +
580D VAL* 4.7 4.0 - - + +
588D GLU* 1.3 82.2 + - - +
590D VAL* 1.3 71.4 + - - +
591D SER* 4.4 4.5 + - - -
625D THR* 3.7 22.6 - - - +
626D GLN* 3.5 39.5 + - + -
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Residues in contact with VAL 590 (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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560D PHE* 4.5 3.6 - - + -
578D SER* 3.1 1.6 + - - -
579D CYS* 2.6 67.1 + - - +
581D MET* 3.8 27.1 - - + -
588D GLU 3.5 0.4 + - - -
589D GLU* 1.3 77.3 + - - +
591D SER* 1.3 61.6 + - - +
592D PHE* 5.7 1.6 - - + -
623D LEU* 3.9 31.6 - - + -
624D GLU 3.3 13.2 - - - +
625D THR* 3.8 15.7 - - + -
645D LEU* 4.5 9.2 - - + -
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Residues in contact with SER 591 (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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399C MET* 6.3 1.3 - - - -
403C LYS* 5.1 10.0 + - - +
576D GLY 4.8 2.9 - - - -
577D TYR 3.2 13.2 - - - -
578D SER* 3.5 16.6 - - - -
589D GLU* 4.4 4.7 + - - -
590D VAL* 1.3 77.6 - - - +
592D PHE* 1.3 68.0 + - - +
623D LEU* 3.6 1.9 - - - -
624D GLU* 2.8 44.4 + - - +
626D GLN* 5.8 1.6 + - - -
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Residues in contact with PHE 592 (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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403C LYS* 6.1 1.0 - - - +
564D ILE* 3.6 27.6 - - + -
566D ILE* 6.0 2.5 - - + -
573D LEU* 3.8 27.8 - - + -
575D THR* 2.4 42.3 - - - +
576D GLY* 4.8 0.2 - - - -
577D TYR* 2.8 46.7 + + + +
578D SER* 5.4 0.2 - - - -
579D CYS* 4.8 3.1 - - - -
590D VAL* 5.7 0.9 - - + -
591D SER* 1.3 79.4 + - - +
593D ALA* 1.3 56.6 + - - +
594D LYS 4.9 0.4 - - - +
595D LEU* 4.5 5.4 - - + -
619D ILE* 4.9 4.9 - - + -
621D ALA* 3.8 15.9 - - + -
622D GLU 3.6 4.3 - - - +
623D LEU* 3.5 16.6 - - + -
645D LEU* 3.8 29.2 - - + -
653D ALA* 6.2 0.4 - - + -
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Residues in contact with ALA 593 (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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575D THR* 3.4 21.0 + - - +
591D SER 3.5 1.0 + - - -
592D PHE* 1.3 73.4 - - - +
594D LYS* 1.3 67.7 + - + +
622D GLU* 2.5 40.7 + - + +
624D GLU* 3.3 34.3 - - + +
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Residues in contact with LYS 594 (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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559D ARG* 4.9 3.8 - - - +
575D THR* 4.2 6.7 - - - -
593D ALA* 1.3 88.3 - - - +
595D LEU* 1.3 67.0 + - - +
596D LEU* 3.7 18.0 + - + +
621D ALA* 3.1 3.9 - - - +
622D GLU* 2.7 71.7 + - - +
624D GLU* 5.3 1.0 + - - -
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Residues in contact with LEU 595 (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 LEU* 3.9 21.5 - - + +
574D THR* 4.5 1.3 - - - -
575D THR* 3.4 34.1 + - - +
592D PHE* 4.5 14.4 - - + -
594D LYS* 1.3 78.3 - - - +
596D LEU* 1.3 61.6 + - - +
609D PRO* 3.4 19.4 - - - +
610D PRO* 3.8 36.0 - - + +
611D MET 4.9 0.7 - - - +
612D PHE* 4.0 17.0 - - - +
613D ALA* 4.2 9.9 - - + -
619D ILE* 4.1 17.3 - - + -
620D ILE 4.3 0.2 - - - -
621D ALA* 3.9 4.5 - - + -
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Residues in contact with LEU 596 (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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561D ILE* 3.8 44.4 - - + -
594D LYS* 4.3 26.7 - - + +
595D LEU* 1.3 78.0 - - - +
597D HIS* 1.3 88.9 + - + +
609D PRO* 3.4 20.3 - - - +
610D PRO* 4.0 2.0 - - - -
620D ILE* 2.8 20.0 + - + +
621D ALA 4.4 5.8 - - - -
622D GLU* 4.6 5.8 - - + +
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Residues in contact with HIS 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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595D LEU 3.9 0.2 - - - -
596D LEU* 1.3 104.1 + - + +
598D LYS* 1.3 67.1 + - - +
605D LYS* 3.4 36.1 - - + +
606D SER* 3.2 24.9 - - - +
607D LYS* 4.8 6.7 - - + -
610D PRO* 3.6 9.3 - - - +
619D ILE* 3.1 11.3 - - - +
620D ILE* 3.1 45.8 + - + +
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Residues in contact with LYS 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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597D HIS* 1.3 77.9 - - - +
599D LEU* 1.3 78.2 + - - +
600D ASP* 4.5 13.5 - - - -
604D ARG 3.0 12.6 - - - +
606D SER* 2.6 36.7 + - - +
610D PRO* 3.7 16.3 - - + +
617D MET* 3.8 36.4 - - + -
618D LYS 3.6 13.9 - - - +
619D ILE* 4.2 0.2 - - - +
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Residues in contact with LEU 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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563D GLN* 3.9 23.3 - - + +
598D LYS* 1.3 82.4 - - - +
600D ASP* 1.3 69.4 + - - +
603D ASN* 3.6 29.4 - - + +
604D ARG 3.2 22.0 - - - +
605D LYS* 5.2 5.6 - - + -
617D MET* 5.3 1.7 - - - +
618D LYS* 3.0 41.3 + - + +
619D ILE* 3.4 43.1 - - - +
620D ILE* 4.0 14.1 - - + +
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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