Contacts of the helix formed by residues 600 - 615 (chain D) in PDB entry 5Y7K
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 600 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594D ILE* 5.2 0.7 - - - +
597D ARG* 2.8 63.5 + - + +
598D LEU 3.9 4.9 - - - +
599D GLY* 1.3 81.6 - - - +
601D PHE* 1.3 72.5 + - - +
602D GLU* 3.3 3.3 - - - +
603D VAL* 3.0 4.3 + - - +
604D GLU* 2.8 44.9 + - - +
682D HIS* 5.9 4.3 - - + -
686D SER* 5.9 1.6 - - - -
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Residues in contact with PHE 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581D ARG* 3.3 59.2 - - + +
593D ALA* 3.3 31.2 - - + -
594D ILE* 4.5 4.2 - - + +
597D ARG* 3.3 43.7 - - - -
600D THR* 1.3 85.4 + - - +
602D GLU* 1.3 55.1 + - - +
604D GLU* 4.1 14.1 - - - -
605D ASP* 2.6 41.2 + - - +
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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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548D ALA* 4.2 19.1 - - + +
550D PRO* 6.2 0.2 - - - -
580D GLY* 5.9 0.7 - - - -
581D ARG 4.0 19.3 + - - +
594D ILE* 3.7 16.2 - - + +
598D LEU* 3.1 17.3 - - - +
599D GLY* 2.9 32.2 + - - +
600D THR 3.7 3.4 - - - +
601D PHE* 1.3 74.6 - - - +
603D VAL* 1.3 67.1 + - + +
605D ASP* 3.9 4.9 - - - +
606D GLN* 3.3 27.1 + - - +
631D TYR* 2.5 45.0 + - - -
634D TYR* 4.5 0.5 - - - -
635D VAL* 4.0 7.5 - - + +
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Residues in contact with VAL 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599D GLY* 3.5 32.1 - - - +
600D THR 3.0 7.4 + - - +
602D GLU* 1.3 76.1 - - + +
604D GLU* 1.3 67.2 + - + +
606D GLN* 3.2 5.9 + - - +
607D ILE* 3.2 27.1 + - + +
634D TYR* 5.1 0.2 - - + -
635D VAL* 4.3 20.6 - - + -
638D MET* 3.8 23.1 - - + +
639D VAL* 3.5 33.4 - - + +
642D SER* 5.5 0.2 - - - -
691D ARG* 4.5 7.2 - - - +
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Residues in contact with GLU 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581D ARG* 4.5 4.9 + - - +
597D ARG* 5.3 1.6 + - - -
600D THR* 2.8 37.6 + - - +
601D PHE* 3.8 19.9 - - - +
603D VAL* 1.3 73.9 - - + +
605D ASP* 1.3 55.4 + - - +
607D ILE* 3.1 13.6 + - + +
608D GLU* 2.7 37.0 + - - +
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Residues in contact with ASP 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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519D LEU* 5.4 7.8 - - - +
524D PHE* 4.6 5.4 - - - -
578D PHE* 3.6 22.6 - - + -
580D GLY* 3.6 6.8 - - - -
581D ARG* 2.8 62.9 + - - +
601D PHE 2.6 20.6 + - - +
602D GLU* 3.9 5.2 - - - +
604D GLU* 1.3 72.6 - - - +
606D GLN* 1.3 59.2 + - + +
608D GLU* 3.7 8.1 - - - +
609D ALA* 2.8 30.0 + - - +
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Residues in contact with GLN 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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544D LEU* 3.5 32.9 - - + +
546D VAL* 3.2 29.6 - - + +
547D TYR 5.7 0.2 - - - +
548D ALA* 4.0 16.2 - - + +
578D PHE* 2.8 44.1 + - - +
580D GLY* 4.6 4.2 - - - +
602D GLU 3.3 13.7 + - - +
603D VAL 3.2 8.3 + - - +
605D ASP* 1.3 77.4 - - - +
607D ILE* 1.3 62.2 + - - +
609D ALA* 3.4 3.5 + - - +
610D ALA* 3.3 16.5 + - - +
626D ILE* 5.0 0.2 - - + -
635D VAL* 4.0 17.0 - - + -
639D VAL* 4.4 11.7 - - + -
647D PHE* 5.0 0.7 - - - -
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Residues in contact with ILE 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 VAL* 3.2 19.4 + - + +
604D GLU* 3.1 12.7 + - + +
606D GLN* 1.3 73.2 - - - +
608D GLU* 1.3 66.0 + - - +
610D ALA* 3.2 12.6 + - - +
611D ARG* 3.2 41.9 + - - +
639D VAL* 3.8 27.1 - - + -
642D SER* 3.3 33.2 - - - +
644D SER* 3.8 15.7 - - - +
646D VAL* 4.2 7.4 - - + +
647D PHE* 4.4 7.2 - - + -
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Residues in contact with GLU 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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519D LEU* 4.1 29.9 - - + +
604D GLU 2.7 19.5 + - - +
605D ASP* 3.8 8.5 - - - +
607D ILE* 1.3 73.5 - - - +
609D ALA* 1.3 62.9 + - - +
611D ARG* 3.1 28.0 + - - +
612D GLN* 2.7 53.2 + - + +
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Residues in contact with ALA 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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517D ILE* 4.9 3.6 - - - -
544D LEU* 5.3 2.0 - - + -
578D PHE* 3.5 40.8 - - + -
605D ASP 2.8 18.3 + - - +
606D GLN* 3.6 6.3 - - - +
607D ILE 3.2 0.2 - - - -
608D GLU* 1.3 76.4 - - - +
610D ALA* 1.3 57.2 + - - +
612D GLN* 3.2 10.1 + - - +
613D PHE* 2.9 42.8 + - + -
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Residues in contact with ALA 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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542D LEU* 4.9 2.0 - - + -
544D LEU* 4.7 4.0 - - + +
606D GLN 3.3 4.3 + - - +
607D ILE 3.2 11.0 + - - +
609D ALA* 1.3 76.1 - - - +
611D ARG* 1.3 64.8 + - - +
613D PHE* 3.2 12.3 + - - +
614D SER* 3.0 24.1 + - - -
624D ILE* 4.5 12.0 - - + +
646D VAL* 3.6 25.4 - - + -
647D PHE* 3.7 23.1 - - + -
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Residues in contact with ARG 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 ILE* 3.4 33.8 + - - +
608D GLU* 3.1 32.8 + - - +
610D ALA* 1.3 77.1 - - - +
612D GLN* 1.3 63.0 + - - +
614D SER* 2.8 22.5 + - - -
615D LYS* 3.2 31.9 + - - +
644D SER* 4.1 18.2 + - - +
646D VAL* 3.9 22.7 - - + +
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Residues in contact with GLN 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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517D ILE* 3.6 41.0 - - + +
518D ILE 5.2 1.0 - - - +
519D LEU* 4.4 10.7 - - - +
608D GLU* 2.7 40.1 + - + +
609D ALA 3.2 6.5 + - - +
611D ARG* 1.3 82.3 - - - +
613D PHE* 1.3 67.1 + - + +
615D LYS* 3.2 25.5 + - - +
616D MET* 3.3 17.0 + - + +
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Residues in contact with PHE 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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517D ILE* 5.2 2.9 - - + -
526D TYR* 3.7 46.9 - + + -
528D MET* 3.4 22.0 - - + -
542D LEU* 3.7 29.8 - - + -
544D LEU* 4.1 15.7 - - + -
576D ALA* 3.7 20.2 - - + -
577D SER 4.7 0.2 - - - -
578D PHE* 4.7 3.8 - + + -
609D ALA* 2.9 36.0 + - + +
610D ALA* 3.2 5.6 + - - +
612D GLN* 1.3 79.2 - - + +
614D SER* 1.3 62.4 + - - +
616D MET* 3.1 33.0 + - + +
617D GLY 4.2 0.3 + - - -
619D VAL* 3.3 18.1 - - + +
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Residues in contact with SER 614 (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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539D LYS* 5.6 1.2 + - - -
610D ALA 3.0 13.1 + - - -
611D ARG* 2.8 24.9 + - - -
613D PHE* 1.3 77.4 - - - +
615D LYS* 1.3 62.6 + - - +
616D MET 3.1 3.9 + - - -
617D GLY* 3.6 10.2 + - - -
619D VAL* 3.8 23.4 - - - +
621D ASN* 3.5 38.7 + - - +
624D ILE* 4.5 4.9 - - - -
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Residues in contact with LYS 615 (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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611D ARG* 3.3 36.2 + - - +
612D GLN* 3.2 19.2 + - - +
613D PHE 3.2 1.0 - - - -
614D SER* 1.3 78.9 + - - +
616D MET* 1.3 59.5 + - - +
617D GLY* 3.5 0.9 - - - -
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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