Contacts of the helix formed by residues 725 - 741 (chain K) in PDB entry 6R1U
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 ASP 725 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723K THR 3.9 1.2 + - - -
724K LEU* 1.3 76.6 - - - +
726K ASP* 1.3 65.4 + - - +
727K LYS* 3.1 21.5 + - - +
728K GLN* 2.8 47.9 + - - +
729K VAL* 3.1 10.6 + - - +
756K ARG* 3.4 3.1 - - - +
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Residues in contact with ASP 726 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725K ASP* 1.3 75.2 - - - +
727K LYS* 1.3 62.4 + - - +
729K VAL* 3.1 4.5 + - - +
730K LEU* 2.9 23.4 + - - +
752K TYR* 3.8 22.6 - - + +
754K VAL* 3.6 26.2 + - + +
756K ARG* 2.8 35.6 + - - +
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Residues in contact with LYS 727 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725K ASP* 3.1 20.8 + - - +
726K ASP* 1.3 78.3 - - - +
728K GLN* 1.3 86.4 + - + +
730K LEU* 3.3 8.3 + - - +
731K GLN* 2.8 60.2 + - + +
752K TYR* 3.5 15.0 + - - +
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Residues in contact with GLN 728 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723K THR 4.4 2.3 - - - +
724K LEU* 3.5 32.5 - - + +
725K ASP* 2.8 48.4 + - - +
727K LYS* 1.3 92.3 - - + +
729K VAL* 1.3 66.3 + - - +
731K GLN* 3.3 12.2 + - - +
732K GLN* 3.1 30.1 + - - +
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Residues in contact with VAL 729 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662K ILE* 4.4 4.0 - - + -
694K PHE* 4.0 11.5 - - + -
713K ILE* 3.9 27.4 - - + -
721K VAL* 3.3 28.5 - - + -
724K LEU* 4.2 5.4 - - + -
725K ASP 3.1 14.3 + - - +
726K ASP 3.1 6.0 + - - +
728K GLN* 1.3 75.0 - - - +
730K LEU* 1.3 62.7 + - - +
732K GLN* 3.2 9.8 + - + +
733K CYS* 3.0 20.4 + - - +
754K VAL* 4.1 20.2 - - + -
756K ARG* 3.6 18.2 - - - +
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Residues in contact with LEU 730 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662K ILE* 3.9 13.2 - - + +
664K LEU* 3.4 33.9 - - + -
726K ASP 2.9 12.4 + - - +
727K LYS* 3.4 11.2 - - - +
729K VAL* 1.3 77.9 - - - +
731K GLN* 1.3 59.0 + - + +
733K CYS* 3.2 0.9 + - - +
734K MET* 2.9 34.6 + - + +
749K PRO* 3.9 22.2 - - + -
752K TYR* 3.6 38.1 - - + -
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Residues in contact with GLN 731 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727K LYS* 2.8 58.5 + - + +
728K GLN* 3.5 13.4 - - - +
729K VAL 3.2 0.4 - - - -
730K LEU* 1.3 81.1 - - + +
732K GLN* 1.3 58.1 + - + +
734K MET* 3.5 6.3 + - - +
735K ALA* 2.9 28.4 + - - +
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Residues in contact with GLN 732 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690K LYS* 4.9 6.5 + - - +
693K LEU* 3.5 25.3 - - + +
694K PHE* 4.0 9.1 - - + -
720K SER* 5.6 1.4 + - - -
721K VAL* 5.4 2.4 - - - +
724K LEU* 3.3 34.7 - - - +
728K GLN* 3.1 14.3 + - - +
729K VAL* 3.2 8.2 + - - +
731K GLN* 1.3 75.4 - - + +
733K CYS* 1.3 60.6 - - - +
735K ALA* 3.7 7.1 - - - +
736K THR* 2.8 31.7 + - - -
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Residues in contact with CYS 733 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662K ILE* 3.9 11.4 - - + -
664K LEU* 3.9 26.9 - - + -
694K PHE* 3.5 34.7 - - + -
697K PHE* 3.8 30.5 - - - -
729K VAL 3.0 9.0 + - - +
730K LEU 3.2 7.6 + - - +
732K GLN* 1.3 76.2 - - - +
734K MET* 1.3 60.4 + - - +
736K THR* 3.2 4.3 + - - -
737K LEU* 2.9 28.0 + - - +
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Residues in contact with MET 734 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664K LEU* 3.8 18.8 - - - -
666K PHE* 3.8 9.4 - - + -
730K LEU* 2.9 33.6 + - + +
731K GLN* 3.9 5.2 - - - +
733K CYS* 1.3 72.7 - - - +
735K ALA* 1.3 61.9 + - - +
737K LEU* 3.3 7.7 + - + +
738K ARG* 3.0 65.4 + - - +
746K VAL* 3.9 13.9 - - + -
747K PRO 3.5 24.7 - - - +
749K PRO* 3.6 24.9 - - + -
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Residues in contact with ALA 735 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731K GLN 2.9 18.6 + - - +
732K GLN* 3.7 9.0 - - - +
733K CYS 3.3 0.2 - - - -
734K MET* 1.3 76.0 - - - +
736K THR* 1.3 63.1 + - - +
738K ARG* 3.5 6.7 + - - +
739K GLU* 3.1 27.5 + - - +
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Residues in contact with THR 736 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470K GLU* 4.9 4.3 + - - +
683K HIS* 3.5 28.8 - - + +
693K LEU* 5.0 4.2 + - - +
694K PHE* 3.9 13.3 - - + -
697K PHE* 4.2 12.1 - - + -
732K GLN 2.8 18.0 + - - -
733K CYS* 3.3 12.3 - - - -
735K ALA* 1.3 73.9 - - - +
737K LEU* 1.3 60.5 + - - +
739K GLU* 3.1 9.5 + - - +
740K LEU* 2.9 46.4 + - + +
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Residues in contact with LEU 737 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664K LEU* 4.4 8.1 - - + -
666K PHE* 3.9 26.9 - - + -
670K PHE* 4.3 6.7 - - + -
681K PHE* 4.4 3.1 - - + -
697K PHE* 3.6 41.1 - - + -
709K LEU* 4.2 11.7 - - + -
733K CYS* 2.9 18.1 + - - +
734K MET* 3.3 15.0 + - - +
736K THR* 1.3 76.0 - - - +
738K ARG* 1.3 58.4 + - - +
740K LEU* 3.1 4.2 + - + +
741K PHE* 2.8 60.2 + - + +
746K VAL* 4.6 12.1 - - + -
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Residues in contact with ARG 738 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734K MET* 3.0 46.7 + - - +
735K ALA* 3.9 6.5 - - - +
736K THR 3.3 0.2 - - - -
737K LEU* 1.3 76.1 - - - +
739K GLU* 1.3 61.0 + - - +
741K PHE 3.5 1.6 - - - +
742K LYS* 3.2 27.9 + - - +
744K GLN 5.4 0.2 - - - +
746K VAL* 2.8 50.7 + - + +
747K PRO 3.7 6.5 + - - -
748K ASP* 3.0 26.5 + - - -
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Residues in contact with GLU 739 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470K GLU* 3.8 32.0 - - + +
471K GLY* 2.7 42.9 + - - -
735K ALA 3.1 17.1 + - - +
736K THR* 3.1 10.0 + - - +
737K LEU 3.1 0.4 - - - -
738K ARG* 1.3 76.9 - - - +
740K LEU* 1.3 62.5 + - - +
741K PHE 3.2 0.9 + - - -
742K LYS* 3.3 33.6 + - - +
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Residues in contact with LEU 740 (chain K).
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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468K ILE* 3.5 40.0 - - + +
469K GLN 3.7 16.6 - - - +
470K GLU* 3.8 6.3 - - + +
472K GLY* 3.4 6.2 - - - -
674K LYS* 2.9 22.2 + - - +
681K PHE* 4.9 5.4 - - + -
682K GLY 5.0 0.2 - - - +
683K HIS* 3.8 26.0 - - + -
697K PHE* 4.0 17.0 - - + -
736K THR* 2.9 43.0 + - + +
737K LEU* 3.7 7.0 - - + +
739K GLU* 1.3 76.7 - - - +
741K PHE* 1.3 73.5 + - + +
742K LYS 3.5 0.2 - - - -
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Residues in contact with PHE 741 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468K ILE* 5.0 1.8 - - + -
670K PHE* 4.0 15.5 - + - -
671K TRP* 3.6 35.7 - - + -
674K LYS* 3.9 35.0 - - + +
675K VAL* 4.1 6.5 - - + -
681K PHE* 3.8 33.0 - + - -
737K LEU* 2.8 30.9 + - + +
738K ARG* 3.5 6.1 - - - +
740K LEU* 1.3 84.6 - - + +
742K LYS* 1.3 62.8 + - - +
743K GLU 3.3 3.1 - - - -
744K GLN* 3.0 51.0 + - + +
746K VAL* 4.0 9.9 - - + +
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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