Contacts of the helix formed by residues 736 - 746 (chain K) in PDB entry 6D6Q
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 LEU 736 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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709K ARG* 5.7 5.2 - - + +
711K LEU* 5.5 7.6 - - + -
728K ALA* 3.5 28.5 - - + +
729K GLU* 4.8 0.7 - - - -
730K SER* 3.8 16.6 - - - +
733K PHE* 3.0 44.7 + - + +
734K PRO 3.3 2.6 + - - -
735K TYR* 1.3 75.3 - - - +
737K ASN* 1.3 76.2 + - - +
738K THR* 3.0 2.2 - - - +
739K LEU* 2.8 18.5 + - - +
740K LEU* 3.2 36.7 - - + +
904K PHE* 4.0 18.4 - - + -
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Residues in contact with ASN 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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725K LEU* 2.9 30.8 + - + +
726K ASP* 4.9 1.5 - - - -
728K ALA* 3.6 7.7 - - - +
729K GLU* 3.2 49.7 - - - +
733K PHE 5.7 0.2 - - - +
734K PRO 4.9 5.1 + - - +
736K LEU* 1.3 79.3 - - - +
738K THR* 1.3 64.5 + - + +
740K LEU* 3.2 7.3 + - - +
741K ARG* 2.9 41.6 + - - +
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Residues in contact with THR 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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633K SER* 5.4 9.0 - - - +
735K TYR* 3.1 43.1 - - + -
736K LEU 5.4 0.9 - - - +
737K ASN* 1.3 80.6 - - + +
739K LEU* 1.3 70.2 + - - +
741K ARG* 3.1 16.3 + - - +
742K ILE* 2.8 36.5 + - - +
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Residues in contact with LEU 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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735K TYR* 2.8 56.1 - - + +
736K LEU* 2.8 13.8 + - - +
738K THR* 1.3 79.5 + - - +
740K LEU* 1.3 55.8 + - - +
742K ILE* 3.2 9.9 + - + +
743K LEU* 2.8 34.1 + - - +
851K TYR* 4.4 18.4 - - + -
852K ILE 4.0 5.4 - - - +
853K LEU* 3.9 21.0 - - + +
863K LEU* 5.8 5.2 - - + -
904K PHE* 3.3 42.6 - - + -
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Residues in contact with LEU 740 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702K LEU* 3.2 20.6 - - + +
705K ALA* 6.4 1.1 - - + -
706K ALA* 4.2 13.7 - - + +
711K LEU* 5.6 0.4 - - + -
713K ILE* 3.9 27.4 - - + -
725K LEU* 3.5 23.5 - - + +
728K ALA* 4.3 14.4 - - + -
736K LEU* 3.2 37.0 - - + +
737K ASN* 3.2 5.1 + - - +
739K LEU* 1.3 75.3 - - - +
741K ARG* 1.3 58.1 + - - +
743K LEU* 4.1 8.5 - - + -
744K ALA* 2.9 27.2 + - - +
904K PHE* 3.4 24.2 - - + -
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Residues in contact with ARG 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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631K THR* 2.7 49.0 + - - +
632K LEU* 4.0 24.1 - - + +
633K SER* 4.1 21.8 - - - +
725K LEU* 4.7 26.7 + - + +
726K ASP* 3.2 25.5 + - - -
737K ASN* 2.9 32.0 + - - +
738K THR* 3.1 16.8 + - - +
740K LEU* 1.3 77.6 - - - +
742K ILE* 1.3 56.7 + - - +
744K ALA* 3.3 5.7 + - - +
745K THR* 2.9 32.0 + - - -
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Residues in contact with ILE 742 (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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633K SER* 3.9 17.0 - - - +
634K SER* 4.0 7.2 - - - +
635K PRO* 3.9 22.4 - - + -
735K TYR* 5.2 5.6 - - - +
738K THR* 2.8 41.5 + - - +
739K LEU* 3.6 8.7 - - + +
741K ARG* 1.3 70.9 - - - +
743K LEU* 1.3 56.8 + - - +
744K ALA 2.9 4.7 - - - -
745K THR* 2.8 27.6 + - - -
746K ARG* 2.9 48.7 + - + +
853K LEU* 4.2 19.1 - - + -
863K LEU* 5.1 9.9 - - + -
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Residues in contact with LEU 743 (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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701K ILE* 5.8 3.1 - - + -
702K LEU* 3.7 22.4 - - + +
705K ALA* 4.8 12.8 - - + -
739K LEU 2.8 26.0 + - - +
740K LEU* 3.6 10.5 - - + +
742K ILE* 1.3 72.8 - - + +
744K ALA* 1.3 58.9 + - - +
746K ARG* 3.8 10.7 - - - +
747K CYS* 3.5 18.5 - - - -
853K LEU* 4.0 40.2 - - + +
854K PHE* 4.0 24.8 - - + -
904K PHE* 3.8 30.5 - - + -
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Residues in contact with ALA 744 (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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632K LEU* 4.6 4.3 - - + -
699K TYR* 5.3 3.1 - - + -
702K LEU* 3.5 11.9 - - + +
721K LEU* 5.1 15.7 - - + -
725K LEU* 5.9 3.1 - - + -
740K LEU 2.9 16.6 + - - +
741K ARG* 3.5 7.9 - - - +
743K LEU* 1.3 74.1 - - - +
745K THR* 1.3 52.2 + - - +
746K ARG 3.0 4.5 - - - -
747K CYS* 2.6 34.6 + - - +
748K MET* 2.8 29.9 - - + +
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Residues in contact with THR 745 (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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632K LEU* 3.3 23.0 - - - +
633K SER 3.9 6.7 + - - +
634K SER* 5.3 4.0 - - - +
741K ARG 2.9 15.0 + - - -
742K ILE* 2.8 15.5 + - - -
744K ALA* 1.3 72.3 - - - +
746K ARG* 1.3 63.2 + - - +
747K CYS 3.1 2.1 + - - -
748K MET* 3.5 21.8 + - - +
57O A 3.8 26.6 + - - +
58O A 3.1 36.5 - - + +
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Residues in contact with ARG 746 (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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634K SER* 4.7 11.1 + - - -
635K PRO* 4.5 10.5 - - - +
742K ILE* 2.9 47.0 + - + +
743K LEU* 3.8 13.5 - - - +
744K ALA 2.9 0.6 + - - -
745K THR* 1.3 80.0 - - - +
747K CYS* 1.3 59.6 + - - +
748K MET 5.0 1.5 - - - +
853K LEU* 4.9 4.9 - - - +
854K PHE* 4.4 27.1 - - + -
863K LEU* 5.5 0.2 - - - +
870K GLU* 3.9 33.0 + - - +
56O A 3.9 22.2 + - - +
57O A 2.6 49.1 + - - +
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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