Contacts of the helix formed by residues 768 - 784 (chain O) in PDB entry 6IY3
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 LYS 768 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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767O LEU* 1.3 80.0 - - - +
769O ASP* 1.3 69.2 + - - +
770O TYR* 3.6 28.5 + - + +
771O GLN* 3.2 24.5 + - - +
772O ILE* 3.3 21.8 + - - +
1000O GLU* 3.2 32.6 + - + -
1002O GLU* 5.7 2.7 + - - -
2000O ADP 4.1 32.9 + - + +
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Residues in contact with ASP 769 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768O LYS* 1.3 76.9 - - - +
770O TYR* 1.3 62.5 + - + +
772O ILE* 3.1 15.5 + - - +
773O LYS* 2.9 48.7 + - - +
999O VAL* 6.4 0.7 - - + -
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Residues in contact with TYR 770 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768O LYS* 3.6 25.0 - - + +
769O ASP* 1.3 75.8 - - + +
771O GLN* 1.3 77.0 + - + +
773O LYS* 3.6 15.1 - - + +
774O GLY 2.9 14.9 + - - -
796O LEU* 3.3 54.1 + - + +
801O GLN* 4.3 2.2 - - - -
994O ARG* 2.7 53.1 + - + +
999O VAL* 3.6 42.1 - - + +
1000O GLU* 3.1 26.1 + - + -
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Residues in contact with GLN 771 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767O LEU* 3.3 27.0 - - + +
768O LYS* 3.2 16.1 + - - +
769O ASP 3.2 0.6 - - - -
770O TYR* 1.3 99.3 + - + +
772O ILE* 1.3 56.4 + - - +
774O GLY* 3.4 0.9 + - - -
775O LEU* 2.9 29.5 + - - +
796O LEU 3.7 12.7 + - - +
797O GLY* 4.0 4.3 - - - -
800O ILE* 4.6 1.5 - - - +
801O GLN* 3.4 34.3 + - + +
2000O ADP 2.7 56.3 + - - -
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Residues in contact with ILE 772 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755O ILE 5.4 0.7 - - - +
756O LYS* 3.3 48.5 - - + +
757O LYS* 6.0 0.2 - - - -
758O GLN* 5.2 9.0 - - + +
766O THR* 5.6 1.8 - - - +
767O LEU* 3.8 26.5 - - + +
768O LYS 3.3 18.6 + - - +
769O ASP* 3.1 16.4 + - - +
771O GLN* 1.3 77.4 - - - +
773O LYS* 1.3 60.2 + - + +
775O LEU* 3.3 10.2 + - + +
776O GLN* 2.9 30.4 + - - +
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Residues in contact with LYS 773 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769O ASP* 2.9 35.8 + - - +
770O TYR* 3.3 15.5 + - + +
772O ILE* 1.3 80.4 - - + +
774O GLY* 1.3 56.2 + - - +
776O GLN* 3.3 17.2 + - - +
777O TRP* 2.9 27.2 + - - +
992O LEU* 5.3 1.1 - - - -
994O ARG* 4.7 2.2 - - - +
1244O LYS* 3.4 41.6 - - + +
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Residues in contact with GLY 774 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770O TYR 2.9 15.9 + - - -
771O GLN 3.9 1.1 - - - -
773O LYS* 1.3 73.4 - - - +
775O LEU* 1.3 60.6 + - - +
777O TRP* 3.2 2.5 + - - +
778O MET* 2.9 41.7 + - - +
801O GLN* 4.5 4.7 - - - -
992O LEU* 3.7 26.5 - - - -
994O ARG* 3.7 4.4 - - - +
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Residues in contact with LEU 775 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755O ILE 5.4 8.3 - - - +
756O LYS 5.5 2.2 - - - +
757O LYS 5.3 2.0 - - - +
758O GLN* 4.8 5.2 - - - -
759O PRO* 4.2 21.5 - - + -
767O LEU* 4.1 22.7 - - + -
771O GLN 2.9 17.8 + - - +
772O ILE* 3.4 9.0 - - + +
774O GLY* 1.3 75.1 - - - +
776O GLN* 1.3 55.5 + - - +
778O MET* 3.3 9.9 + - + +
779O VAL* 2.9 46.3 + - + +
801O GLN* 4.8 0.9 - - + +
804O SER* 3.4 40.4 - - - +
805O LEU* 3.9 9.4 - - + +
808O TYR* 4.7 5.8 - - + -
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Residues in contact with GLN 776 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754O ASP* 3.1 49.3 + - + +
755O ILE 4.7 15.7 + - - +
756O LYS* 5.2 13.9 - - - +
772O ILE* 2.9 12.7 + - + +
773O LYS* 3.4 22.2 - - - +
775O LEU* 1.3 76.9 - - - +
777O TRP* 1.3 57.1 + - - +
779O VAL* 3.4 7.3 + - - +
780O SER* 3.0 26.7 + - - -
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Residues in contact with TRP 777 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748O ALA* 5.9 3.2 - - - +
773O LYS 2.9 14.2 + - - +
774O GLY* 3.2 8.3 + - - +
776O GLN* 1.3 76.3 - - - +
778O MET* 1.3 70.2 + - + +
780O SER* 3.2 13.6 + - - -
781O LEU* 2.8 60.6 + - + +
789O ILE 3.2 32.5 - - - -
790O LEU* 4.5 2.5 - - + -
920O LEU* 6.2 0.4 - - + -
989O PRO* 3.3 24.2 + - - +
990O PHE 3.2 12.6 - - - -
991O LEU 3.2 19.3 - - - -
992O LEU* 3.5 34.5 - - + -
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Residues in contact with MET 778 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774O GLY* 2.9 28.7 + - - +
775O LEU* 3.3 8.3 + - + +
777O TRP* 1.3 90.5 - - + +
779O VAL* 1.3 61.3 + - - +
781O LEU* 3.2 17.3 + - + +
782O PHE* 3.0 26.5 + - - +
790O LEU* 4.8 17.0 - - + -
801O GLN* 3.7 49.1 - - + +
802O THR* 5.7 1.8 - - - -
805O LEU* 3.6 37.9 - - + +
920O LEU* 4.3 11.7 - - - -
922O LEU* 5.7 1.6 - - - -
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Residues in contact with VAL 779 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753O GLU 4.6 7.6 - - - +
754O ASP* 5.5 0.7 - - - -
755O ILE* 5.4 11.7 - - + +
775O LEU* 2.9 32.2 + - + +
776O GLN* 3.7 7.4 - - - +
778O MET* 1.3 77.2 - - - +
780O SER* 1.3 56.2 + - - +
782O PHE* 3.2 6.9 + - - +
783O ASN* 2.9 48.6 + - - +
805O LEU* 6.2 2.7 - - + -
808O TYR* 3.6 56.3 - - + +
813O LYS* 4.8 0.7 - - - -
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Residues in contact with SER 780 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748O ALA 3.7 5.4 + - - -
749O HIS* 6.0 1.0 - - - -
751O ILE* 4.8 6.8 + - - +
753O GLU 4.9 2.2 - - - -
754O ASP* 4.6 10.3 - - - -
776O GLN 3.0 15.3 + - - -
777O TRP* 3.2 18.8 + - - -
779O VAL* 1.3 78.1 - - - +
781O LEU* 1.3 49.7 + - - +
783O ASN* 3.6 9.2 - - - +
784O ASN* 2.8 59.3 + - - -
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Residues in contact with LEU 781 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748O ALA* 6.3 2.0 - - + -
777O TRP* 2.8 66.9 + - + +
778O MET* 3.2 21.7 + - + +
780O SER* 1.3 77.4 - - - +
782O PHE* 1.3 57.6 + - - +
784O ASN* 3.4 6.4 + - - +
785O HIS 3.0 21.3 + - - -
786O LEU* 3.2 34.5 + - + +
788O GLY* 3.7 29.6 - - - +
920O LEU* 4.9 8.7 - - + -
989O PRO 4.7 4.3 - - - +
990O PHE* 5.0 2.2 - - + +
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Residues in contact with PHE 782 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778O MET 3.0 12.8 + - - +
779O VAL* 3.2 8.7 + - - +
781O LEU* 1.3 76.3 - - - +
783O ASN* 1.3 63.0 + - - +
785O HIS* 3.2 30.2 + + - +
786O LEU 5.3 0.9 - - - -
805O LEU* 6.1 3.6 - - + -
808O TYR* 6.4 0.4 - - + -
809O LEU* 3.6 33.0 - - + -
813O LYS* 3.6 43.3 - - + -
815O ILE* 5.2 10.8 - - + -
889O VAL* 5.8 4.3 - - + -
890O HIS* 5.0 7.4 - + + -
918O TYR* 3.5 40.8 - + - -
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Residues in contact with ASN 783 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750O ARG* 3.8 2.3 + - - -
751O ILE* 3.8 24.9 - - + +
753O GLU* 3.0 40.2 + - - +
779O VAL* 2.9 42.3 + - - +
780O SER* 3.7 6.0 - - - +
781O LEU 3.3 0.2 - - - -
782O PHE* 1.3 79.1 - - - +
784O ASN* 1.3 56.6 + - - +
785O HIS* 3.1 22.8 + - - -
808O TYR* 5.4 0.2 + - - -
813O LYS* 2.5 31.2 + - - +
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Residues in contact with ASN 784 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683O LEU* 3.8 2.4 - - - +
747O VAL 3.4 15.5 - - - +
748O ALA* 2.5 37.4 + - - +
750O ARG* 2.8 39.6 + - - +
751O ILE* 3.4 19.8 + - - +
780O SER* 2.8 38.0 + - - +
781O LEU* 3.9 7.9 - - - +
782O PHE 3.3 0.2 - - - -
783O ASN* 1.3 70.3 - - - +
785O HIS* 1.3 64.3 - - - +
786O LEU* 3.2 17.1 + - + +
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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