Contacts of the helix formed by residues 669 - 689 (chain A) in PDB entry 2YD0
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 GLU 669 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633A SER* 3.5 26.4 + - - +
636A ARG* 3.9 6.3 - - - +
667A GLU* 2.9 16.3 + - - +
668A THR* 1.3 108.5 + - - +
670A ILE* 1.3 68.6 + - - +
671A MET 3.2 1.1 + - - +
672A PRO* 3.2 10.6 - - + +
673A VAL* 3.1 22.9 + - - +
727A LEU* 4.9 0.2 - - - -
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Residues in contact with ILE 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ASP* 5.4 7.2 - - + +
399A TYR* 4.2 21.5 - - + -
668A THR 4.2 0.8 + - - -
669A GLU* 1.3 74.1 + - - +
671A MET* 1.3 67.6 + - + +
673A VAL 3.5 0.2 + - - -
674A PHE* 2.8 68.1 + - + +
723A SER* 3.2 47.7 + - - +
726A MET* 3.9 18.6 - - + -
727A LEU* 3.9 18.5 - - + +
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Residues in contact with MET 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ASP* 3.4 24.9 - - + +
399A TYR* 3.7 37.7 - - + +
401A PHE* 5.1 5.2 - - + -
402A GLY* 4.8 12.3 - - - -
405A PHE* 6.4 0.7 - - + -
633A SER* 5.1 2.7 - - - -
634A ASN* 3.8 17.7 - - - +
637A ALA* 4.2 14.1 - - + -
669A GLU* 4.8 0.2 - - - +
670A ILE* 1.3 95.8 - - + +
672A PRO* 1.4 67.1 - - + +
674A PHE* 3.5 14.1 + - + +
675A GLN* 2.8 30.8 + - + +
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Residues in contact with PRO 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A SER* 3.7 25.1 - - - +
636A ARG* 4.2 3.4 - - + +
637A ALA* 4.0 15.0 - - + +
640A ILE* 3.6 4.5 - - + +
663A TYR* 3.4 22.2 - - - +
664A LEU* 3.5 11.4 - - - +
667A GLU* 3.3 23.6 - - - +
669A GLU* 3.2 23.3 - - + +
671A MET* 1.4 91.4 - - + +
673A VAL* 1.3 62.2 + - - -
675A GLN* 4.2 1.6 - - + -
676A GLY 3.0 19.1 + - - -
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Residues in contact with VAL 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A LEU* 4.2 7.8 - - + +
667A GLU* 3.7 20.6 - - + -
668A THR 4.6 0.2 - - - -
669A GLU 3.1 21.7 + - - +
670A ILE 4.0 2.2 - - - +
672A PRO* 1.3 76.5 - - - +
674A PHE* 1.3 65.9 + - - +
676A GLY* 3.4 1.6 + - - -
677A LEU* 3.1 28.1 + - + +
707A LEU* 4.3 28.7 - - + +
710A LEU* 3.6 25.4 - - + -
727A LEU* 4.1 19.5 - - + -
731A LEU* 4.5 6.1 - - + -
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Residues in contact with PHE 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670A ILE* 2.8 44.6 + - + +
671A MET* 3.8 15.3 - - + +
673A VAL* 1.3 79.1 - - - +
675A GLN* 1.3 56.4 + - - +
677A LEU* 3.2 17.1 + - + +
678A ASN* 2.8 38.6 + - - +
726A MET* 3.9 17.5 - - + -
727A LEU* 3.6 26.2 - - + -
730A GLN* 3.6 37.2 - - + -
731A LEU* 6.0 0.2 - - + -
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Residues in contact with GLN 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A GLY* 5.3 3.5 - - - -
405A PHE* 3.2 28.0 - - - +
637A ALA* 3.4 34.8 - - + +
640A ILE* 4.4 4.0 - - + -
641A ASN* 3.6 16.8 - - + +
671A MET* 2.8 20.7 + - - +
672A PRO* 3.8 4.3 - - + +
673A VAL 3.2 0.4 - - - -
674A PHE* 1.3 74.5 - - - +
676A GLY* 1.3 67.4 + - - +
678A ASN* 3.1 20.8 + - - +
679A GLU* 2.7 57.3 + - - +
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Residues in contact with GLY 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640A ILE* 4.0 16.8 - - - +
664A LEU* 4.1 17.9 - - - -
672A PRO 3.0 14.1 + - - -
673A VAL 3.8 3.4 - - - -
675A GLN* 1.3 75.8 - - - +
677A LEU* 1.3 56.6 + - - +
679A GLU* 3.0 4.0 + - - +
680A LEU* 2.9 39.8 + - - +
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Residues in contact with LEU 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673A VAL* 3.1 25.5 + - + +
674A PHE* 3.5 26.0 - - + +
675A GLN 3.1 0.6 - - - -
676A GLY* 1.3 71.9 - - - +
678A ASN* 1.3 66.3 + - - +
680A LEU* 4.4 1.6 - - - +
681A ILE* 2.9 57.9 + - + +
703A LEU* 4.1 17.3 - - + -
707A LEU* 3.7 26.2 - - + -
730A GLN* 5.4 11.0 - - + +
731A LEU* 5.2 4.7 - - + -
734A LEU* 4.1 22.0 - - + -
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Residues in contact with ASN 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A ASP* 5.3 6.9 + - - -
674A PHE* 2.8 24.2 + - - +
675A GLN* 3.1 29.2 + - - +
677A LEU* 1.3 78.1 - - - +
679A GLU* 1.3 59.9 + - - +
681A ILE* 5.7 0.4 - - - +
682A PRO* 3.0 25.0 - - - +
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Residues in contact with GLU 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640A ILE* 4.2 8.7 - - + -
641A ASN* 2.9 26.3 + - - -
644A PHE* 3.6 43.6 - - + +
645A GLN* 5.3 2.3 + - - +
675A GLN* 2.7 41.5 + - - +
676A GLY 3.0 6.0 + - - +
678A ASN* 1.3 81.3 - - - +
680A LEU* 1.3 59.3 + - + +
682A PRO* 4.0 6.0 - - - +
683A MET* 3.1 27.4 - - - +
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Residues in contact with LEU 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A PHE* 4.2 13.5 - - + -
658A LEU* 4.0 27.1 - - + -
661A SER* 4.1 13.2 - - - +
664A LEU* 4.9 2.0 - - + -
676A GLY* 2.9 23.9 + - - +
677A LEU* 4.3 1.1 - - - +
679A GLU* 1.3 79.5 - - + +
681A ILE* 1.3 68.1 + - - +
682A PRO 3.2 2.0 - - - -
683A MET* 3.1 17.0 + - + +
684A TYR* 4.7 0.7 - - - -
699A PHE* 3.4 36.8 - - + -
702A PHE* 4.7 7.9 - - + -
703A LEU* 4.0 29.6 - - + -
706A LEU* 4.2 16.2 - - + -
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Residues in contact with ILE 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A LEU* 2.9 48.0 + - + +
678A ASN* 5.7 0.4 - - - +
680A LEU* 1.3 71.4 - - - +
682A PRO* 1.3 71.1 - - + +
684A TYR* 3.1 44.4 + - + +
685A LYS* 3.0 24.1 + - + +
703A LEU* 4.3 9.2 - - + -
734A LEU* 4.3 11.2 - - + -
841A ARG* 3.5 28.7 - - - +
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Residues in contact with PRO 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A LEU 3.7 0.4 - - - +
678A ASN* 3.0 28.9 - - - +
679A GLU* 4.2 6.5 - - - +
680A LEU 3.5 1.8 - - - -
681A ILE* 1.3 99.1 - - + +
683A MET* 1.3 61.6 + - + +
685A LYS* 3.5 11.7 - - + +
686A LEU* 3.2 27.6 + - + +
881A GLN* 5.6 3.4 - - + +
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Residues in contact with MET 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A PHE* 3.7 33.4 - - + -
654A ILE* 4.6 3.8 - - + -
658A LEU* 4.8 6.1 - - - -
679A GLU 3.1 22.4 - - - +
680A LEU* 3.1 16.3 + - + +
682A PRO* 1.3 78.2 - - + +
684A TYR* 1.3 63.2 + - - +
686A LEU* 3.3 14.6 + - - +
687A MET* 3.4 23.5 + - + +
699A PHE* 3.7 30.1 - - + -
921A TRP* 3.7 43.5 - - + -
922A MET* 5.0 1.2 - - - +
929A ILE* 4.9 2.7 - - - -
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Residues in contact with TYR 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680A LEU 3.6 4.9 + - - -
681A ILE* 3.1 55.6 + - + +
683A MET* 1.3 77.1 - - - +
685A LYS* 1.3 83.5 + - - +
687A MET* 3.5 12.3 - - - +
688A GLU* 2.9 42.5 + - - +
696A GLU* 4.8 3.1 - - + +
699A PHE* 3.8 24.4 - + + -
700A LYS* 3.2 34.3 - - + -
703A LEU* 3.7 17.0 - - + -
734A LEU* 4.3 1.7 - - - +
737A VAL* 5.7 0.5 - - - +
738A HIS* 3.1 28.4 + + - -
841A ARG* 5.4 0.2 + - - -
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Residues in contact with LYS 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681A ILE* 3.0 27.6 + - + +
682A PRO* 3.5 12.8 - - + +
684A TYR* 1.3 95.7 - - + +
686A LEU* 1.3 64.5 + - - +
688A GLU* 2.6 40.2 + - - +
689A LYS* 3.6 18.1 + - - +
807A ARG* 4.6 11.4 - - - +
841A ARG* 2.7 51.1 + - + +
843A PRO* 4.5 2.8 - - - +
881A GLN* 3.8 38.6 - - + +
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Residues in contact with LEU 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682A PRO 3.2 16.4 + - - +
683A MET* 3.7 7.2 - - - +
684A TYR 3.3 0.2 - - - -
685A LYS* 1.3 74.3 - - - +
687A MET* 1.3 62.0 + - - +
689A LYS* 3.3 15.1 + - - +
690A ARG* 3.6 14.0 - - - +
880A ASN 4.6 0.4 - - - +
881A GLN* 3.3 32.7 - - + +
882A PHE 4.6 0.2 - - - +
883A SER* 4.3 6.8 - - - +
918A ASN* 3.6 46.4 - - + +
921A TRP* 4.3 17.0 - - + -
922A MET* 3.9 27.1 - - + -
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Residues in contact with MET 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683A MET* 3.5 23.6 - - + +
684A TYR* 3.5 12.6 - - - +
686A LEU* 1.3 74.2 - - - +
688A GLU* 1.3 57.3 + - - +
690A ARG* 2.8 33.4 + - - +
692A MET* 4.0 22.7 - - + +
695A VAL* 4.0 21.3 - - + +
696A GLU* 3.8 40.8 - - + +
699A PHE* 4.2 21.3 - - + -
921A TRP* 5.7 0.4 - - + -
922A MET* 3.7 16.8 - - + +
926A PHE* 4.7 7.6 - - + -
929A ILE* 4.5 16.6 - - + -
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Residues in contact with GLU 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684A TYR* 2.9 30.0 + - - +
685A LYS* 2.6 39.8 + - - +
687A MET* 1.3 75.0 - - - +
689A LYS* 1.3 63.6 + - + +
690A ARG 3.5 6.8 + - - +
696A GLU* 3.5 16.0 + - - +
700A LYS* 2.6 37.4 + - - +
738A HIS* 5.3 0.5 - - - -
841A ARG 4.1 0.7 - - - +
843A PRO* 3.7 35.1 - - + +
846A TYR* 4.2 10.0 + - - -
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Residues in contact with LYS 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A LYS* 3.6 23.2 + - - +
686A LEU 3.3 5.4 + - - +
687A MET 3.0 1.6 + - - -
688A GLU* 1.3 78.7 + - - +
690A ARG* 1.3 64.5 + - + +
840A GLY 3.8 21.0 + - - -
841A ARG 4.7 5.5 + - - -
842A ASN 6.0 0.4 - - - -
843A PRO* 6.0 0.8 - - - +
846A TYR* 3.4 57.5 + - + -
881A GLN* 2.8 59.4 + - - +
882A PHE* 4.6 15.2 - - + -
883A SER* 6.0 0.7 - - - -
884A THR* 5.8 0.3 - - - +
887A ARG* 5.8 2.6 + - - -
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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
------------------------------------------------------------
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