Contacts of the helix formed by residues 744 - 763 (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 SER 744 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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738D GLU* 2.7 31.3 + - - -
742D ILE 3.5 0.2 - - - -
743D ALA* 1.3 77.9 - - - +
745D SER* 1.3 59.7 + - - +
746D THR* 4.1 6.0 + - - -
747D ALA* 3.0 19.1 + - - +
748D HIS* 2.7 32.9 + - - +
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Residues in contact with SER 745 (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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743D ALA 3.4 3.8 + - - -
744D SER* 1.3 73.3 - - - +
746D THR* 1.3 65.9 + - - +
748D HIS* 4.0 4.8 + - - +
749D GLN* 3.2 40.4 + - - +
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Residues in contact with THR 746 (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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724C VAL* 3.6 24.1 - - - +
725C ASP* 3.6 37.5 + - + +
744D SER* 4.1 6.4 + - - -
745D SER* 1.3 79.3 - - - +
747D ALA* 1.3 62.4 + - - +
749D GLN* 3.3 11.8 + - - +
750D HIS* 2.9 28.1 + - - +
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Residues in contact with ALA 747 (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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724C VAL* 3.6 15.5 - - + +
735D TYR* 4.3 8.2 - - + -
738D GLU* 3.6 26.9 - - + +
742D ILE* 3.9 10.3 - - + -
744D SER* 3.0 21.5 + - - +
746D THR* 1.3 81.9 + - - +
748D HIS* 1.3 56.7 + - - +
750D HIS* 3.1 1.8 + - - +
751D ILE* 2.8 34.3 + - - +
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Residues in contact with HIS 748 (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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48D TYR* 3.2 31.6 + + - -
49D LEU* 4.2 11.4 + - + +
629D TRP* 6.0 1.8 - + - -
741D GLY 6.0 0.7 - - - -
742D ILE 3.8 15.8 + - - +
743D ALA* 4.2 10.3 - - - +
744D SER 2.7 22.5 + - - +
745D SER* 4.0 4.6 + - - +
747D ALA* 1.3 73.9 - - - +
749D GLN* 1.3 66.9 + - - +
751D ILE* 3.3 8.3 - - + +
752D TYR* 3.2 61.9 + + - -
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Residues in contact with GLN 749 (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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49D LEU* 3.7 40.5 - - + +
50D LYS* 2.8 41.2 + - - +
745D SER* 3.2 34.5 + - - +
746D THR* 3.8 9.7 - - - +
747D ALA 3.3 0.2 - - - -
748D HIS* 1.3 81.2 - - - +
750D HIS* 1.3 54.4 + - - +
753D THR* 2.7 38.3 + - - +
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Residues in contact with HIS 750 (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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723C LEU 4.5 0.2 - - - -
724C VAL* 3.8 29.8 - - + +
727C GLY* 4.8 5.6 - - - -
728C VAL 2.9 34.4 + - - -
729C ASP* 3.8 22.0 - - + +
730C PHE* 3.5 25.9 - + - -
733D MET* 4.6 7.2 - - + -
735D TYR* 2.5 31.9 + + + +
746D THR 2.9 18.7 + - - +
747D ALA 3.1 4.0 + - - +
749D GLN* 1.3 75.2 - - - +
751D ILE* 1.3 59.3 + - - +
753D THR* 3.5 6.2 + - - -
754D HIS* 2.9 27.2 + - - +
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Residues in contact with ILE 751 (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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629D TRP* 4.0 12.3 - - + -
653D VAL* 3.8 22.4 - - + -
703D ILE* 3.6 37.0 - - + -
735D TYR* 3.0 23.4 + - + +
742D ILE* 3.9 17.9 - - + +
747D ALA 2.8 16.2 + - - +
748D HIS* 3.3 17.9 - - - +
750D HIS* 1.3 75.7 - - - +
752D TYR* 1.3 75.8 + - + +
754D HIS* 3.2 2.6 + - - +
755D MET* 2.8 39.3 + - + +
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Residues in contact with TYR 752 (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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45D LEU* 4.5 3.4 - - + -
48D TYR* 3.6 17.7 + + + -
49D LEU* 4.0 14.8 - - + -
563D TRP* 3.4 45.8 + + + +
627D TRP* 4.2 10.5 - + - -
629D TRP* 3.9 19.6 - + - -
748D HIS* 3.2 54.5 + + - +
750D HIS 3.4 0.2 - - - -
751D ILE* 1.3 86.8 - - + +
753D THR* 1.3 58.5 + - - +
755D MET* 3.3 24.7 - - + -
756D SER* 2.7 38.4 + - - -
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Residues in contact with THR 753 (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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729C ASP* 5.0 10.3 - - + -
45D LEU* 4.1 15.7 - - + +
49D LEU* 3.5 14.9 - - - +
749D GLN* 2.7 24.9 + - - +
750D HIS* 3.7 7.0 - - - -
752D TYR* 1.3 77.4 - - - +
754D HIS* 1.3 62.2 + - - +
756D SER* 3.4 2.3 + - - -
757D HIS* 3.3 43.3 + - + +
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Residues in contact with HIS 754 (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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729C ASP* 2.6 30.0 + - - +
730C PHE 3.1 25.1 - - - -
731C GLN* 3.5 20.4 + - - -
701D LEU* 4.5 23.3 - - + +
703D ILE* 4.8 3.4 - - + -
731D GLN* 6.0 1.0 - - - +
732D ALA 4.7 1.6 + - - -
733D MET* 3.5 33.2 - - + +
735D TYR* 4.2 7.9 - - - +
750D HIS* 2.9 19.3 + + - +
751D ILE* 3.2 5.1 + - - +
753D THR* 1.3 77.0 - - - +
755D MET* 1.3 62.3 + - + +
757D HIS* 3.2 7.0 + - + +
758D PHE* 3.1 21.1 + - + +
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Residues in contact with MET 755 (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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563D TRP* 4.0 12.8 - - + -
627D TRP* 4.1 17.5 - - + -
629D TRP* 5.1 1.1 - - + -
651D ILE* 3.8 37.2 - - + -
653D VAL* 3.9 16.4 - - + -
701D LEU* 4.5 1.6 - - + -
703D ILE* 3.9 18.2 - - + -
751D ILE* 2.8 34.2 + - + +
752D TYR* 3.3 43.5 - - + +
754D HIS* 1.3 71.0 - - - +
756D SER* 1.3 57.8 + - - +
758D PHE* 3.3 4.4 + - - +
759D ILE* 2.9 33.1 + - - +
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Residues in contact with SER 756 (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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45D LEU* 3.7 17.8 - - - +
563D TRP* 3.0 26.1 + - - -
566D TYR* 3.7 20.4 - - - -
567D LEU* 5.5 1.3 - - - -
752D TYR 2.7 22.9 + - - -
753D THR 3.7 4.9 - - - -
754D HIS 3.2 0.4 - - - -
755D MET* 1.3 76.8 - - - +
757D HIS* 1.3 60.5 + - - +
759D ILE* 3.3 2.5 + - - +
760D LYS* 2.8 39.7 + - - +
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Residues in contact with HIS 757 (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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729C ASP* 3.1 30.9 + - + +
753D THR* 3.3 28.9 + - + +
754D HIS* 3.2 8.8 + - + +
756D SER* 1.3 81.5 - - - +
758D PHE* 1.3 61.5 + - - +
760D LYS* 3.4 17.0 + - + +
761D GLN* 3.1 26.7 + - - +
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Residues in contact with PHE 758 (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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649D CYS* 4.0 20.4 - - + -
650D GLY 3.6 17.3 - - - -
651D ILE* 3.5 24.7 - - + -
699D GLU* 3.6 31.2 - - + -
700D TYR 4.6 0.4 - - - -
701D LEU* 3.8 31.4 - - + -
731D GLN* 4.1 23.3 - - + -
754D HIS* 3.1 13.4 + - + +
755D MET 3.3 6.3 + - - +
757D HIS* 1.3 78.1 - - - +
759D ILE* 1.3 63.9 + - + +
761D GLN* 3.2 24.0 + - + +
762D CYS* 3.2 22.7 + - - +
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Residues in contact with ILE 759 (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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543D LEU* 4.4 15.9 - - + -
563D TRP* 3.9 15.0 - - + -
567D LEU* 4.6 8.7 - - + -
573D ILE* 3.9 27.8 - - + -
625D ALA* 4.3 22.9 - - + -
627D TRP* 5.8 0.2 - - + -
649D CYS* 4.7 5.6 - - - -
650D GLY* 6.1 0.7 - - - -
651D ILE* 3.8 24.0 - - + -
755D MET 2.9 19.8 + - - +
756D SER* 3.9 5.8 - - - +
758D PHE* 1.3 79.8 - - + +
760D LYS* 1.3 67.7 + - + +
762D CYS* 3.2 3.6 + - - +
763D PHE* 3.1 32.5 + - + +
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Residues in contact with LYS 760 (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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566D TYR* 3.6 18.6 - - - +
567D LEU* 6.0 1.1 - - + -
571D GLU* 3.1 36.7 + - + +
756D SER* 2.8 29.7 + - - +
757D HIS* 4.0 16.6 - - + +
758D PHE 3.4 0.2 - - - -
759D ILE* 1.3 75.3 - - + +
761D GLN* 1.3 58.7 + - - +
764D SER 3.3 1.7 + - - -
765D LEU* 2.7 51.0 + - + +
766D PRO* 3.0 27.4 + - - -
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Residues in contact with GLN 761 (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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699D GLU* 3.1 27.0 + - - +
757D HIS 3.1 17.5 + - - +
758D PHE* 3.2 30.6 + - + +
760D LYS* 1.3 76.5 - - - +
762D CYS* 1.3 76.3 + - - +
764D SER* 3.2 13.9 + - - +
765D LEU 5.3 0.9 - - - -
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Residues in contact with CYS 762 (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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623D ARG* 4.8 1.9 - - - +
648D LYS* 3.1 49.6 - - - +
649D CYS* 2.0 52.7 - - + -
699D GLU* 4.7 3.4 - - - -
758D PHE* 3.2 19.4 + - + +
759D ILE 3.2 4.2 + - - +
761D GLN* 1.3 89.1 - - - +
763D PHE* 1.3 67.4 + - + +
764D SER* 3.5 3.3 + - - -
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Residues in contact with PHE 763 (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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541D PRO* 3.6 13.5 - - + -
542D LEU 3.5 21.1 - - - -
543D LEU* 4.7 2.0 - - + -
573D ILE* 3.6 47.1 - - + -
623D ARG* 2.6 74.3 + - + +
624D ILE 4.1 0.4 - - - -
625D ALA* 3.6 24.5 - - + -
649D CYS* 4.5 0.2 - - - -
759D ILE* 3.1 25.1 + - + +
762D CYS* 1.3 89.0 - - + +
764D SER* 1.3 67.0 + - - +
765D LEU* 3.1 14.7 + - + -
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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