Contacts of the helix formed by residues 719 - 736 (chain A) in PDB entry 2Y48
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 719 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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718A ILE* 1.3 79.6 - - - +
720A ASP* 1.3 64.2 + - - +
721A ASP* 3.4 10.8 + - - +
722A VAL* 3.1 29.1 + - - +
723A ILE* 3.2 17.0 + - - +
750A ARG* 4.4 2.7 - - - +
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Residues in contact with ASP 720 (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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718A ILE 3.7 0.2 + - - -
719A SER* 1.3 72.4 - - - +
721A ASP* 1.3 60.4 + - - +
723A ILE* 3.3 7.2 + - - +
724A VAL* 2.9 38.1 + - + +
746A THR* 5.5 4.0 - - - +
747A VAL* 6.1 0.4 - - - -
748A VAL* 3.3 25.9 + - + +
750A ARG* 3.1 33.7 + - - +
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Residues in contact with ASP 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A SER* 3.2 9.2 + - - +
720A ASP* 1.3 75.3 - - - +
722A VAL* 1.3 56.6 + - + +
723A ILE 3.1 0.3 + - - -
724A VAL* 3.1 7.4 + - - +
725A GLY* 2.7 33.6 + - - -
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Residues in contact with VAL 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A ILE* 3.8 21.3 - - + -
719A SER* 3.1 18.7 + - - +
721A ASP* 1.3 74.9 - - + +
723A ILE* 1.3 62.3 + - - +
725A GLY* 3.1 3.5 + - - -
726A ARG* 3.1 51.0 + - + +
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Residues in contact with ILE 723 (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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662A VAL* 3.7 32.3 - - + -
691A LEU* 4.4 5.3 - - + +
707A VAL* 5.7 0.7 - - + -
715A MET* 3.5 46.2 - - + +
718A ILE* 3.5 32.5 - - + +
719A SER 3.2 5.0 + - - +
720A ASP* 3.6 7.4 - - - +
721A ASP 3.1 1.0 - - - -
722A VAL* 1.3 75.9 - - - +
724A VAL* 1.3 64.2 + - - +
725A GLY 3.1 0.3 + - - -
726A ARG* 3.2 9.3 + - - +
727A CYS* 3.0 20.8 + - - +
748A VAL* 4.1 26.9 - - + -
750A ARG* 4.6 2.5 - - - +
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Residues in contact with VAL 724 (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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662A VAL* 4.6 9.4 - - + -
664A LEU* 3.5 26.9 - - + -
720A ASP* 2.9 20.2 + - + +
721A ASP* 3.8 4.7 - - - +
723A ILE* 1.3 74.9 - - - +
725A GLY* 1.3 63.8 + - - +
727A CYS* 3.3 7.2 - - - +
728A LEU* 3.1 25.7 + - + +
743A PRO* 3.9 13.9 - - + -
746A THR* 3.8 35.2 - - + +
748A VAL* 4.7 6.1 - - + -
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Residues in contact with GLY 725 (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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721A ASP 2.7 13.7 + - - -
722A VAL* 3.4 6.1 - - - -
723A ILE 3.0 0.6 - - - -
724A VAL* 1.3 74.4 - - - +
726A ARG* 1.3 53.8 + - - +
728A LEU* 2.8 32.0 + - - +
729A ALA* 3.0 13.0 + - - +
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Residues in contact with ARG 726 (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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690A GLU* 3.0 35.8 + - - +
691A LEU* 4.1 11.9 - - + -
715A MET* 3.8 22.5 - - - -
718A ILE* 4.3 14.9 - - - +
722A VAL* 3.1 37.8 + - + +
723A ILE* 3.2 4.5 + - - +
725A GLY* 1.3 73.3 - - - +
727A CYS* 1.3 61.1 + - - +
729A ALA* 3.4 9.8 - - - +
730A ILE* 3.0 32.5 + - + +
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Residues in contact with CYS 727 (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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662A VAL* 4.3 13.0 - - - -
664A LEU* 3.7 29.2 - - + -
691A LEU* 3.1 35.2 - - - +
694A PHE* 4.5 6.1 - - - -
705A ALA* 4.4 6.1 - - - -
723A ILE 3.0 13.1 + - - +
724A VAL* 3.3 13.7 - - - +
726A ARG* 1.3 75.3 - - - +
728A LEU* 1.3 64.8 + - + +
730A ILE* 3.4 4.8 + - - +
731A LEU* 3.1 28.9 + - - +
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Residues in contact with LEU 728 (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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664A LEU* 5.2 1.6 - - + -
666A PHE* 4.2 17.7 - - + -
724A VAL* 3.2 20.2 - - + +
725A GLY* 2.8 14.6 + - - +
727A CYS* 1.3 74.2 - - + +
729A ALA* 1.3 67.5 + - - +
731A LEU* 2.9 9.5 + - + +
732A LYS* 2.8 43.1 + - - +
740A VAL* 4.1 18.4 - - + -
741A PRO 4.2 9.6 - - - +
742A GLN* 3.4 28.0 - - - +
743A PRO* 4.0 20.6 - - + -
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Residues in contact with ALA 729 (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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725A GLY 3.0 11.3 + - - +
726A ARG* 3.4 16.6 - - - +
728A LEU* 1.3 76.1 - - - +
730A ILE* 1.3 64.1 + - + +
732A LYS* 3.2 12.9 + - - +
733A GLY* 3.0 18.5 + - - -
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Residues in contact with ILE 730 (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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678A PHE* 6.2 0.9 - - + -
680A HIS* 3.3 57.9 - - + +
690A GLU* 4.6 2.7 - - + +
691A LEU* 4.2 24.0 - - + -
694A PHE* 4.2 14.6 - - + -
726A ARG* 3.0 21.2 + - + +
727A CYS 3.8 4.3 - - - +
729A ALA* 1.3 78.7 - - + +
731A LEU* 1.3 65.1 + - + +
733A GLY* 3.2 4.6 + - - -
734A ILE* 3.0 35.0 + - + +
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Residues in contact with LEU 731 (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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664A LEU* 4.3 15.0 - - + -
666A PHE* 4.4 9.2 - - + -
670A PHE* 3.9 17.7 - - + -
678A PHE* 3.7 32.5 - - + -
694A PHE* 3.8 22.4 - - + -
703A LEU* 3.8 15.7 - - + -
727A CYS 3.1 18.7 + - - +
728A LEU* 2.9 12.2 + - + +
730A ILE* 1.3 76.6 - - + +
732A LYS* 1.3 51.8 + - - +
734A ILE* 3.2 3.3 + - + +
735A PHE* 2.8 49.7 + - + +
740A VAL* 3.8 14.1 - - + -
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Residues in contact with LYS 732 (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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728A LEU* 2.8 38.1 + - - +
729A ALA* 3.4 11.4 - - - +
731A LEU* 1.3 67.5 - - - +
733A GLY* 1.3 66.2 + - - +
735A PHE 2.9 0.2 + - - -
736A GLY* 2.6 34.4 + - - -
737A SER* 3.8 38.0 + - - +
740A VAL* 3.4 41.2 + - + +
742A GLN* 5.7 2.5 + - - -
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Residues in contact with GLY 733 (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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365A ALA 5.8 1.3 - - - -
366A ASN 4.5 6.3 - - - +
367A GLY* 3.4 27.6 - - - +
729A ALA 3.0 9.5 + - - -
730A ILE* 3.4 5.8 - - - -
732A LYS* 1.3 79.4 - - - +
734A ILE* 1.3 60.6 + - - +
736A GLY 4.5 1.0 + - - -
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Residues in contact with ILE 734 (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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363A TYR* 3.3 67.5 - - + +
364A GLU 4.7 0.7 - - - +
365A ALA 5.8 1.1 - - - +
367A GLY* 4.0 17.1 - - - +
678A PHE* 5.0 7.0 - - + -
679A GLY 5.3 0.7 - - - +
680A HIS* 4.5 7.4 - - + -
730A ILE* 3.0 44.0 + - + +
731A LEU* 3.2 6.9 + - + +
732A LYS 3.1 0.2 - - - -
733A GLY* 1.3 78.8 - - - +
735A PHE* 1.3 88.9 + - + +
736A GLY 3.8 0.2 - - - -
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Residues in contact with PHE 735 (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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363A TYR* 5.3 5.8 - - - -
670A PHE* 3.5 43.1 - + + +
671A TRP* 3.7 30.1 - - + -
672A ASP* 4.5 6.1 - - + -
678A PHE* 3.7 32.3 - + - -
703A LEU* 5.4 0.2 - - + -
731A LEU* 2.8 27.4 + - + +
734A ILE* 1.3 98.5 - - + +
736A GLY* 1.3 60.5 + - - +
739A ALA* 3.7 14.6 - - + +
740A VAL* 4.2 5.4 - - + -
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Residues in contact with GLY 736 (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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732A LYS* 2.6 18.2 + - - -
733A GLY 4.5 1.2 + - - -
734A ILE 3.8 0.8 - - - -
735A PHE* 1.3 74.5 - - - +
737A SER* 1.3 52.9 + - - -
738A SER* 2.6 19.0 + - - -
739A ALA* 2.9 13.4 + - - -
740A VAL* 3.9 10.2 - - - +
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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