Contacts of the helix formed by residues 753 - 769 (chain A) in PDB entry 4YZ9
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 TYR 753 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680A HIS* 3.5 42.1 - - + +
685A VAL* 4.1 6.8 - - + +
752A THR* 1.3 83.2 - - - +
754A THR* 1.3 87.1 + - + +
756A ASP* 2.9 17.7 + - - +
757A ILE* 3.3 18.3 + - + +
820A ARG 4.4 6.0 + - - -
821A PRO 4.5 3.6 - - - -
822A SER* 3.6 43.2 + - - -
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Residues in contact with THR 754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A GLU* 4.1 3.3 + - - -
752A THR* 2.7 20.9 + - - +
753A TYR* 1.3 112.0 - - + +
755A VAL* 1.3 63.4 + - - +
757A ILE* 3.3 13.8 + - - +
758A PHE 3.3 6.6 + - - -
817A PRO* 3.4 42.4 - - + +
818A GLN* 5.3 1.6 - - - -
820A ARG* 3.2 23.4 + - + +
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Residues in contact with VAL 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A VAL* 4.9 1.6 - - + -
687A ARG* 4.4 13.0 - - - +
738A ILE* 5.7 0.7 - - + -
739A ALA* 4.1 16.0 - - + +
741A GLU* 3.9 19.3 - - + +
742A MET* 3.5 46.0 - - + -
751A PRO* 4.0 13.2 - - + -
752A THR 3.2 10.5 + - - +
753A TYR 3.1 0.8 - - - -
754A THR* 1.3 79.9 + - - +
756A ASP* 1.3 72.0 + - - +
758A PHE* 3.3 13.7 + - - +
759A SER* 3.3 15.1 + - - +
820A ARG* 4.3 0.2 - - - +
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Residues in contact with ASP 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A LEU* 4.0 12.3 - - + +
680A HIS* 3.0 27.5 + - + +
685A VAL* 3.3 11.4 - - - +
686A HIS* 2.8 33.4 + - - +
687A ARG* 2.9 28.9 + - - -
689A LEU* 4.0 6.6 - - + +
753A TYR 2.9 8.1 + - - +
755A VAL* 1.3 75.7 - - - +
757A ILE* 1.3 54.7 + - - +
759A SER* 3.2 9.0 + - - -
760A ALA* 2.7 35.3 + - - +
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Residues in contact with ILE 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A THR* 6.2 0.4 - - + -
676A LEU* 4.3 7.0 - - + -
680A HIS* 4.3 9.9 - - + -
753A TYR* 3.6 23.8 - - + +
754A THR* 3.6 9.9 - - - +
755A VAL 3.2 0.8 - - - -
756A ASP* 1.3 76.2 - - - +
758A PHE* 1.3 59.2 + - - +
760A ALA* 3.3 6.6 + - + +
761A GLY 2.8 23.7 + - - -
812A MET* 3.6 37.2 - - + +
820A ARG* 4.0 8.7 - - + -
821A PRO 3.3 29.4 - - - +
823A ALA* 3.6 30.7 - - + +
826A VAL* 4.9 4.0 - - + -
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Residues in contact with PHE 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A TRP 4.2 4.3 - - - -
738A ILE 3.5 18.8 - - - -
739A ALA* 3.6 17.9 - - + -
740A PRO* 3.7 9.9 - - + -
754A THR 3.3 3.4 + - - -
755A VAL 3.6 8.5 - - - +
756A ASP 3.2 0.2 - - - -
757A ILE* 1.3 78.1 - - - +
759A SER* 1.3 65.2 + - - +
761A GLY* 3.1 10.0 + - - -
762A CYS* 3.2 26.3 + - - -
775A PHE* 3.4 30.1 - + - -
785A ILE* 3.9 19.5 - - + -
812A MET 3.3 10.6 + - - -
813A ILE* 3.2 39.2 - - - +
815A MET* 3.9 3.6 - - + -
820A ARG* 3.8 29.6 - - - +
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Residues in contact with SER 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A ARG 5.4 2.8 + - - -
688A ASP 5.4 0.2 - - - -
689A LEU* 3.3 36.8 + - - +
737A TRP* 2.6 26.1 + - - +
738A ILE* 4.6 2.4 - - - -
739A ALA 4.8 0.2 + - - -
755A VAL* 3.3 14.0 + - - +
756A ASP* 3.2 10.0 + - - -
758A PHE* 1.3 79.6 - - - +
760A ALA* 1.3 62.6 + - - +
762A CYS* 3.1 9.2 + - - +
763A VAL* 3.0 26.0 + - - +
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Residues in contact with ALA 760 (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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672A THR* 6.0 3.6 - - + -
673A THR* 5.8 1.6 - - + +
676A LEU* 4.3 10.5 - - + -
689A LEU* 4.0 16.7 - - + +
756A ASP 2.7 20.7 + - - +
757A ILE* 3.6 11.7 - - + +
758A PHE 3.3 0.2 - - - -
759A SER* 1.3 72.8 - - - +
761A GLY* 1.3 58.0 + - - +
763A VAL* 3.0 7.2 + - - +
764A PHE* 2.8 47.3 + - + -
812A MET* 4.8 4.9 - - - -
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Residues in contact with GLY 761 (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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757A ILE 2.8 14.4 + - - -
758A PHE 3.1 4.8 + - - -
760A ALA* 1.3 75.7 - - - +
762A CYS* 1.3 58.8 + - - +
764A PHE* 3.3 3.8 + - - +
765A TYR* 3.3 17.3 + - - +
809A ILE* 3.8 10.8 - - - +
812A MET* 3.7 23.5 - - - +
813A ILE* 3.6 18.6 - - - -
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Residues in contact with CYS 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A GLY 4.6 1.8 - - - -
737A TRP* 3.6 11.9 - - + -
758A PHE* 3.2 37.3 + - - -
759A SER* 3.1 9.7 + - - +
761A GLY* 1.3 75.7 - - - +
763A VAL* 1.3 58.2 + - - +
765A TYR* 3.5 2.9 + - - +
766A TYR* 3.0 28.1 + - - +
773A HIS* 3.6 37.5 - - + +
774A PRO* 4.0 13.4 - - + +
775A PHE* 4.0 13.5 - - - -
813A ILE* 4.2 4.0 - - - -
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Residues in contact with VAL 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A LEU* 3.6 29.8 - - + -
669A LEU* 4.4 11.0 - - + -
672A THR* 5.3 3.8 - - + -
689A LEU* 5.0 2.2 - - + -
690A LYS* 4.2 7.4 - - - +
691A PRO* 4.1 12.8 - - + -
694A ILE* 3.7 18.8 - - + -
737A TRP* 4.0 16.2 - - + -
759A SER 3.0 16.1 + - - +
760A ALA* 3.0 12.0 + - - +
762A CYS* 1.3 74.2 - - - +
764A PHE* 1.3 67.0 + - + +
766A TYR* 3.1 8.0 + - + +
767A VAL* 3.0 21.8 + - - +
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Residues in contact with PHE 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A LEU* 3.9 28.3 - - + -
672A THR* 5.7 4.7 - - + -
673A THR* 3.2 28.9 - - - -
760A ALA* 2.8 36.8 + - + -
761A GLY 3.6 8.5 - - - +
763A VAL* 1.3 78.2 - - + +
765A TYR* 1.3 62.3 + - - +
767A VAL* 3.2 1.7 + - - +
768A ILE* 3.0 30.2 + - + +
808A LEU* 3.9 18.2 - - + -
809A ILE* 4.0 14.8 - - + -
812A MET* 3.7 15.5 - - + -
826A VAL* 4.0 9.9 - - + -
831A PHE* 4.1 17.7 - + - -
832A PHE* 3.8 24.9 - + - -
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Residues in contact with TYR 765 (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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761A GLY 3.3 6.8 + - - +
762A CYS 3.9 1.6 - - - +
764A PHE* 1.3 77.9 - - - +
766A TYR* 1.3 52.0 + - - +
768A ILE* 4.6 2.2 - - + +
769A SER* 2.4 47.9 + - - -
772A SER* 3.6 30.9 - - - -
773A HIS 3.8 11.4 - - - -
774A PRO* 3.6 30.7 - - + -
791A SER 3.5 10.7 + - - -
792A LEU* 3.3 40.9 - - + -
793A ASP* 3.6 3.5 + - - -
794A CYS* 3.1 39.7 + - + +
795A LEU* 4.2 14.4 - - + -
809A ILE* 3.8 19.9 - - + +
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Residues in contact with TYR 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A LEU* 4.3 3.4 - - + -
650A GLN* 3.6 25.2 - - + +
653A VAL* 3.6 31.2 - - + +
654A GLU* 3.7 19.5 + - - +
691A PRO* 3.9 27.4 - - + -
737A TRP* 4.1 21.5 - + + -
762A CYS 3.0 18.4 + - - +
763A VAL* 3.1 8.9 + - - +
765A TYR* 1.3 77.0 - - - +
767A VAL* 1.3 65.3 + - + +
770A GLU* 3.2 1.9 + - - -
771A GLY* 2.9 50.4 + - - -
772A SER 3.2 23.3 + - - +
773A HIS* 5.4 2.2 - + + -
781A ARG* 6.1 2.2 - - - -
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Residues in contact with VAL 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A LEU* 3.8 33.2 - - + -
652A TYR* 4.9 7.2 - - + -
653A VAL* 4.0 15.1 - - + +
665A PRO* 3.6 41.2 - - + +
668A LEU* 4.5 1.6 - - + -
669A LEU* 3.8 22.2 - - + -
763A VAL 3.0 15.7 + - - +
764A PHE 3.8 3.1 - - - +
766A TYR* 1.3 77.6 - - + +
768A ILE* 1.3 66.8 + - + +
770A GLU* 3.2 16.6 + - - +
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Residues in contact with ILE 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A PRO* 5.8 4.5 - - + -
666A ILE* 5.8 2.5 - - + -
669A LEU* 4.4 7.0 - - + -
764A PHE* 3.0 19.3 + - + +
765A TYR* 4.1 4.0 - - + +
767A VAL* 1.3 76.6 - - + +
769A SER* 1.3 60.6 + - - +
770A GLU* 3.4 8.5 + - - +
795A LEU* 3.9 24.2 - - + -
802A ASP* 5.4 4.0 - - - +
805A ALA* 3.9 14.4 - - + -
809A ILE* 4.0 14.6 - - + -
831A PHE* 3.5 39.9 - - + -
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Residues in contact with SER 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A TYR* 2.4 37.7 + - - -
766A TYR 3.7 0.3 + - - -
768A ILE* 1.3 72.4 - - - +
770A GLU* 1.3 69.7 + - - +
772A SER* 3.2 42.0 + - - -
794A CYS* 3.9 27.3 - - - -
795A LEU* 6.3 0.7 - - - -
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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
------------------------------------------------------------
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