Contacts of the helix formed by residues 800 - 817 (chain A) in PDB entry 4Z4H
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 PRO 800 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667A TYR* 3.9 24.7 - - + -
707A VAL* 4.6 2.7 - - + -
765A TYR* 3.3 18.4 - - + +
783A THR* 3.9 26.2 - - + +
786A LEU* 4.0 14.8 - - + +
787A CYS* 3.6 9.1 - - - -
799A ILE* 1.3 90.3 - - + +
801A ALA* 1.3 66.6 + - - +
802A PRO* 4.0 16.4 - - + -
803A ALA* 2.9 20.9 + - + +
804A TYR* 2.9 10.0 + - - +
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Residues in contact with ALA 801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A TYR* 4.8 1.3 - - + +
786A LEU 3.1 9.8 + - - +
787A CYS* 4.5 0.8 - - - +
789A THR* 3.3 36.6 - - - +
790A TYR* 4.0 10.3 - - - +
799A ILE 3.4 2.9 + - - -
800A PRO* 1.3 68.6 - - - +
802A PRO* 1.3 64.2 - - + +
804A TYR* 2.9 9.6 + - - +
805A TYR* 2.7 54.2 + - + -
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Residues in contact with PRO 802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A PHE* 4.5 5.8 - - + +
594A LEU 4.1 3.8 - - - -
595A GLY* 3.6 23.1 - - - +
615A VAL* 3.0 27.3 - - + +
625A TYR* 3.4 35.0 - - + +
667A TYR* 4.4 14.4 - - + -
786A LEU* 4.6 12.8 - - + +
789A THR* 4.9 0.4 - - - +
800A PRO* 3.4 14.4 - - + -
801A ALA* 1.3 95.3 - - + +
803A ALA* 1.3 61.1 + - - +
805A TYR* 4.1 1.5 - - + -
806A ALA 3.1 8.8 + - - -
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Residues in contact with ALA 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A GLY* 4.1 7.9 - - - -
596A ALA 4.9 0.9 - - - +
597A ASP* 5.0 0.5 - - - +
667A TYR* 4.6 18.6 - - + +
669A ASP* 4.7 13.9 - - + -
707A VAL* 4.9 4.7 - - + -
799A ILE* 3.8 15.7 - - + -
800A PRO* 2.9 19.1 + - + +
802A PRO* 1.3 77.0 - - - +
804A TYR* 1.3 66.1 + - - +
806A ALA* 3.4 12.6 + - - +
807A HIS* 3.1 20.8 + - - -
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Residues in contact with TYR 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790A TYR* 3.3 36.8 - + + -
797A VAL* 3.8 24.2 - - + -
798A SER* 4.6 1.8 - - - -
799A ILE* 3.7 27.7 - - + +
800A PRO 2.9 11.2 + - - +
801A ALA* 2.9 8.3 + - - +
803A ALA* 1.3 78.9 - - - +
805A TYR* 1.3 62.1 + - - +
807A HIS* 3.1 17.4 + + + +
808A LEU* 3.2 20.1 + - + +
4B A 3.5 20.3 + - - -
5B C 2.6 40.7 + - - -
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Residues in contact with TYR 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A VAL* 4.0 11.7 - - + -
623A ASN 4.8 0.5 + - - -
625A TYR* 3.5 40.2 - + + -
789A THR 3.3 9.7 + - - -
790A TYR* 3.5 30.9 - + - -
791A VAL* 3.0 44.2 + - + +
792A ARG* 5.1 1.1 - - + -
801A ALA* 2.7 36.7 + - + +
802A PRO* 3.7 5.4 - - + +
803A ALA 3.3 0.2 - - - -
804A TYR* 1.3 69.1 - - - +
806A ALA* 1.3 66.9 + - - +
808A LEU* 3.0 15.5 + - + +
809A VAL* 2.9 26.0 + - - +
856A MET* 4.0 10.4 - - + +
858A PHE* 3.7 23.7 - + + -
859A ALA* 6.3 0.9 - - + -
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Residues in contact with ALA 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A GLY 3.8 21.3 - - - +
596A ALA 3.9 1.8 - - - -
597A ASP* 3.8 25.7 - - + +
613A ALA* 3.3 17.7 - - - +
615A VAL* 4.0 11.1 - - + +
802A PRO 3.1 13.2 + - - +
803A ALA 3.5 10.1 - - - +
804A TYR 3.2 0.2 - - - -
805A TYR* 1.3 76.2 - - - +
807A HIS* 1.3 61.4 + - - +
809A VAL* 3.4 0.4 + - - -
810A ALA* 3.0 20.4 + - - +
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Residues in contact with HIS 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A ASP* 3.3 25.1 + - - -
599A THR* 4.8 1.6 + - - -
669A ASP* 3.0 39.3 + - - -
799A ILE* 3.9 16.2 - - + +
803A ALA 3.1 23.5 + - - -
804A TYR* 3.1 14.3 + + + +
805A TYR 3.1 0.4 - - - -
806A ALA* 1.3 76.4 - - - +
808A LEU* 1.3 65.8 - - + +
810A ALA* 3.2 3.1 + - - +
811A PHE* 2.9 51.0 + + + -
901A MG 4.6 2.9 - - - -
10B C 5.7 8.2 + - - -
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Residues in contact with LEU 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790A TYR* 3.6 21.5 - - - +
792A ARG* 3.4 39.7 - - - +
804A TYR* 3.6 17.3 - - + +
805A TYR* 3.0 28.8 + - + +
807A HIS* 1.3 77.9 - - + +
809A VAL* 1.3 57.2 + - - +
811A PHE* 3.5 12.1 + - + +
812A ARG* 3.0 28.8 + - - +
858A PHE* 3.9 28.6 - - + +
859A ALA* 4.8 0.7 - - - -
1D C 5.6 9.0 - - - +
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Residues in contact with VAL 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A ALA* 3.5 19.1 - - + -
615A VAL* 3.8 8.5 - - + -
627A ALA* 3.5 25.4 - - + -
628A THR 4.0 6.5 - - - +
629A VAL* 3.9 19.7 - - + +
805A TYR 2.9 18.9 + - - +
806A ALA* 3.6 5.2 - - - +
808A LEU* 1.3 76.4 - - - +
810A ALA* 1.3 63.4 + - - +
812A ARG* 3.3 4.5 + - - +
813A ALA* 3.1 21.1 + - - +
857A TYR* 4.0 13.5 + - - +
858A PHE* 3.6 24.5 - - + -
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Residues in contact with ALA 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A ASP* 4.4 4.3 - - - +
599A THR* 3.4 27.8 - - - +
611A ILE* 3.8 30.6 - - + +
613A ALA* 4.1 9.0 - - + +
806A ALA 3.0 17.0 + - - +
807A HIS 3.2 3.8 + - - +
809A VAL* 1.3 77.3 - - - +
811A PHE* 1.3 58.1 + - - +
813A ALA* 3.3 4.6 + - - +
814A ARG* 3.0 26.2 + - - +
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Residues in contact with PHE 811 (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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599A THR* 4.0 27.6 - - + -
807A HIS* 2.9 45.3 + + + +
808A LEU* 3.9 11.9 - - + +
810A ALA* 1.3 74.6 - - - +
812A ARG* 1.3 64.9 + - - +
814A ARG* 3.3 13.1 + - + +
815A TYR* 3.1 26.6 + - - -
9B G 5.5 0.9 - - - -
10B C 4.4 14.1 - + - -
1D C 3.2 80.5 - + - +
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Residues in contact with ARG 812 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A TYR* 3.5 7.9 + - - -
533A LYS* 3.8 26.8 - - - +
537A ASP* 2.9 27.6 + - - +
808A LEU 3.0 17.3 + - - +
809A VAL* 3.6 5.6 - - - +
810A ALA 3.3 0.2 - - - -
811A PHE* 1.3 74.6 - - - +
813A ALA* 1.3 64.7 + - - +
815A TYR* 2.9 15.8 + - - +
816A HIS* 2.9 43.5 + - + -
857A TYR* 3.2 43.7 + - + -
858A PHE* 4.3 14.1 + - + -
859A ALA 4.3 2.4 + - - -
1B U 3.3 24.5 + - - -
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Residues in contact with ALA 813 (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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611A ILE* 3.9 11.2 - - + -
629A VAL* 3.7 26.5 - - + -
809A VAL 3.1 12.9 + - - +
810A ALA 3.3 9.6 + - - +
812A ARG* 1.3 76.2 - - - +
814A ARG* 1.3 62.4 + - - +
816A HIS* 3.0 25.5 + - - +
817A LEU* 3.0 17.2 + - - +
846A VAL* 3.9 16.8 - - + +
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Residues in contact with ARG 814 (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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599A THR* 3.2 33.9 + - + +
600A HIS 3.5 19.4 + - - -
601A PRO* 3.5 5.9 - - - -
602A PRO* 5.7 1.9 - - - +
608A LYS* 4.2 7.6 - - - +
609A PRO* 3.1 25.6 + - - +
611A ILE* 3.6 19.7 - - + +
810A ALA 3.0 13.2 + - - +
811A PHE* 3.4 19.5 - - + +
813A ALA* 1.3 75.3 - - - +
815A TYR* 1.3 61.3 + - - +
817A LEU* 3.3 11.8 + - - +
818A VAL* 3.3 15.9 + - + +
821A GLU* 2.7 47.1 + - - +
1D C 6.1 0.9 - - - -
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Residues in contact with TYR 815 (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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529A TYR* 3.7 34.3 - + + -
530A ALA* 3.8 37.5 - - + +
533A LYS* 5.6 1.8 - - + -
811A PHE 3.1 17.8 + - - +
812A ARG* 2.9 21.8 + - - +
814A ARG* 1.3 73.6 - - + +
816A HIS* 1.3 61.7 + - + +
817A LEU 3.0 5.5 + - - -
818A VAL* 3.4 28.0 + - + +
1B U 4.0 11.3 - + - -
1D C 3.5 36.0 - - - -
2D A 2.9 30.2 + - - -
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Residues in contact with HIS 816 (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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530A ALA 5.3 1.8 - - - -
533A LYS* 3.7 18.7 + - + -
534A ARG* 4.3 11.5 - - + +
537A ASP* 3.1 37.3 + - + +
538A THR* 3.9 15.1 - - + +
812A ARG* 2.9 39.2 + - + -
813A ALA* 3.0 15.9 + - - +
815A TYR* 1.3 77.4 - - - +
817A LEU* 1.3 59.7 + - - +
818A VAL 3.5 0.6 + - - +
820A LYS* 3.9 24.3 + - - +
845A ALA* 3.5 26.6 + - - +
846A VAL* 4.3 7.6 + - + -
848A VAL* 4.3 10.5 - - + -
857A TYR* 4.8 1.6 - + - -
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Residues in contact with LEU 817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A PRO* 4.3 8.3 - - + -
611A ILE* 3.9 25.4 - - + -
631A VAL* 4.0 12.1 - - + -
813A ALA 3.0 11.2 + - - +
814A ARG 3.3 6.5 + - - +
815A TYR 3.0 0.8 - - - -
816A HIS* 1.3 77.8 - - - +
818A VAL* 1.3 64.8 + - - +
819A ASP 3.1 1.2 + - - -
820A LYS* 2.9 19.6 + - + +
821A GLU* 3.4 30.5 - - + +
842A LEU* 3.7 31.9 - - + +
845A ALA* 3.5 28.7 - - + -
846A VAL* 3.6 16.4 - - + -
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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