Contacts of the helix formed by residues 802 - 819 (chain A) in PDB entry 4P5Q
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 THR 802 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743A VAL* 3.4 16.4 - - - +
794A GLU* 4.9 0.2 + - - -
800A LYS* 3.8 25.4 + - + +
801A PHE* 1.3 80.0 - - - +
803A SER* 1.3 64.8 + - - +
804A ALA* 3.0 20.9 + - - +
805A SER* 2.7 27.2 + - - -
806A ASP 3.2 4.2 + - - -
865A ARG* 4.0 15.0 - - - +
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Residues in contact with SER 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A SER* 3.3 36.0 + - - -
741A GLY 5.9 0.7 - - - -
742A TYR 4.3 7.3 + - - -
743A VAL* 3.9 8.1 - - - +
802A THR* 1.3 74.9 - - - +
804A ALA* 1.3 56.1 + - - +
806A ASP* 3.1 12.8 + - - +
807A VAL* 2.9 30.3 + - - +
870A LYS* 6.6 0.2 - - - -
871A PHE* 4.0 4.7 - - - -
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Residues in contact with ALA 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A THR* 3.0 11.9 + - - +
803A SER* 1.3 78.8 - - - +
805A SER* 1.3 57.2 + - - +
807A VAL* 3.3 9.2 + - - +
808A TRP 3.1 17.0 + - - -
865A ARG* 3.8 37.0 - - + +
868A ARG* 3.0 23.5 + - + +
870A LYS* 5.3 10.5 - - + +
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Residues in contact with SER 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A VAL* 4.4 1.9 - - - +
792A SER* 3.3 29.7 + - - -
794A GLU* 3.9 4.9 + - - -
795A ALA* 4.4 5.4 - - - -
800A LYS 4.1 6.3 - - - -
801A PHE* 3.4 14.6 - - - +
802A THR* 2.7 37.2 + - - -
804A ALA* 1.3 73.9 - - - +
806A ASP* 1.3 65.8 + - - +
808A TRP* 3.4 5.2 + - - +
809A SER* 3.1 23.0 + - - -
868A ARG* 3.9 4.7 - - - +
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Residues in contact with ASP 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A MET* 3.6 19.2 - - + +
738A SER* 6.0 1.0 - - - -
742A TYR 4.2 2.8 - - - +
743A VAL* 3.4 17.6 - - - +
744A HIS* 2.8 27.0 + - - +
745A ARG* 3.1 26.2 + - - -
747A LEU* 3.7 7.2 - - + +
802A THR 3.2 4.5 + - - +
803A SER* 3.1 14.2 + - - +
805A SER* 1.3 76.3 + - - +
807A VAL* 1.3 58.5 + - - +
809A SER* 3.2 10.1 + - - -
810A TYR* 2.8 27.2 + - - +
871A PHE* 3.7 14.3 - - + -
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Residues in contact with VAL 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A SER* 2.9 17.4 + - - +
804A ALA* 3.5 13.5 - - - +
805A SER 3.2 0.4 - - - -
806A ASP* 1.3 74.2 - - - +
808A TRP* 1.3 67.1 + - - +
810A TYR* 3.1 5.2 + - - +
811A GLY 3.0 17.2 + - - -
860A CYS* 3.5 24.6 - - + +
868A ARG* 4.0 16.6 - - + -
869A PRO* 3.5 28.5 - - + +
870A LYS* 4.7 1.8 - - + -
871A PHE* 3.6 35.0 - - + +
874A ILE* 4.0 5.6 - - + -
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Residues in contact with TRP 808 (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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789A ARG 4.9 1.6 + - - -
790A TRP 3.7 15.8 - - - -
791A THR 3.6 9.0 + - - -
792A SER* 3.6 18.2 - - - -
793A PRO* 3.4 31.0 - - + -
804A ALA 3.1 11.2 + - - +
805A SER 3.4 10.1 - - - +
807A VAL* 1.3 76.0 - - - +
809A SER* 1.3 65.3 + - - +
811A GLY* 3.0 12.8 + - - -
812A ILE* 3.1 24.0 + - + +
825A TYR* 4.5 10.8 + - - -
837A VAL* 3.6 29.6 - - + -
842A ARG* 3.8 13.9 - - - -
860A CYS 3.4 12.5 + - - +
861A TRP* 3.2 55.2 + + + -
862A GLN 3.9 5.6 - - - -
863A LYS* 4.9 0.4 - - - -
868A ARG* 3.6 13.9 - - - +
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Residues in contact with SER 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A ARG* 5.4 4.7 + - - -
747A LEU* 3.4 33.0 + - - +
790A TRP* 2.7 28.1 + - - +
791A THR* 4.6 1.9 - - - -
805A SER 3.1 12.4 + - - -
806A ASP* 3.4 13.6 + - - -
808A TRP* 1.3 78.2 - - - +
810A TYR* 1.3 57.7 + - - +
812A ILE* 3.0 8.4 + - - +
813A VAL* 2.9 28.9 + - - +
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Residues in contact with TYR 810 (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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727A LEU* 2.8 36.9 + - + +
730A ILE* 3.8 22.0 - - + -
731A ALA* 3.7 26.5 - - + -
734A MET* 4.9 0.2 - - + -
747A LEU* 3.7 11.4 - - + +
806A ASP 2.8 13.9 + - - +
807A VAL 3.1 8.7 + - - +
809A SER* 1.3 78.5 - - - +
811A GLY* 1.3 58.2 + - - +
813A VAL* 3.1 7.6 + - + +
814A LEU* 2.8 43.0 + - + +
856A LEU* 4.8 2.2 - - + -
860A CYS* 4.2 5.4 - - - -
871A PHE* 3.7 24.7 - + + -
874A ILE* 3.6 29.8 - - + -
878A LEU* 3.2 15.6 - - - +
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Residues in contact with GLY 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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807A VAL 3.0 7.5 + - - -
808A TRP 3.0 9.2 + - - -
810A TYR* 1.3 75.8 - - - +
812A ILE* 1.3 61.6 + - - +
814A LEU* 3.3 9.6 + - - +
815A TRP 3.0 17.5 + - - -
857A MET* 4.0 4.9 - - - +
860A CYS* 3.6 20.2 - - - +
861A TRP* 3.3 23.9 - - - -
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Residues in contact with ILE 812 (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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789A ARG 3.8 15.3 - - - +
790A TRP* 3.4 29.6 - - + +
808A TRP* 3.1 27.0 + - + +
809A SER 3.0 7.5 + - - +
811A GLY* 1.3 76.2 - - - +
813A VAL* 1.3 56.5 + - - +
815A TRP* 3.1 5.2 + - + +
816A GLU* 2.8 26.0 + - - +
824A PRO* 3.5 26.2 - - + -
825A TYR* 3.7 22.9 - - + +
843A LEU* 3.9 9.0 - - + -
861A TRP* 3.3 25.3 - - + +
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Residues in contact with VAL 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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707A LEU* 5.1 0.2 - - + -
727A LEU* 4.7 2.7 - - + -
730A ILE* 4.0 32.5 - - + -
747A LEU* 3.9 13.2 - - + +
748A ALA* 3.7 37.7 - - - +
749A ALA* 4.7 10.3 - - - +
752A ILE* 4.9 1.3 - - + -
790A TRP* 4.9 0.4 - - + -
809A SER 2.9 18.2 + - - +
810A TYR* 3.5 11.9 - - + +
812A ILE* 1.3 75.0 - - - +
814A LEU* 1.3 58.8 + - - +
816A GLU* 3.1 9.8 + - - +
817A VAL* 2.8 35.9 + - + +
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Residues in contact with LEU 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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727A LEU* 3.4 42.1 - - + +
810A TYR* 2.8 22.5 + - + +
811A GLY* 3.4 9.4 - - - +
813A VAL* 1.3 76.9 - - - +
815A TRP* 1.3 60.7 + - - +
817A VAL* 3.4 1.0 + - - +
818A MET* 3.0 38.5 + - + +
853A LEU* 3.7 18.2 - - + +
856A LEU* 3.7 36.3 - - + -
857A MET* 3.5 31.9 - - + +
878A LEU* 5.7 0.2 - - + -
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Residues in contact with TRP 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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811A GLY 3.0 12.7 + - - +
812A ILE* 3.4 8.5 - - - +
814A LEU* 1.3 78.3 - - - +
816A GLU* 1.3 69.6 + - + +
818A MET 3.4 1.0 + - - -
819A SER* 2.8 42.2 + - - -
822A GLU* 3.7 38.6 - - + -
823A ARG 3.7 5.8 - - - -
824A PRO* 3.6 24.5 - - + -
826A TRP* 4.1 25.1 - + - -
843A LEU* 3.5 32.6 - - + +
844A PRO* 2.8 30.6 + - + -
846A PRO* 3.7 17.9 - - + +
857A MET* 3.8 19.2 - - - +
861A TRP* 4.1 8.3 - + + -
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Residues in contact with GLU 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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708A ASP* 4.7 7.1 - - - +
711A LEU* 4.9 0.9 - - - -
712A ARG* 5.4 1.9 + - - -
749A ALA* 2.9 38.7 + - + +
750A ARG 4.8 0.9 + - - -
790A TRP* 2.9 42.4 + - - -
812A ILE 2.8 18.2 + - - +
813A VAL* 3.1 15.7 + - - +
815A TRP* 1.3 78.7 - - + +
817A VAL* 1.3 62.5 + - - +
819A SER* 3.3 1.7 + - - -
820A TYR 3.1 3.6 + - - -
821A GLY* 2.8 31.7 + - - +
822A GLU 4.1 12.9 - - - +
824A PRO* 3.8 19.7 - - + +
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Residues in contact with VAL 817 (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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707A LEU* 3.8 29.4 - - + -
711A LEU* 3.7 15.6 - - + +
723A LEU* 3.9 31.9 - - + +
726A MET* 4.8 5.4 - - + -
727A LEU* 3.8 36.6 - - + -
730A ILE* 4.8 0.9 - - + -
749A ALA* 5.3 1.1 - - + -
813A VAL* 2.8 27.5 + - + +
814A LEU 3.8 4.0 - - - +
816A GLU* 1.3 74.1 - - + +
818A MET* 1.3 58.0 + - - +
819A SER 3.1 0.2 - - - -
820A TYR* 3.0 23.9 + - - -
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Residues in contact with MET 818 (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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720A VAL* 4.8 8.3 - - + -
723A LEU* 3.8 31.6 - - + -
727A LEU* 3.9 16.6 - - - -
814A LEU* 3.0 23.6 + - + +
817A VAL* 1.3 75.3 - - - +
819A SER* 1.3 57.3 + - - +
820A TYR* 3.3 12.8 + - - -
846A PRO* 3.5 29.0 - - + +
847A MET 4.5 7.1 + - - +
848A ASP 5.5 0.4 - - - +
849A CYS* 4.2 8.1 - - + -
850A PRO* 4.0 17.5 - - + -
853A LEU* 3.8 28.7 - - + -
857A MET* 3.9 14.4 - - + -
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Residues in contact with SER 819 (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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715A ASP* 4.7 2.3 - - - +
815A TRP* 2.8 38.1 + - - -
816A GLU 3.8 2.5 - - - -
818A MET* 1.3 77.5 - - - +
820A TYR* 1.3 70.6 + - - +
821A GLY 3.2 1.0 + - - -
822A GLU* 3.4 29.9 + - - +
846A PRO* 3.2 22.5 - - - +
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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