Contacts of the helix formed by residues 781 - 802 (chain E) in PDB entry 3T06
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 ASN 781 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780E PRO* 1.3 79.9 - - - +
782E LEU* 1.3 67.4 + - - +
783E PRO* 3.1 6.5 - - - -
784E GLU* 2.8 38.0 + - + +
785E LEU* 3.0 9.9 + - - +
828E VAL* 3.3 24.3 + - - +
831E GLN* 2.5 43.5 + - - +
832E PHE* 3.2 25.8 - - - +
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Residues in contact with LEU 782 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753E LEU* 4.3 9.4 - - + +
756E LEU* 4.0 22.0 - - + -
757E ASP* 3.6 42.8 - - + +
761E TYR* 4.0 20.0 - - + -
779E PHE* 4.1 21.0 + - + -
780E PRO 3.9 0.4 - - - -
781E ASN* 1.3 75.8 + - - +
783E PRO* 1.3 70.8 - - + +
785E LEU* 4.3 10.1 - - + -
786E ILE* 2.9 41.1 + - + +
832E PHE* 4.0 22.4 - - + -
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Residues in contact with PRO 783 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757E ASP* 6.1 0.4 - - - +
761E TYR* 4.8 22.4 - - + +
762E GLN* 6.1 1.1 - - - +
779E PHE 5.3 0.9 - - - +
780E PRO 5.3 1.1 - - - +
781E ASN* 3.3 6.7 - - - -
782E LEU* 1.3 95.6 - - + +
784E GLU* 1.3 72.0 - - - +
786E ILE* 3.6 8.1 - - + +
787E GLU* 3.0 28.2 + - - +
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Residues in contact with GLU 784 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780E PRO 4.7 1.2 - - - +
781E ASN* 2.8 37.3 + - + +
783E PRO* 1.3 87.7 - - - +
785E LEU* 1.3 58.3 + - - +
787E GLU* 3.8 7.6 - - - +
788E ILE* 3.1 31.4 + - - +
828E VAL* 4.4 16.8 - - + -
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Residues in contact with LEU 785 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753E LEU* 4.3 13.2 - - + -
781E ASN 3.0 14.1 + - - +
782E LEU* 3.8 7.0 - - + +
784E GLU* 1.3 73.8 - - - +
786E ILE* 1.3 66.2 + - - +
787E GLU 3.1 1.6 + - - -
788E ILE* 3.4 10.5 + - + +
789E HIS* 3.3 25.1 - - + +
825E LEU* 5.6 2.0 - - + -
828E VAL* 3.5 28.2 - - + +
829E ALA* 4.5 6.7 - - + -
832E PHE* 3.4 46.9 - - + -
878E GLU* 3.4 39.7 - - + +
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Residues in contact with ILE 786 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750E LEU* 3.8 8.8 - - + +
753E LEU* 3.6 47.1 - - + +
754E ARG* 3.9 28.3 - - + +
757E ASP* 3.8 26.2 - - + +
782E LEU* 2.9 29.1 + - + +
783E PRO* 3.6 6.3 - - + +
785E LEU* 1.3 77.3 - - - +
787E GLU* 1.3 59.9 + - - +
789E HIS 3.5 0.2 + - - -
790E ASN* 2.8 30.5 + - + +
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Residues in contact with GLU 787 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783E PRO 3.0 16.8 + - - +
784E GLU* 3.8 9.2 - - - +
785E LEU 3.1 0.8 - - - -
786E ILE* 1.3 77.7 - - - +
788E ILE* 1.3 69.4 + - - +
790E ASN* 3.4 23.4 + - - +
791E SER* 2.9 33.2 + - - -
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Residues in contact with ILE 788 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784E GLU 3.1 20.2 + - - +
785E LEU* 3.4 8.0 + - + +
787E GLU* 1.3 79.0 - - - +
789E HIS* 1.3 80.6 + - + +
791E SER* 3.1 14.3 + - - -
792E TRP* 3.2 9.6 + - + +
816E ARG* 3.8 34.6 + - - +
824E GLU* 4.2 15.0 - - + +
825E LEU* 3.7 37.0 - - + -
828E VAL* 3.8 35.7 - - + -
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Residues in contact with HIS 789 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746E GLU* 3.0 25.9 + - - +
749E HIS* 3.6 23.3 - + + -
750E LEU* 3.8 20.4 - - + -
753E LEU* 3.7 12.3 - - + -
785E LEU* 3.3 18.7 + - + +
786E ILE 4.0 1.3 - - - +
787E GLU 3.4 0.2 - - - -
788E ILE* 1.3 89.2 - - + +
790E ASN* 1.3 59.4 + - - +
792E TRP* 3.1 6.9 + + - +
793E CYS* 2.7 31.4 + - - +
825E LEU* 5.1 1.3 - - + +
878E GLU* 2.8 29.0 + - - -
881E ARG* 4.4 4.0 - - + -
882E LEU* 4.8 4.0 - - + +
885E TYR* 3.6 22.4 + + - -
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Residues in contact with ASN 790 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750E LEU* 3.9 13.9 - - + +
754E ARG* 3.4 27.6 + - - +
786E ILE* 2.8 26.3 + - + +
787E GLU* 3.4 21.5 + - - +
789E HIS* 1.3 72.9 - - - +
791E SER* 1.3 63.4 + - - +
793E CYS* 3.7 3.2 - - - +
794E GLU* 3.0 37.7 + - - +
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Residues in contact with SER 791 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787E GLU* 2.9 27.9 + - - -
788E ILE 3.1 9.2 + - - -
790E ASN* 1.3 80.2 - - - +
792E TRP* 1.3 61.6 + - - +
794E GLU* 3.3 8.7 + - - +
795E ALA* 3.1 24.9 + - - +
816E ARG* 3.7 14.7 + - - -
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Residues in contact with TRP 792 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742E LEU* 4.6 3.8 - - + -
746E GLU* 3.6 22.7 - - - -
788E ILE* 3.2 9.8 + - + +
789E HIS* 3.1 10.7 + + - +
791E SER* 1.3 79.3 + - - +
793E CYS* 1.3 65.6 + - - +
794E GLU 3.0 1.8 - - - -
795E ALA* 3.2 7.1 + - + +
796E MET* 3.1 46.7 + - + +
812E LEU* 3.2 35.0 + - + +
813E MET* 3.7 29.8 - - + -
815E ALA* 5.4 2.9 - - + -
816E ARG* 3.4 36.7 - - + +
817E PHE* 3.7 23.3 - + - -
885E TYR* 3.4 33.9 - + - -
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Residues in contact with CYS 793 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743E PHE 5.1 0.9 - - - -
746E GLU* 4.1 12.7 - - + +
747E ALA* 3.8 38.1 - - - -
750E LEU* 4.6 13.2 - - + -
789E HIS 2.7 21.2 + - - +
790E ASN* 3.7 10.5 - - - +
792E TRP* 1.3 71.8 - - - +
794E GLU* 1.3 58.7 + - + +
796E MET* 3.5 14.1 - - - +
797E LYS* 3.1 36.6 + - - +
800E ARG* 5.7 0.2 + - - -
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Residues in contact with GLU 794 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790E ASN* 3.0 31.8 + - - +
791E SER* 3.4 11.0 - - - +
792E TRP 3.0 0.2 - - - -
793E CYS* 1.3 75.4 - - + +
795E ALA* 1.3 66.3 + - - +
796E MET 3.1 1.3 - - - -
797E LYS* 3.1 36.7 + - - +
798E LYS* 3.0 21.3 + - - +
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Residues in contact with ALA 795 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791E SER 3.1 13.5 + - - +
792E TRP* 3.2 11.0 + - + +
794E GLU* 1.3 75.6 - - - +
796E MET* 1.3 62.3 + - - +
798E LYS* 3.2 18.2 + - - +
799E LEU* 3.2 16.5 + - - +
812E LEU* 3.8 23.2 - - + +
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Residues in contact with MET 796 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742E LEU* 3.9 27.8 - - + -
743E PHE* 3.9 39.9 - - + +
746E GLU* 3.8 27.8 - - + -
792E TRP* 3.1 58.6 + - + +
793E CYS* 3.5 11.4 - - - +
795E ALA* 1.3 74.0 - - - +
797E LYS* 1.3 66.2 + - - +
798E LYS 3.1 0.9 + - - -
799E LEU* 3.2 5.4 + - - +
800E ARG* 3.1 27.0 + - - +
812E LEU* 4.0 14.8 - - + -
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Residues in contact with LYS 797 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793E CYS* 3.1 21.9 + - - +
794E GLU* 3.1 35.7 + - - +
796E MET* 1.3 78.1 - - - +
798E LYS* 1.3 62.2 + - - +
800E ARG* 3.6 34.6 + - - +
801E GLU* 3.3 33.0 + - - +
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Residues in contact with LYS 798 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794E GLU 3.0 11.7 + - - +
795E ALA* 3.3 14.6 - - - +
796E MET 3.1 0.4 - - - -
797E LYS* 1.3 77.8 - - - +
799E LEU* 1.3 63.9 + - + +
801E GLU* 3.0 55.9 + - - +
802E GLU* 3.7 16.8 + - - +
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Residues in contact with LEU 799 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743E PHE* 4.9 3.6 - - + -
795E ALA 3.2 9.0 + - - +
796E MET* 3.2 8.5 + - - +
798E LYS* 1.3 77.0 - - + +
800E ARG* 1.3 61.6 + - - +
801E GLU 3.0 6.1 + - - -
802E GLU* 3.3 40.9 + - - +
803E GLY 4.0 2.3 - - - +
806E ILE* 4.6 27.4 - - + +
807E LYS 6.0 0.7 - - - +
808E GLU 4.2 19.1 - - - +
809E ILE* 4.9 2.9 - - + -
812E LEU* 4.0 31.4 - - + -
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Residues in contact with ARG 800 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720E VAL* 5.0 21.5 - - + +
740E ASN* 5.3 10.5 - - - +
743E PHE* 4.1 32.2 - - + +
796E MET* 3.1 16.4 + - - +
797E LYS* 3.6 43.8 + - - +
799E LEU* 1.3 76.6 - - - +
801E GLU* 1.3 62.2 + - - +
802E GLU 3.4 0.2 - - - -
803E GLY 3.5 14.6 - - - +
804E PRO* 4.4 3.6 - - + +
806E ILE* 4.2 23.1 - - + +
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Residues in contact with GLU 801 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797E LYS* 3.3 23.8 + - - +
798E LYS* 3.0 41.0 + - - +
799E LEU 3.0 0.4 - - - -
800E ARG* 1.3 79.8 - - - +
802E GLU* 1.3 57.0 + - - +
803E GLY 3.0 7.3 + - - -
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Residues in contact with GLU 802 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798E LYS* 3.7 18.9 + - - +
799E LEU* 3.4 31.0 - - + +
801E GLU* 1.3 76.8 - - - +
803E GLY* 1.3 61.2 + - - +
805E ILE 4.6 4.7 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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