Contacts of the helix formed by residues 818 - 832 (chain A) in PDB entry 3NC0
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 GLU 818 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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773A ALA* 5.7 4.0 - - + +
777A VAL* 5.1 11.2 - - + -
781A LEU* 6.0 0.9 - - + -
814A HIS 5.2 2.7 - - - +
815A ILE* 2.8 30.1 + - + +
817A ALA* 1.3 101.8 - - + +
819A ILE* 1.3 66.0 + - - +
820A PRO* 3.2 2.9 - - - -
821A GLN* 2.9 39.8 + - + +
822A ILE* 2.9 32.9 + - + +
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Residues in contact with ILE 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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808A VAL* 4.6 10.8 - - + -
815A ILE* 3.5 11.8 + - + +
816A THR* 3.8 16.2 - - - +
818A GLU* 1.3 77.4 - - - +
820A PRO* 1.3 63.3 - - + +
822A ILE* 4.4 11.7 - - + -
823A PHE* 2.7 53.8 + - + +
855A VAL* 3.5 38.1 - - + -
859A CYS* 4.2 13.7 - - + -
862A ALA* 3.8 25.4 - - + -
863A PHE* 5.3 1.8 - - + -
866A ILE* 6.2 2.9 - - + -
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Residues in contact with PRO 820 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816A THR 4.1 4.7 - - - +
817A ALA* 3.7 17.0 - - - +
818A GLU 3.3 3.8 - - - -
819A ILE* 1.3 98.4 - - + +
821A GLN* 1.3 64.5 + - + +
823A PHE* 4.1 2.7 - - + +
824A ASP* 3.2 22.0 + - - +
862A ALA* 5.1 4.0 - - + -
865A ALA* 5.7 7.6 - - + -
866A ILE* 5.3 17.9 - - + -
870A GLN* 5.6 3.5 + - - +
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Residues in contact with GLN 821 (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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781A LEU* 3.4 44.1 - - + +
817A ALA 5.3 0.4 + - - +
818A GLU* 2.9 35.3 + - - +
820A PRO* 1.3 80.3 - - + +
822A ILE* 1.3 63.1 + - - +
824A ASP* 3.6 12.8 - - - +
825A ALA* 3.8 6.6 + - - +
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Residues in contact with ILE 822 (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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777A VAL* 5.7 3.8 - - + -
781A LEU* 4.5 6.3 - - + -
785A LEU* 3.7 29.2 - - + -
804A MET* 4.2 28.7 - - + -
807A ILE* 5.2 0.2 - - + -
808A VAL* 5.5 2.0 - - + -
815A ILE* 4.0 27.1 - - + -
818A GLU* 2.9 28.8 + - + +
819A ILE* 3.8 11.7 - - + +
821A GLN* 1.3 72.6 - - - +
823A PHE* 1.3 73.4 + - + +
824A ASP 2.9 3.0 + - - -
825A ALA* 3.0 15.4 + - - +
826A VAL* 3.3 23.0 + - + +
851A LEU* 5.5 4.5 - - + -
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Residues in contact with PHE 823 (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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819A ILE* 2.7 35.1 + - + +
820A PRO* 4.2 2.0 - - + +
822A ILE* 1.3 79.1 - - + +
824A ASP* 1.3 61.4 + - - +
826A VAL* 4.2 7.6 - - + -
827A PHE* 2.7 64.0 + + + +
828A GLU* 5.6 0.2 - - - +
848A PHE* 5.9 1.3 - + - -
851A LEU* 4.4 17.5 - - + -
852A LEU* 3.6 26.0 - - + -
855A VAL* 4.0 27.1 - - + -
863A PHE* 3.9 22.2 - + - -
866A ILE* 5.7 2.0 - - + -
870A GLN* 4.6 20.0 - - - +
874A VAL* 4.5 6.7 - - + -
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Residues in contact with ASP 824 (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 GLN* 3.8 15.0 + - - -
820A PRO 3.2 18.1 + - - +
821A GLN* 3.6 9.2 - - - +
822A ILE 2.9 1.4 + - - -
823A PHE* 1.3 79.0 - - - +
825A ALA* 1.3 67.2 + - - +
826A VAL 4.4 0.3 - - - -
827A PHE 4.1 1.7 + - - -
828A GLU* 4.5 9.7 + - - +
829A CYS* 5.0 0.9 + - - +
870A GLN* 5.5 3.0 - - - +
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Residues in contact with ALA 825 (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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781A LEU* 6.4 0.4 - - + -
785A LEU* 4.0 37.5 - - + +
786A ILE* 4.3 7.6 - - + +
789A GLN* 3.6 30.0 - - + +
821A GLN 3.8 5.6 + - - +
822A ILE 3.0 9.0 + - - +
824A ASP* 1.3 84.6 - - - +
826A VAL* 1.3 58.0 + - + +
829A CYS* 3.2 22.5 - - - +
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Residues in contact with VAL 826 (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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785A LEU* 4.0 25.8 - - + -
788A TYR* 3.5 25.4 - - + -
800A VAL* 4.8 1.8 - - + -
801A LEU* 3.7 27.4 - - + -
822A ILE* 3.5 22.2 - - + +
823A PHE* 4.2 4.7 - - + -
825A ALA* 1.3 82.0 - - + +
827A PHE* 1.3 79.4 + - - +
828A GLU 3.7 0.2 - - - -
829A CYS* 3.4 3.6 - - - -
830A THR* 2.7 31.6 + - - -
848A PHE* 6.0 0.4 - - + -
851A LEU* 4.2 14.6 - - + -
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Residues in contact with PHE 827 (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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823A PHE* 2.7 68.2 + + + +
826A VAL* 1.3 82.4 - - - +
828A GLU* 1.3 79.8 + - + +
830A THR* 3.6 1.6 - - - -
831A LEU* 2.8 39.3 + - + +
848A PHE* 3.8 32.2 - + - -
852A LEU* 4.8 3.6 - - + -
870A GLN* 5.9 6.5 - - + +
873A LEU* 3.7 32.8 - - + -
874A VAL* 3.9 34.8 - - + -
877A SER* 4.4 5.4 - - - -
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Residues in contact with GLU 828 (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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823A PHE 4.1 1.6 + - - -
824A ASP 4.5 6.1 + - - +
826A VAL 3.7 0.2 - - - -
827A PHE* 1.3 89.1 - - - +
829A CYS* 1.3 61.7 + - - +
831A LEU* 3.2 8.6 + - + +
832A ASN* 3.1 37.9 + - - +
870A GLN* 5.7 4.9 + - - +
873A LEU* 3.4 32.6 - - + +
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Residues in contact with CYS 829 (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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788A TYR* 4.1 10.1 - - - -
789A GLN* 4.4 11.7 - - + +
796A ARG* 3.6 35.7 + - - +
824A ASP 5.0 1.0 + - - +
825A ALA 3.2 25.0 + - - +
826A VAL 3.4 7.3 + - - -
827A PHE 3.2 1.0 - - - -
828A GLU* 1.3 79.7 - - - +
830A THR* 1.3 69.8 + - - +
832A ASN* 3.6 11.8 + - - +
833A MET* 3.5 16.6 + - - +
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Residues in contact with THR 830 (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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788A TYR* 2.8 36.1 + - - +
801A LEU* 3.9 17.0 - - + +
826A VAL* 2.7 26.7 + - - +
827A PHE 3.6 2.0 - - - -
829A CYS* 1.3 75.4 - - - +
831A LEU* 1.3 65.9 + - - +
833A MET* 3.0 25.1 + - - +
834A ILE* 3.5 9.1 + - + +
844A HIS* 4.5 13.7 - - + +
848A PHE* 4.0 22.9 - - + -
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Residues in contact with LEU 831 (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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827A PHE* 2.8 38.2 + - + +
828A GLU* 3.4 12.8 - - + +
830A THR* 1.3 77.3 - - - +
832A ASN* 1.3 57.1 + - - +
834A ILE* 3.1 29.9 + - + +
835A ASN* 3.1 28.5 + - + +
848A PHE* 4.1 15.4 - - + -
873A LEU* 4.0 27.4 - - + +
877A SER* 3.6 26.7 - - - +
880A TRP* 5.1 7.9 - - + -
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Residues in contact with ASN 832 (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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828A GLU* 3.1 29.4 + - - +
829A CYS* 3.9 8.8 - - - +
830A THR 3.2 0.6 - - - -
831A LEU* 1.3 75.2 - - - +
833A MET* 1.3 59.6 + - + +
835A ASN* 3.1 23.6 + - - +
836A LYS* 3.1 34.4 + - - +
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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
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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