Contacts of the helix formed by residues 867 - 882 (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 PRO 867 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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865A ALA 3.9 1.3 - - - +
866A ILE* 1.3 92.9 - - + +
868A PRO* 1.3 75.7 - - + +
869A ALA* 4.2 9.2 - - + +
870A GLN* 2.9 34.3 + - + +
871A PHE* 2.9 11.9 + - - +
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Residues in contact with PRO 868 (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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866A ILE 4.4 1.6 - - - +
867A PRO* 1.3 86.9 - - + +
869A ALA* 1.3 56.7 + - - +
871A PHE* 3.8 10.0 - - + +
872A LYS* 3.0 31.4 + - - +
918A TYR* 4.1 5.9 + - - +
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Residues in contact with ALA 869 (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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867A PRO* 3.0 8.2 + - + -
868A PRO* 1.3 82.4 - - - +
870A GLN* 1.3 59.7 + - - +
872A LYS* 3.8 8.7 + - - +
873A LEU* 3.4 18.5 + - - +
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Residues in contact with GLN 870 (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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820A PRO* 5.6 4.0 + - - +
823A PHE* 4.6 24.0 - - - +
824A ASP* 5.5 2.2 - - - +
827A PHE* 5.9 6.5 - - + -
828A GLU* 5.7 4.5 + - - +
866A ILE* 3.1 39.8 - - + +
867A PRO* 2.9 27.6 + - + +
869A ALA* 1.3 77.2 - - - +
871A PHE* 1.3 66.9 + - - +
873A LEU* 3.0 25.3 + - + +
874A VAL* 3.1 15.0 + - + +
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Residues in contact with PHE 871 (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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860A PHE* 5.3 3.4 - + - -
863A PHE* 3.4 48.9 - + + +
864A LEU* 5.6 3.4 - - + -
866A ILE* 3.9 9.8 - - + +
867A PRO 2.9 15.0 + - - +
868A PRO* 3.8 8.7 - - + +
870A GLN* 1.3 77.5 - - - +
872A LYS* 1.3 67.3 + - - +
874A VAL* 2.8 20.4 + - + +
875A LEU* 3.0 21.7 + - + -
900A LEU* 4.8 15.3 - - + -
904A VAL* 6.0 0.4 - - + -
914A PHE* 3.7 27.8 - + - -
918A TYR* 3.7 34.5 - + - -
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Residues in contact with LYS 872 (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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868A PRO 3.0 19.0 + - - +
869A ALA* 3.8 8.1 - - - +
871A PHE* 1.3 76.9 - - - +
873A LEU* 1.3 65.0 + - - +
874A VAL 3.0 0.5 + - - -
875A LEU* 3.1 2.9 + - - +
876A ASP* 2.9 46.5 + - - +
917A THR* 6.2 0.6 - - - +
918A TYR* 3.6 31.3 - - + +
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Residues in contact with LEU 873 (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* 3.7 20.3 - - + -
828A GLU* 3.4 40.6 - - + +
831A LEU* 4.0 14.9 - - + +
869A ALA 3.4 10.1 + - - +
870A GLN* 3.0 18.0 + - + +
872A LYS* 1.3 79.2 - - - +
874A VAL* 1.3 60.0 + - - +
876A ASP* 4.2 5.8 - - + +
877A SER* 3.3 20.3 + - - -
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Residues in contact with VAL 874 (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* 4.5 10.3 - - + -
827A PHE* 3.9 23.6 - - + -
852A LEU* 3.8 30.4 - - + +
863A PHE* 4.1 18.6 - - + -
866A ILE* 4.4 12.3 - - + -
870A GLN* 3.4 17.3 - - + +
871A PHE* 2.8 18.9 + - + +
873A LEU* 1.3 74.8 - - - +
875A LEU* 1.3 66.4 + - - +
877A SER* 3.0 19.1 + - - -
878A ILE* 3.3 13.0 + - + +
900A LEU* 6.5 0.4 - - + -
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Residues in contact with LEU 875 (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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871A PHE* 3.0 18.6 + - + +
872A LYS* 3.8 8.3 - - - +
874A VAL* 1.3 76.6 - - - +
876A ASP* 1.3 62.2 + - - +
878A ILE* 2.9 39.9 + - + +
879A ILE* 3.2 13.8 + - + +
897A LEU* 4.4 13.9 - - + -
900A LEU* 3.5 25.4 - - + -
914A PHE* 3.4 35.2 - - + -
918A TYR* 3.8 24.7 - - + -
922A ILE* 4.0 10.8 - - + -
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Residues in contact with ASP 876 (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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872A LYS* 2.9 44.2 + - - +
873A LEU* 4.3 6.3 - - + +
875A LEU* 1.3 81.0 - - - +
877A SER* 1.3 61.4 + - - +
879A ILE* 3.4 18.4 - - - +
880A TRP* 3.1 20.3 + - - +
918A TYR* 5.0 5.0 - - - -
925A HIS* 5.0 7.7 + - - -
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Residues in contact with SER 877 (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* 4.4 5.8 - - - -
831A LEU* 3.6 19.0 - - - +
848A PHE* 3.5 27.7 - - - -
849A PHE* 3.5 10.9 - - - -
852A LEU* 4.4 4.1 - - - +
873A LEU 3.3 15.1 + - - -
874A VAL* 3.0 16.7 + - - -
876A ASP* 1.3 78.6 - - - +
878A ILE* 1.3 54.6 + - - +
880A TRP* 3.0 11.3 - - - +
881A ALA 3.0 20.8 + - - -
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Residues in contact with ILE 878 (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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849A PHE* 5.0 1.3 - - - -
852A LEU* 3.8 18.4 - - + -
856A ASN* 6.1 0.4 - - - -
863A PHE* 6.2 2.2 - - + -
874A VAL* 3.8 12.3 - - + +
875A LEU* 2.9 34.8 + - + +
877A SER* 1.3 73.2 - - - +
879A ILE* 1.3 67.5 + - + +
880A TRP 3.1 1.1 - - - -
881A ALA* 2.8 24.1 + - - +
882A PHE* 3.2 10.2 + - + -
893A GLY* 3.4 27.1 - - - +
896A ILE* 3.5 24.9 - - + -
897A LEU* 3.9 18.2 - - + +
900A LEU* 4.1 12.6 - - + -
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Residues in contact with ILE 879 (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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875A LEU* 3.4 22.2 - - + +
876A ASP* 3.4 22.9 - - + +
878A ILE* 1.3 76.8 - - + +
880A TRP* 1.3 64.7 + - - +
882A PHE* 3.2 32.5 + - + -
883A LYS* 3.3 29.2 + - + +
897A LEU* 5.4 1.8 - - + -
922A ILE* 4.9 18.4 - - + -
925A HIS* 3.4 55.4 - - + +
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Residues in contact with TRP 880 (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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831A LEU* 5.1 7.9 - - + -
834A ILE* 2.6 30.9 + - + +
835A ASN* 3.7 24.0 - - + +
836A LYS 4.9 3.6 - - - -
837A ASP 3.2 26.5 - - - -
838A PHE* 3.3 37.8 - + - -
849A PHE* 4.4 10.5 - + - -
876A ASP 3.1 9.0 + - - +
877A SER* 3.0 16.6 - - - +
878A ILE 3.1 0.2 - - - -
879A ILE* 1.3 80.2 - - - +
881A ALA* 1.3 51.4 + - - +
883A LYS* 3.5 19.1 + - + +
884A HIS* 2.7 41.3 + + - -
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Residues in contact with ALA 881 (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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849A PHE* 3.8 29.6 - - + -
877A SER 3.0 5.8 + - - +
878A ILE* 2.8 12.4 + - - +
880A TRP* 1.3 77.4 - - - +
882A PHE* 1.3 57.7 + - - +
884A HIS* 2.9 38.7 + - - +
889A VAL* 3.8 8.5 - - - +
890A ALA* 3.3 7.8 + - - -
893A GLY* 3.7 20.4 - - - +
896A ILE* 5.9 0.2 - - + -
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Residues in contact with PHE 882 (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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878A ILE* 3.2 23.9 + - + -
879A ILE* 3.2 39.0 + - + -
881A ALA* 1.3 76.8 - - - +
883A LYS* 1.3 57.1 + - + +
884A HIS 3.3 2.5 - - - -
890A ALA* 3.3 27.9 - - - +
893A GLY 4.5 2.0 - - - -
894A LEU* 3.7 28.9 - - + +
897A LEU* 3.7 24.0 - - + -
922A ILE 5.3 0.2 - - - -
925A HIS* 3.8 29.4 - - + -
926A ILE* 3.6 18.6 - - + -
929A VAL* 3.8 21.2 - - + +
935A HIS* 3.6 16.5 - - - -
942A HIS* 5.1 2.8 - - + -
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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