Contacts of the helix formed by residues 891 - 902 (chain A) in PDB entry 4N78
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 SER 891 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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716A VAL* 4.5 10.2 - - - +
885A PRO* 3.5 11.7 - - - -
889A HIS 3.8 1.4 - - - -
890A GLY* 1.3 77.3 - - - +
892A LYS* 1.3 61.1 + - - +
893A ALA* 3.7 7.3 + - - +
894A LEU* 3.3 28.7 + - - +
895A ASN* 2.9 31.0 + - - -
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Residues in contact with LYS 892 (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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885A PRO* 3.3 32.6 - - + +
891A SER* 1.3 73.9 - - - +
893A ALA* 1.3 63.2 + - - +
895A ASN* 3.2 10.1 + - + +
896A LEU* 3.0 37.8 + - + +
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Residues in contact with ALA 893 (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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738A ILE* 4.7 20.4 - - + +
739A HIS 5.7 4.0 - - - +
891A SER* 3.3 7.3 + - - +
892A LYS* 1.3 79.3 - - - +
894A LEU* 1.3 59.1 + - + +
896A LEU* 3.4 8.1 + - - +
897A ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 894 (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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716A VAL* 3.8 30.5 - - + +
719A GLY 4.1 17.7 - - - +
720A SER* 4.0 12.1 - - - +
723A LEU* 4.0 27.1 - - + -
728A ARG* 4.9 1.3 - - - +
738A ILE* 4.7 9.2 - - + -
739A HIS 6.1 0.4 - - - +
889A HIS* 3.5 29.4 - - + +
891A SER* 3.3 22.6 + - - +
892A LYS 3.3 0.2 - - - -
893A ALA* 1.3 76.7 - - + +
895A ASN* 1.3 67.5 + - - +
897A ALA* 4.2 2.0 - - - -
898A TYR* 2.9 37.4 + - + -
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Residues in contact with ASN 895 (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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882A ASN* 5.6 2.6 - - - +
885A PRO* 3.6 28.1 - - - +
888A LEU* 3.5 15.7 - - + +
889A HIS* 3.1 44.2 + - - +
891A SER 2.9 26.1 + - - +
892A LYS* 3.4 11.2 - - + +
894A LEU* 1.3 76.5 - - - +
896A LEU* 1.3 60.3 + - + +
898A TYR* 4.3 0.7 - - - +
899A SER* 2.9 32.2 + - - -
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Residues in contact with LEU 896 (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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892A LYS* 3.0 36.5 + - + +
893A ALA* 3.6 9.4 - - - +
895A ASN* 1.3 77.5 - - + +
897A ALA* 1.3 66.9 + - - +
899A SER* 3.2 7.7 + - - -
900A SER* 2.9 32.4 + - - +
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Residues in contact with ALA 897 (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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723A LEU* 4.3 16.8 - - + -
727A LEU* 4.8 4.8 - - + +
738A ILE* 4.0 26.9 - - + -
893A ALA 2.9 16.4 + - - +
894A LEU* 3.3 8.7 + - - +
896A LEU* 1.3 76.3 - - - +
898A TYR* 1.3 57.8 + - + +
900A SER* 3.3 6.1 + - - -
901A ILE* 3.0 31.7 + - - +
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Residues in contact with TYR 898 (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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719A GLY* 2.6 34.2 + - - -
722A LEU* 3.3 12.8 - - + +
723A LEU* 3.0 36.3 + - + -
804A ILE* 3.8 19.9 - - + +
889A HIS* 3.5 37.2 - + + +
894A LEU* 2.9 34.0 + - + +
897A ALA* 1.3 73.5 - - - +
899A SER* 1.3 65.9 + - - +
901A ILE* 3.1 16.8 + - + +
902A TYR* 3.0 56.1 + + + -
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Residues in contact with SER 899 (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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797A GLU* 5.2 11.9 + - - +
889A HIS* 5.2 1.9 - - - -
895A ASN 2.9 22.1 + - - -
896A LEU* 3.4 11.7 - - - -
898A TYR* 1.3 76.5 - - - +
900A SER* 1.3 61.9 + - - +
902A TYR* 3.5 4.5 + - - +
903A GLY* 3.2 18.9 + - - -
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Residues in contact with SER 900 (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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896A LEU* 2.9 17.7 + - - +
897A ALA* 3.6 8.5 - - - -
899A SER* 1.3 73.2 - - - +
901A ILE* 1.3 67.6 - - - +
903A GLY* 3.0 14.6 + - - -
904A SER* 3.9 7.1 + - - -
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Residues in contact with ILE 901 (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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723A LEU* 3.8 20.2 - - + -
724A ASP* 5.0 9.2 - - + +
727A LEU* 3.6 29.4 - - + -
897A ALA 3.0 18.1 + - - +
898A TYR* 3.1 21.3 + - + +
900A SER* 1.3 78.4 - - - +
902A TYR* 1.3 83.1 + - + +
903A GLY 3.5 0.3 + - - -
904A SER* 3.7 16.7 + - - -
905A TYR* 3.9 9.7 - - + -
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Residues in contact with TYR 902 (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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796A VAL* 4.0 27.6 - - + -
797A GLU* 3.7 51.1 - - + +
800A GLY* 3.2 27.0 - - - -
889A HIS* 4.6 5.2 - + - -
898A TYR* 3.0 53.9 + + + +
899A SER 3.8 3.1 - - - +
901A ILE* 1.3 88.9 - - + +
903A GLY* 1.3 62.7 + - - +
904A SER 3.1 2.2 - - - -
905A TYR* 3.3 25.1 + + + +
906A ARG* 3.6 15.5 - - - +
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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
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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