Contacts of the helix formed by residues 840 - 850 (chain A) in PDB entry 3NKO
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 840 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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839A ARG* 1.3 76.7 - - - +
841A TYR* 1.3 65.2 + - - +
842A SER* 3.5 9.7 + - - -
843A GLU* 2.9 45.4 + - - +
844A ILE* 3.1 20.3 + - - +
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Residues in contact with TYR 841 (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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541A PRO* 3.3 45.1 - - + +
542A THR 3.5 21.4 + - - -
543A LEU* 3.5 26.9 - - + -
544A PRO* 3.3 11.4 - - - +
834A TYR 5.9 2.0 - - - -
839A ARG 3.8 1.2 + - - -
840A SER* 1.3 73.1 - - - +
842A SER* 1.3 56.9 + - - +
844A ILE* 3.1 14.0 + - + +
845A LEU* 2.9 42.1 + - + +
848A LYS* 4.8 4.3 - - - -
1010A EDO 2.5 36.7 + - - -
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Residues in contact with SER 842 (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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528A GLY 3.9 15.6 + - - +
531A ASN* 2.9 33.0 + - - +
532A HIS 5.9 0.2 - - - -
541A PRO* 4.1 10.6 - - - +
840A SER* 3.2 8.4 + - - -
841A TYR* 1.3 78.9 - - - +
843A GLU* 1.3 61.8 + - - +
845A LEU* 3.1 10.3 + - - +
846A THR* 3.0 26.2 + - - -
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Residues in contact with GLU 843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A ARG* 3.1 30.4 + - + -
840A SER* 2.9 49.6 + - - +
842A SER* 1.3 77.4 - - - +
844A ILE* 1.3 58.1 + - - +
846A THR* 3.3 8.9 + - - -
847A LEU* 3.0 25.8 + - - +
1028A EDO 3.1 31.2 + - - +
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Residues in contact with ILE 844 (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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784A LEU* 4.8 2.5 - - + -
834A TYR* 3.6 35.2 - - + +
837A THR* 3.7 34.3 - - + +
839A ARG* 4.0 13.9 - - + +
840A SER 3.1 14.0 + - - +
841A TYR* 3.1 20.5 + - + +
843A GLU* 1.3 76.9 - - - +
845A LEU* 1.3 58.1 + - - +
847A LEU* 3.0 11.9 + - + +
848A LYS* 2.8 44.3 + - + +
1028A EDO 4.1 12.1 - - - +
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Residues in contact with LEU 845 (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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526A THR* 3.6 20.6 - - + +
527A HIS 3.5 25.1 - - - +
528A GLY* 4.0 7.4 - - - -
529A SER* 3.8 14.6 - - - +
541A PRO* 3.7 28.3 - - + -
841A TYR* 2.9 34.2 + - + +
842A SER* 3.1 7.8 + - - +
844A ILE* 1.3 77.2 - - - +
846A THR* 1.3 62.2 + - - +
848A LYS* 3.2 8.3 + - + +
849A THR* 3.1 27.4 + - - +
1010A EDO 3.7 23.6 - - - +
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Residues in contact with THR 846 (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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501A PRO* 5.1 12.1 - - + -
529A SER* 2.7 22.6 + - - +
530A LEU* 6.0 0.4 - - + -
532A HIS* 3.5 28.4 + - + +
842A SER 3.0 13.3 + - - -
843A GLU* 3.5 11.4 - - - -
845A LEU* 1.3 77.2 - - - +
847A LEU* 1.3 61.1 + - - +
849A THR* 3.0 22.5 + - - +
850A TYR* 3.3 9.0 + - - +
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Residues in contact with LEU 847 (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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768A THR* 5.3 0.2 - - + -
784A LEU* 3.6 50.7 - - + +
786A VAL* 3.5 31.5 - - + +
822A VAL* 5.0 1.0 - - - +
834A TYR* 3.7 38.8 - - + +
843A GLU 3.0 14.7 + - - +
844A ILE* 3.3 12.8 - - + +
846A THR* 1.3 74.1 - - - +
848A LYS* 1.3 62.3 + - - +
850A TYR* 3.2 21.0 + - - +
1020A EDO 3.7 13.0 - - - -
1028A EDO 4.1 11.4 - - - +
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Residues in contact with LYS 848 (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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526A THR* 5.8 0.2 - - + -
543A LEU* 5.9 0.2 - - - +
821A ARG* 3.5 0.9 - - - +
822A VAL* 3.2 23.6 + - + -
823A ARG* 2.9 36.1 + - + +
826A GLU* 2.8 27.4 + - - +
832A ASP* 3.0 8.7 + - - -
833A PHE* 3.0 29.2 + - - +
834A TYR* 4.0 15.5 - - + -
841A TYR* 4.8 3.4 - - - -
844A ILE* 2.8 35.1 + - + +
845A LEU* 3.2 10.7 + - + +
847A LEU* 1.3 73.5 - - - +
849A THR* 1.3 59.7 + - - +
850A TYR 3.3 0.4 + - - -
1010A EDO 2.9 39.2 + - - +
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Residues in contact with THR 849 (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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202A ARG* 4.9 2.1 + - - -
503A PHE* 6.1 0.7 - - - +
504A GLU* 4.9 5.8 - - - +
507A GLU* 3.8 18.1 - - - +
526A THR* 3.8 30.5 - - + +
529A SER* 3.9 9.6 + - - -
530A LEU* 6.1 0.5 - - - +
821A ARG* 3.1 31.6 - - - +
823A ARG* 4.8 1.8 - - + -
845A LEU 3.1 13.4 + - - +
846A THR* 3.0 18.7 + - - +
847A LEU 3.2 0.2 - - - -
848A LYS* 1.3 77.5 - - + +
850A TYR* 1.3 65.6 + - - +
851A LEU* 3.5 1.7 + - - +
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Residues in contact with TYR 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A PRO* 6.4 2.0 - - + -
502A PRO* 6.1 2.7 - - + -
786A VAL* 3.2 32.9 - - + +
787A SER* 5.3 0.4 - - - -
820A ALA 4.1 1.6 - - - +
821A ARG* 3.4 18.9 - - - -
822A VAL 4.5 1.2 + - - -
846A THR 3.3 9.6 + - - +
847A LEU* 3.2 17.8 + - - +
848A LYS 3.3 0.5 - - - +
849A THR* 1.3 80.0 - - - +
851A LEU* 1.3 69.6 + - - +
852A HIS* 2.8 44.4 + - + -
853A THR 5.1 0.2 + - - -
1020A EDO 3.3 39.6 + - - -
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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