Contacts of the helix formed by residues 810 - 818 (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 TRP 810 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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706A ARG* 3.5 31.3 - - + +
707A VAL* 3.9 22.7 - - + -
797A ASN* 3.4 37.7 - - - -
800A SER* 3.5 29.8 + - - -
802A ASN* 3.4 32.1 - - + +
803A SER* 3.5 13.6 + - - +
805A GLU 3.1 18.4 + - - -
806A ASP 3.3 21.5 - - - -
807A GLU* 3.1 11.8 + - + +
808A SER 3.5 0.8 - - - -
809A LYS* 1.3 81.8 - - + +
811A VAL* 1.3 81.3 + - + +
812A GLU 3.4 2.0 - - - +
813A GLU* 3.3 16.6 + - - +
814A LEU* 3.2 21.4 + - + +
1017A EDO 5.4 0.7 + - - -
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Residues in contact with VAL 811 (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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707A VAL* 3.8 37.5 - - + +
710A TYR* 3.9 20.9 - - + -
807A GLU* 3.0 44.6 + - + +
810A TRP* 1.3 96.6 - - + +
812A GLU* 1.3 67.2 + - - +
814A LEU* 3.1 5.3 + - - +
815A MET* 3.0 32.0 + - - +
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Residues in contact with GLU 812 (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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710A TYR* 4.4 12.3 + - + +
715A LEU* 3.5 32.3 - - + +
718A LYS* 2.9 34.5 + - - -
719A TYR* 4.5 7.8 + - - +
807A GLU 4.7 1.2 + - - -
808A SER 5.8 0.4 - - - +
810A TRP 3.4 0.8 - - - +
811A VAL* 1.3 76.4 - - - +
813A GLU* 1.3 57.6 - - - +
815A MET* 3.1 9.4 + - - +
816A LYS* 2.9 53.6 + - - +
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Residues in contact with GLU 813 (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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802A ASN* 4.9 8.7 - - - +
809A LYS 4.6 9.4 - - - +
810A TRP* 3.3 16.5 + - - +
811A VAL 3.2 0.2 - - - -
812A GLU* 1.3 78.1 - - - +
814A LEU* 1.3 62.5 + - - +
816A LYS* 3.5 12.5 + - - +
817A MET* 3.4 20.1 + - - +
1017A EDO 3.3 26.8 + - - +
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Residues in contact with LEU 814 (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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707A VAL* 3.9 24.2 - - + -
791A LEU* 5.5 4.3 - - + -
792A PRO* 5.1 4.3 - - + -
797A ASN* 4.6 0.2 - - - +
799A GLU* 3.4 36.8 - - + +
800A SER* 3.9 24.2 - - - +
810A TRP* 3.2 12.4 + - + +
811A VAL* 3.1 9.2 + - - +
813A GLU* 1.3 77.6 - - - +
815A MET* 1.3 63.7 + - + +
817A MET* 3.2 10.4 + - - +
818A HIS* 3.3 36.9 - - + -
1017A EDO 4.1 10.3 - - - -
1023A EDO 3.8 30.3 - - - +
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Residues in contact with MET 815 (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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707A VAL* 4.7 3.4 - - + -
711A PHE* 3.4 38.4 - - + -
715A LEU* 3.4 25.4 - - - -
719A TYR* 3.7 15.9 - - - +
789A PHE* 3.2 37.3 - - + -
791A LEU* 3.9 29.2 - - + -
811A VAL* 3.0 27.8 + - + +
812A GLU* 3.1 9.2 + - - +
814A LEU* 1.3 77.1 - - + +
816A LYS* 1.3 62.1 + - + +
818A HIS 3.0 10.9 + - - -
819A THR 3.1 9.7 + - - -
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Residues in contact with LYS 816 (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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479A LYS* 3.8 11.6 - - - +
789A PHE* 4.8 0.9 - - + -
812A GLU* 2.9 41.2 + - - +
813A GLU* 3.8 10.1 - - - +
814A LEU 3.3 0.2 - - - -
815A MET* 1.3 76.0 - - + +
817A MET* 1.3 61.5 + - + +
818A HIS 3.2 0.5 + - - -
819A THR* 3.3 22.7 - - - +
854A TYR* 3.8 54.0 - - + +
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Residues in contact with MET 817 (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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423A TYR* 4.1 8.3 - - - +
429A PRO* 3.4 21.2 - - + +
431A ARG* 2.9 53.3 + - - +
446A LEU* 4.3 6.7 - - - -
477A ASP* 3.8 10.1 - - - +
479A LYS* 4.2 12.6 - - - +
813A GLU 3.4 9.8 + - - +
814A LEU 3.2 11.1 + - - +
815A MET 3.2 0.4 - - - -
816A LYS* 1.3 79.7 - - - +
818A HIS* 1.3 64.8 + - + +
819A THR 3.4 0.7 - - - -
1016A EDO 4.2 20.4 - - - +
1017A EDO 3.9 23.6 - - - +
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Residues in contact with HIS 818 (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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427A HIS 3.9 9.2 - - - -
428A LEU 4.4 0.2 - - - -
429A PRO* 3.5 37.8 - - + +
430A LYS* 4.6 2.6 + - - +
431A ARG* 4.7 0.4 - - - +
762A HIS* 6.0 0.4 - - - -
789A PHE* 3.5 1.9 - - - -
790A ILE* 3.0 38.5 + - - +
791A LEU* 4.2 10.1 - - + -
792A PRO* 3.7 27.9 - - + +
799A GLU* 2.8 28.9 + - - -
814A LEU* 3.3 35.2 + - + +
815A MET 3.0 8.9 + - - +
817A MET* 1.3 84.8 - - + +
819A THR* 1.3 65.9 + - - +
820A ALA* 4.2 0.3 - - - +
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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