Contacts of the helix formed by residues 714 - 724 (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 VAL 714 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710A TYR* 2.9 45.8 + - + +
713A ARG* 1.3 116.1 - - + +
715A LEU* 1.3 64.1 + - + +
716A VAL 3.6 0.9 - - - -
717A LYS* 3.6 6.7 + - - +
718A LYS* 3.1 29.8 + - + +
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Residues in contact with LEU 715 (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* 3.2 38.2 + - + +
711A PHE* 3.3 16.1 + - + +
714A VAL* 1.3 78.7 - - + +
716A VAL* 1.3 60.6 + - - +
718A LYS* 3.1 15.3 + - + +
719A TYR* 2.8 53.4 + - + +
811A VAL* 4.6 0.2 - - + -
812A GLU* 3.5 38.1 - - + +
815A MET* 3.4 33.4 - - + -
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Residues in contact with VAL 716 (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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629A TYR* 4.0 13.0 - - - +
631A ILE* 4.1 16.8 - - + -
681A LEU* 3.7 25.8 - - + -
711A PHE* 3.1 47.5 + - + +
712A GLN* 4.2 8.0 + - - +
714A VAL 3.6 0.2 - - - -
715A LEU* 1.3 74.8 - - - +
717A LYS* 1.3 64.7 + - - +
719A TYR* 3.2 12.2 + - + +
720A ALA* 3.0 21.1 + - - +
726A VAL* 3.9 3.7 - - + +
728A VAL* 4.1 18.6 - - + -
767A ILE* 5.8 0.2 - - + -
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Residues in contact with LYS 717 (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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631A ILE* 5.0 4.3 - - + -
632A SER 4.4 0.2 + - - -
633A LYS* 2.6 31.9 + - - +
634A GLN* 4.1 2.0 - - - +
635A ALA* 3.0 31.5 + - + +
637A VAL* 3.7 30.5 - - + -
681A LEU* 4.6 5.7 - - + +
712A GLN 5.1 0.6 + - - -
713A ARG 4.5 4.6 + - - +
714A VAL 3.6 8.8 + - - +
715A LEU 3.2 0.4 - - - -
716A VAL* 1.3 80.2 - - - +
718A LYS* 1.3 57.9 + - - +
720A ALA* 3.1 8.8 + - + -
721A SER* 2.9 38.8 + - - -
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Residues in contact with LYS 718 (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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714A VAL* 3.1 21.0 + - + +
715A LEU* 3.1 22.2 + - + +
717A LYS* 1.3 78.8 - - - +
719A TYR* 1.3 67.4 + - - +
721A SER* 3.5 5.8 + - - -
722A GLU* 3.1 52.1 + - + +
812A GLU* 2.9 39.3 + - - -
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Residues in contact with TYR 719 (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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711A PHE* 4.1 13.0 - + - -
715A LEU* 2.8 41.1 + - + +
716A VAL* 3.5 10.1 - - - +
718A LYS* 1.3 90.0 - - - +
720A ALA* 1.3 60.4 + - - +
722A GLU* 3.1 13.4 + - - -
723A ARG* 2.9 46.3 + - - +
726A VAL* 3.8 16.6 - - + -
767A ILE* 3.5 35.9 - - + -
787A SER* 5.8 0.9 - - - -
789A PHE* 4.0 12.8 - + - -
812A GLU* 4.5 6.1 + - - +
815A MET* 3.7 20.4 - - - +
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Residues in contact with ALA 720 (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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631A ILE* 3.6 40.4 - - + +
632A SER 3.8 7.4 - - - +
633A LYS* 3.5 5.4 - - - -
716A VAL 3.0 13.0 + - - +
717A LYS* 3.1 10.3 + - + +
719A TYR* 1.3 75.3 - - - +
721A SER* 1.3 61.6 + - - +
724A ASN* 3.1 4.2 + - - -
725A GLY* 2.5 36.0 + - - -
726A VAL* 3.8 4.6 - - + +
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Residues in contact with SER 721 (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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633A LYS* 3.7 33.7 + - - -
717A LYS* 2.9 30.5 + - - -
718A LYS* 3.7 8.1 - - - -
720A ALA* 1.3 79.9 - - - +
722A GLU* 1.3 63.4 + - - +
723A ARG 3.6 0.2 + - - -
724A ASN 4.0 1.7 + - - -
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Residues in contact with GLU 722 (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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718A LYS* 3.1 49.2 + - + +
719A TYR* 3.1 13.5 + - - +
721A SER* 1.3 80.2 - - - +
723A ARG* 1.3 66.9 - - + +
724A ASN 3.5 0.6 + - - -
773A PHE* 5.2 5.0 - - - +
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Residues in contact with ARG 723 (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 TYR* 2.9 28.7 + - - +
722A GLU* 1.3 84.9 - - + +
724A ASN* 1.3 71.3 + - - +
725A GLY 3.7 5.9 - - - +
726A VAL* 4.0 4.2 - - - +
767A ILE* 3.0 33.1 + - - +
768A THR 3.6 0.4 - - - -
769A SER* 2.7 43.9 + - - +
770A CYS 4.8 2.1 + - - +
773A PHE* 4.4 16.0 - - - +
775A GLN 4.7 2.1 - - - +
777A ALA 5.3 0.2 + - - -
785A SER* 2.9 38.6 + - - -
786A VAL* 3.9 1.4 - - - +
787A SER* 3.1 26.6 + - - -
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Residues in contact with ASN 724 (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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633A LYS* 3.6 33.3 - - + +
634A GLN* 5.4 1.2 + - - +
720A ALA 3.1 5.5 + - - -
721A SER 4.0 1.8 + - - -
722A GLU 3.5 2.4 - - - -
723A ARG* 1.3 82.7 - - - +
725A GLY* 1.3 59.3 + - - +
773A PHE* 3.0 25.8 + - + +
774A THR* 3.5 9.5 + - - +
775A GLN 3.4 3.5 - - - +
776A PRO* 3.4 33.5 - - - +
777A ALA 3.1 20.8 + - - -
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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