Contacts of the helix formed by residues 761 - 767 (chain A) in PDB entry 5NK4
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 761 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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655A LYS* 4.7 5.5 - - - -
659A ASP* 4.0 16.0 + - - -
760A LEU* 1.3 81.0 - - - +
762A ARG* 1.3 64.2 + - - +
763A VAL 3.2 1.0 + - - -
764A LEU* 3.6 3.3 + - - +
765A GLU* 3.0 47.7 + - - +
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Residues in contact with ARG 762 (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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646A LYS* 3.7 18.4 - - - +
659A ASP* 3.6 46.8 + - + +
660A PHE* 5.3 2.2 - - - +
663A GLU* 3.6 20.6 + - - -
757A ASP* 2.8 28.4 + - - -
758A PHE 2.8 34.1 + - - -
759A GLY* 4.1 13.7 - - - -
760A LEU 3.1 2.8 + - - +
761A SER* 1.3 80.8 + - - +
763A VAL* 1.3 69.1 + - - +
765A GLU* 3.9 10.1 - - - -
766A ASP* 3.0 63.2 + - - +
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Residues in contact with VAL 763 (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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735A TYR* 4.5 1.6 - - - +
737A HIS* 4.2 9.0 - - + +
738A ARG* 4.3 7.0 - - - +
739A ASP* 3.5 30.1 - - + +
757A ASP* 3.8 29.6 - - - +
758A PHE* 3.6 9.0 - - - -
759A GLY* 3.4 41.1 - - - +
760A LEU 3.8 4.9 - - - +
761A SER 3.1 1.4 - - - -
762A ARG* 1.3 87.1 - - - +
764A LEU* 1.3 64.1 + - + +
766A ASP* 4.2 1.4 - - - +
767A ASP* 3.5 20.8 + - - +
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Residues in contact with LEU 764 (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 ARG* 3.8 37.5 - - + +
739A ASP* 3.9 18.4 - - + -
760A LEU 4.6 0.8 + - - +
761A SER* 3.6 4.9 + - - +
763A VAL* 1.3 76.5 - - + +
765A GLU* 1.3 61.3 + - - +
766A ASP 3.5 0.2 + - - -
767A ASP* 3.6 2.6 + - - -
770A ALA* 3.4 10.9 - - + +
778A LYS* 2.9 37.3 + - + +
779A ILE* 3.6 26.7 - - + -
780A PRO* 3.6 28.0 - - + -
794A PHE* 4.3 7.4 - - + -
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Residues in contact with GLU 765 (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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655A LYS* 4.2 23.0 + - - -
659A ASP* 4.4 2.9 - - - +
761A SER* 3.0 45.2 + - - +
762A ARG* 4.0 6.8 - - - +
764A LEU* 1.3 79.0 - - + +
766A ASP* 1.3 65.2 + - - +
778A LYS* 3.2 31.5 + - + -
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Residues in contact with ASP 766 (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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646A LYS* 5.2 1.4 + - - -
762A ARG* 3.0 57.7 + - - +
763A VAL 4.3 1.6 - - - +
765A GLU* 1.3 81.8 - - - +
767A ASP* 1.3 63.2 + - - +
768A PRO* 3.3 8.8 - - - +
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Residues in contact with ASP 767 (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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739A ASP* 2.6 33.6 - - - +
743A ARG* 2.7 29.8 + - - -
744A ASN* 3.9 3.1 + - - -
757A ASP* 5.3 2.0 - - - +
763A VAL 3.5 9.6 + - - +
764A LEU* 3.6 3.6 + - - +
765A GLU 3.4 1.4 - - - -
766A ASP* 1.3 77.3 - - - +
768A PRO* 1.3 66.9 - - - +
769A GLU* 2.9 23.9 + - - +
770A ALA* 3.0 16.5 + - + +
778A LYS* 2.9 22.8 + - - -
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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