Contacts of the helix formed by residues 737 - 746 (chain E) in PDB entry 6NYY
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 ASP 737 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543E LYS* 5.5 4.5 + - - -
546E GLU* 4.0 18.7 - - - +
591E LEU* 5.8 0.9 - - - -
592E LEU* 3.1 17.2 - - - +
593E LYS* 3.9 6.5 - - + +
736E LEU* 1.3 75.1 - - - +
738E LYS* 1.3 80.6 + - - +
739E ASN* 3.2 27.9 + - + +
740E ASP* 3.2 25.1 + - - +
741E MET* 3.3 19.2 + - - +
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Residues in contact with LYS 738 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583E TRP* 4.1 26.2 - - + -
590E PRO* 3.9 22.6 - - - +
591E LEU* 3.3 27.1 - - - +
592E LEU* 2.9 16.3 + - + +
609E LEU* 6.0 3.4 - - + +
737E ASP* 1.3 83.0 + - - +
739E ASN* 1.3 62.6 + - - +
741E MET* 3.2 16.0 + - - +
742E VAL* 3.2 20.2 + - + +
748E ARG* 4.9 8.7 - - - +
752E GLU* 5.5 6.9 - - - +
753E LYS 5.9 0.2 + - - -
754E SER* 4.9 15.2 - - - -
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Residues in contact with ASN 739 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737E ASP* 3.2 21.3 + - + +
738E LYS* 1.3 80.8 - - - +
740E ASP* 1.3 62.5 + - - +
742E VAL* 3.7 8.4 + - - +
743E GLU* 3.5 29.3 + - - +
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Residues in contact with ASP 740 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729E LEU* 5.4 2.3 - - + +
733E LYS* 3.8 25.4 + - - +
735E VAL 4.0 5.4 - - - +
736E LEU* 3.7 23.2 - - + +
737E ASP* 3.2 32.6 + - - +
738E LYS 3.2 0.4 - - - -
739E ASN* 1.3 81.7 - - - +
741E MET* 1.3 63.0 + - - +
743E GLU* 3.4 15.0 + - - +
744E LEU* 3.4 26.7 + - + +
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Residues in contact with MET 741 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579E ALA* 3.9 30.7 - - + +
583E TRP* 3.6 24.9 - - + -
591E LEU* 3.8 20.9 - - + -
726E VAL* 4.0 16.8 - - + -
736E LEU* 3.8 26.9 - - + -
737E ASP 3.4 14.1 - - - +
738E LYS* 3.2 6.3 + - - +
740E ASP* 1.3 75.3 - - - +
742E VAL* 1.3 61.0 + - - +
744E LEU* 3.4 6.2 + - - +
745E LEU* 3.0 60.1 + - + +
746E GLY 3.9 0.7 - - - +
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Residues in contact with VAL 742 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583E TRP* 3.9 15.9 - - + -
738E LYS* 3.2 23.2 + - + +
739E ASN* 4.0 9.6 - - - +
740E ASP 3.3 0.2 - - - -
741E MET* 1.3 76.5 - - - +
743E GLU* 1.3 60.2 + - + +
746E GLY* 2.8 45.0 + - - +
747E PRO* 4.2 11.7 - - + -
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Residues in contact with GLU 743 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733E LYS* 5.3 5.0 + - - -
739E ASN* 3.5 18.1 + - - +
740E ASP* 3.4 17.9 + - - +
741E MET 3.3 0.4 - - - -
742E VAL* 1.3 78.2 - - + +
744E LEU* 1.3 61.9 + - + +
746E GLY 4.8 0.2 - - - -
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Residues in contact with LEU 744 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725E LYS* 4.0 37.1 + - + +
726E VAL* 3.8 33.2 - - + +
729E LEU* 3.7 33.0 - - + -
736E LEU* 5.1 3.8 - - + -
740E ASP 3.4 17.5 + - - +
741E MET* 4.0 11.2 - - - +
742E VAL 3.2 0.6 - - - -
743E GLU* 1.3 83.4 - - + +
745E LEU* 1.3 73.8 + - + +
746E GLY 3.8 0.2 - - - -
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Residues in contact with LEU 745 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580E VAL* 4.5 8.3 - - + -
583E TRP* 4.1 26.4 + - + +
584E TYR* 3.6 32.4 + - + +
722E ASP* 3.8 35.7 - - + +
725E LYS* 5.2 2.0 - - + -
726E VAL* 4.3 6.7 - - + -
741E MET* 3.0 39.3 + - + +
744E LEU* 1.3 91.9 - - + +
746E GLY* 1.3 62.7 + - - +
747E PRO 4.3 4.2 - - - +
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Residues in contact with GLY 746 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583E TRP* 3.3 16.8 - - - -
742E VAL* 2.8 27.3 + - - -
743E GLU 4.8 0.2 - - - -
744E LEU 3.8 1.0 - - - -
745E LEU* 1.3 79.4 - - - +
747E PRO* 1.3 78.1 - - - +
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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