Contacts of the helix formed by residues 666 - 677 (chain A) in PDB entry 5WRZ
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 PRO 666 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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664A LYS 3.5 4.7 - - - +
665A LEU* 1.4 93.6 - - + +
667A LYS* 1.3 66.7 + - - +
668A PRO* 3.4 3.6 - - + -
669A VAL* 3.0 25.4 + - + +
670A GLN* 3.0 10.9 + - - +
801A ILE 5.8 1.1 - - - +
802A LYS* 6.3 0.7 - - - -
803A VAL* 4.1 27.4 - - + +
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Residues in contact with LYS 667 (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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665A LEU 3.7 1.9 + - - -
666A PRO* 1.3 71.2 - - - +
668A PRO* 1.3 67.7 - - + +
670A GLN* 3.2 19.5 + - + +
671A ASP* 2.9 59.7 + - - +
674A LYS* 3.6 16.6 - - - +
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Residues in contact with PRO 668 (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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666A PRO* 3.5 9.2 - - + -
667A LYS* 1.3 94.7 - - + +
669A VAL* 1.3 55.6 + - - +
671A ASP* 3.3 9.5 + - + +
672A LEU 2.9 23.2 + - - -
803A VAL* 4.0 18.4 - - + -
806A ARG* 6.0 1.8 - - - +
835A ASP* 3.7 33.0 - - + +
837A PHE* 3.5 23.6 - - + -
1004A LYS* 5.7 0.7 + - - +
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Residues in contact with VAL 669 (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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665A LEU* 4.2 14.4 - - + -
666A PRO* 3.0 21.5 + - + +
668A PRO* 1.3 75.4 - - - +
670A GLN* 1.3 59.4 + - - +
672A LEU* 3.2 6.4 + - + +
673A ILE* 3.0 30.1 + - + +
794A TYR* 3.9 33.0 - - + -
801A ILE* 3.8 27.1 - - + +
803A VAL* 3.9 15.0 - - + +
837A PHE* 3.8 22.9 - - + -
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Residues in contact with GLN 670 (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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662A LYS 4.5 3.6 + - - +
663A SER* 3.2 37.1 + - - -
665A LEU* 2.6 32.0 + - + +
666A PRO 3.0 12.1 + - - +
667A LYS* 3.5 20.6 + - - +
669A VAL* 1.3 77.1 - - - +
671A ASP* 1.3 63.5 + - - +
673A ILE* 3.3 2.8 + - - +
674A LYS* 3.0 38.0 + - - +
788A ASP* 5.0 1.0 - - - +
790A ILE* 3.9 28.2 - - + +
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Residues in contact with ASP 671 (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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667A LYS* 2.9 56.7 + - - +
668A PRO* 3.3 7.0 + - + +
670A GLN* 1.3 72.3 - - - +
672A LEU* 1.3 61.6 + - - +
674A LYS* 3.4 15.6 + - - +
675A MET* 3.0 26.2 + - - +
1004A LYS* 4.3 20.7 + - - +
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Residues in contact with LEU 672 (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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668A PRO 2.9 15.1 + - - +
669A VAL* 3.2 9.2 + - - +
671A ASP* 1.3 76.8 - - - +
673A ILE* 1.3 58.8 + - + +
675A MET* 3.3 11.4 + - + +
676A ILE* 3.0 42.3 + - + +
801A ILE* 4.1 33.4 - - + -
837A PHE* 4.0 25.6 - - + -
873A LEU* 5.3 2.2 - - + -
918A LEU* 3.8 36.3 - - + -
1002A LEU* 3.9 25.6 - - + -
1004A LYS* 5.6 1.7 - - + +
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Residues in contact with ILE 673 (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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669A VAL* 3.0 21.7 + - + +
670A GLN 3.3 4.2 + - - +
672A LEU* 1.3 77.4 - - + +
674A LYS* 1.3 62.8 + - - +
676A ILE* 3.4 9.2 + - + +
677A PHE* 3.0 28.0 + - + +
790A ILE* 3.8 34.8 - - + +
793A ASN* 3.9 22.0 - - + +
794A TYR* 3.9 29.8 - - + +
797A LEU* 3.3 33.4 - - + -
801A ILE* 4.4 6.5 - - + -
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Residues in contact with LYS 674 (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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667A LYS* 3.6 15.2 - - - +
670A GLN* 3.0 25.6 + - - +
671A ASP* 3.5 30.5 + - - +
673A ILE* 1.3 76.8 - - - +
675A MET* 1.3 62.1 + - - +
677A PHE* 4.0 1.4 - - - -
678A ASP* 3.4 26.0 + - - +
790A ILE* 3.8 23.5 - - + +
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Residues in contact with MET 675 (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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671A ASP* 3.0 11.9 + - + +
672A LEU* 3.5 21.8 - - + +
674A LYS* 1.3 76.5 - - - +
676A ILE* 1.3 63.7 + - + +
678A ASP* 3.4 17.7 + - - +
681A SER* 4.8 4.5 + - - -
866A THR* 4.6 24.0 + - + +
867A THR* 6.0 1.2 - - - +
916A ILE* 4.3 20.9 - - - +
918A LEU* 3.8 31.0 - - + -
1004A LYS* 3.5 29.4 - - + +
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Residues in contact with ILE 676 (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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672A LEU* 3.0 21.8 + - + +
673A ILE* 3.5 16.6 - - + +
675A MET* 1.3 77.9 - - + +
677A PHE* 1.3 71.7 + - + +
678A ASP 3.6 0.7 + - - -
682A MET* 4.1 9.2 - - - +
774A ALA* 5.1 0.3 - - - +
797A LEU* 3.8 39.7 - - + -
866A THR 4.4 10.0 - - - +
867A THR* 5.0 6.8 - - - +
869A PHE* 3.9 11.9 - - + -
870A ALA* 4.2 26.3 + - + +
873A LEU* 4.4 10.5 - - + -
918A LEU* 3.8 28.9 - - + -
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Residues in contact with PHE 677 (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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673A ILE* 3.0 24.8 + - + +
674A LYS* 4.0 2.7 - - - +
676A ILE* 1.3 85.4 - - + +
678A ASP* 1.3 62.2 + - - +
679A VAL* 3.1 5.5 + - - +
682A MET* 3.6 10.1 - - - +
774A ALA* 4.2 13.0 - - + -
777A LEU* 4.3 15.3 - - + -
778A LEU* 3.3 44.9 - - + +
793A ASN* 3.4 48.7 - - + +
796A LYS* 4.6 4.9 - - + -
797A LEU* 3.6 31.4 - - + -
870A ALA* 4.0 17.5 - - + -
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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