Contacts of the helix formed by residues 500 - 507 (chain A) in PDB entry 2QR8
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 GLU 500 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A GLY* 1.3 71.2 - - - -
501A LEU* 1.3 66.2 + - - +
502A LEU* 3.4 14.1 - - - +
503A ASP* 3.1 33.0 + - + +
504A LYS* 3.2 23.2 + - - +
542A PRO* 3.4 26.7 - - - +
543A SER* 3.4 25.4 + - - +
545A ILE 3.9 4.3 - - - +
546A LEU* 3.9 11.7 - - + +
700A LYS* 3.4 23.7 + - - +
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Residues in contact with LEU 501 (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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499A GLY 3.6 1.4 + - - -
500A GLU* 1.3 72.8 - - - +
502A LEU* 1.3 68.7 + - - +
504A LYS* 3.3 2.4 + - - +
505A ILE* 3.0 40.0 + - + +
519A VAL* 4.0 13.7 - - + -
523A ILE* 4.3 8.1 - - + -
542A PRO 6.0 0.4 - - - +
545A ILE* 3.0 30.6 + - + +
546A LEU* 4.5 2.2 - - - +
547A TYR* 3.7 30.6 - - + +
557A ILE* 3.5 45.5 - - + -
607A LEU* 4.1 20.9 - - + -
611A MET* 4.9 1.6 - - - -
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Residues in contact with LEU 502 (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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500A GLU* 3.4 11.7 + - - +
501A LEU* 1.3 82.3 - - - +
503A ASP* 1.3 64.6 + - - +
505A ILE* 3.7 3.8 - - + -
506A LEU* 2.9 44.2 + - + +
542A PRO* 3.8 18.5 + - + -
545A ILE 4.8 0.2 + - - -
607A LEU* 4.0 16.8 - - + +
610A THR* 3.8 11.0 - - + -
611A MET* 3.7 38.8 - - + +
699A VAL* 4.4 7.0 - - + -
703A MET* 3.6 31.9 - - + -
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Residues in contact with ASP 503 (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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500A GLU* 3.1 31.6 + - + +
502A LEU* 1.3 76.8 - - - +
504A LYS* 1.3 63.8 + - + +
506A LEU* 3.3 7.2 + - - +
507A ARG* 3.2 53.8 + - - +
696A PRO* 3.8 22.5 - - - +
700A LYS* 3.7 26.9 + - - +
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Residues in contact with LYS 504 (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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498A GLY 3.5 28.3 - - - +
499A GLY* 4.7 4.9 - - - -
500A GLU 3.2 12.9 + - - +
501A LEU 3.7 7.0 - - - +
503A ASP* 1.3 76.2 - - + +
505A ILE* 1.3 61.4 + - - +
507A ARG* 3.0 23.5 + - - +
508A GLN* 3.3 25.0 + - - +
547A TYR* 4.2 14.6 - - + -
550A GLU* 3.9 17.6 + - - +
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Residues in contact with ILE 505 (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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501A LEU* 3.0 35.9 + - + +
502A LEU* 3.7 5.2 - - + +
504A LYS* 1.3 74.3 - - - +
506A LEU* 1.3 59.1 + - - +
507A ARG 3.3 0.7 + - - -
508A GLN* 3.3 21.0 + - - +
511A PHE* 3.6 46.1 - - + +
519A VAL* 4.2 7.0 - - + -
547A TYR* 3.6 24.5 - - + +
611A MET* 4.1 23.6 - - + -
692A ARG* 3.0 31.4 + - - +
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Residues in contact with LEU 506 (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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502A LEU* 2.9 41.3 + - + +
503A ASP* 3.7 7.9 - - - +
504A LYS 3.3 0.2 - - - -
505A ILE* 1.3 71.7 - - - +
507A ARG* 1.3 58.9 + - - +
508A GLN 3.4 1.4 + - - -
509A LYS* 5.2 1.6 - - - -
610A THR* 3.7 23.8 - - + +
614A GLY* 3.8 16.4 - - - +
692A ARG* 4.0 20.4 + - - +
693A GLN 5.2 6.0 - - - +
694A ASP* 4.2 12.6 - - - +
696A PRO* 4.0 25.4 - - + +
699A VAL* 3.8 38.8 - - + -
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Residues in contact with ARG 507 (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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503A ASP* 3.2 37.2 + - - +
504A LYS* 3.0 18.2 + - - +
506A LEU* 1.3 74.3 - - - +
508A GLN* 1.3 61.3 + - - +
509A LYS* 3.6 22.9 + - - +
694A ASP* 5.3 2.0 - - - +
696A PRO* 3.6 35.1 - - + +
697A HIS* 4.4 12.3 + - - +
700A LYS* 6.1 1.0 - - - +
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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