Contacts of the helix formed by residues 633 - 638 (chain B) in PDB entry 1D0N
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 LYS 633 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B GLN* 3.0 29.5 + - - +
375B THR* 4.8 6.7 - - - +
377B GLY 3.5 20.9 - - - +
378B LEU* 3.9 3.1 - - - -
379B GLY* 3.4 31.2 - - - +
380B LEU* 4.0 23.7 - - + +
629B ARG 5.5 1.2 + - - -
630B LEU* 3.4 34.9 + - + +
632B ASP* 1.3 77.4 - - + +
634B LYS* 1.3 53.0 - - - +
635B MET 3.2 2.0 - - - -
636B ASP* 2.8 16.5 + - + +
637B ALA* 2.7 35.2 + - - +
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Residues in contact with LYS 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B GLN 5.9 2.6 + - - +
545B SER* 5.9 1.6 + - - -
630B LEU* 3.0 36.6 + - + +
631B LYS* 5.8 0.9 - - - -
632B ASP* 3.0 4.2 - - - +
633B LYS* 1.3 77.4 - - - +
635B MET* 1.3 58.3 + - - +
637B ALA 3.9 0.2 - - - -
638B HIS* 2.9 37.5 + - - +
676B THR* 6.0 0.7 - - - -
677B TRP* 5.3 11.7 - - + -
678B ASP* 2.7 49.8 + - - +
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Residues in contact with MET 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B ILE* 3.7 24.9 - - + +
390B VAL* 3.5 32.3 - - + -
392B ARG* 3.0 51.8 - - - +
409B GLN* 4.4 13.5 - - - -
632B ASP 3.9 3.0 + - - +
633B LYS 3.2 0.6 - - - -
634B LYS* 1.3 80.7 - - - +
636B ASP* 1.3 60.9 + - - +
638B HIS 4.2 4.5 - - - -
639B PRO* 3.3 25.3 - - - +
640B PRO* 4.4 12.6 - - + -
732B TRP* 4.2 24.5 - - + -
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Residues in contact with ASP 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ARG* 3.6 16.0 + - - -
360B PRO* 3.8 12.0 - - - +
363B ARG* 3.9 4.7 + - - -
379B GLY* 3.8 25.8 + - - -
380B LEU* 4.4 6.1 - - + +
382B TYR 4.4 10.3 - - - +
383B LEU* 3.3 19.4 - - - +
384B SER* 5.3 2.3 + - - +
387B ILE* 5.0 3.8 - - - +
392B ARG* 2.4 30.9 + - - +
632B ASP 3.8 0.7 - - - +
633B LYS* 2.8 30.6 + - + +
635B MET* 1.3 77.3 - - - +
637B ALA* 1.3 63.3 + - - +
638B HIS 3.5 0.3 + - - -
639B PRO* 3.7 9.2 - - - +
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Residues in contact with ALA 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B PRO* 3.9 17.3 - - - +
363B ARG* 3.9 16.7 + - - +
380B LEU* 3.9 19.9 - - + +
630B LEU* 3.9 17.0 - - + -
633B LYS 2.7 18.6 + - - +
634B LYS 4.1 0.2 - - - +
636B ASP* 1.3 73.5 - - - +
638B HIS* 1.3 86.0 + - + +
639B PRO* 3.8 0.7 - - - -
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Residues in contact with HIS 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B GLN* 6.0 6.6 - - + -
630B LEU* 4.1 16.2 - - + +
634B LYS* 2.9 18.6 + - - +
635B MET* 3.5 6.6 - - - +
637B ALA* 1.3 104.7 + - + +
639B PRO* 1.3 68.5 - - - +
640B PRO* 3.6 3.1 - - - +
676B THR* 5.6 1.2 - - - +
677B TRP* 3.3 83.0 + + + +
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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