Contacts of the helix formed by residues 404 - 408 (chain A) in PDB entry 3DYQ
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 404 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A CYS* 4.9 2.4 + - - +
263A MET* 3.5 35.5 - - - +
400A CYS 3.1 18.4 + - - -
401A CYS 2.8 17.0 + - - -
402A ASP 3.3 1.4 + - - -
403A ILE* 1.3 75.7 - - - +
405A ASN* 1.3 69.3 + - - +
406A GLU 3.1 2.5 - - - -
407A VAL* 2.8 26.0 + - - +
408A ARG* 3.9 6.9 + - - +
461A LEU* 4.8 4.3 - - - -
465A PHE* 4.7 4.9 - - - -
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Residues in contact with ASN 405 (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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251A PHE* 3.6 26.1 - - - -
256A HIS* 5.0 5.9 + - - -
259A CYS* 4.2 16.8 - - - +
402A ASP 5.4 3.6 + - - +
403A ILE 3.3 4.0 + - - -
404A SER* 1.3 77.3 + - - +
406A GLU* 1.3 60.5 + - + +
408A ARG* 3.0 37.2 + - - +
413A ALA* 3.4 11.6 - - - +
416A TRP* 3.4 54.4 + - + +
900A PCG 4.7 14.9 + - - +
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Residues in contact with GLU 406 (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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403A ILE 4.6 1.6 + - - -
404A SER 3.0 1.2 + - - -
405A ASN* 1.3 78.4 - - + +
407A VAL* 1.3 61.4 + - - +
408A ARG 3.1 6.3 + - - +
413A ALA* 4.0 18.0 - - - +
417A VAL* 3.5 14.9 - - - +
453A GLN* 2.9 32.2 + - - +
457A ILE* 4.2 12.3 - - + -
461A LEU* 4.0 9.6 - - + +
482A PRO* 4.3 10.9 - - - +
483A LEU* 3.6 24.6 - - + +
486A SER* 2.5 32.7 + - - +
490A TYR* 3.6 13.5 + - - -
900A PCG 4.1 6.7 + - - +
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Residues in contact with VAL 407 (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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199A PRO* 4.6 7.3 - - + +
263A MET* 3.9 15.7 - - + -
404A SER* 2.8 20.5 + - - +
406A GLU* 1.3 73.7 - - - +
408A ARG* 1.3 61.6 + - - +
409A PRO* 4.6 0.7 - - - +
461A LEU* 5.6 0.4 - - + +
465A PHE* 4.0 25.8 - - + -
478A ILE 4.6 1.6 - - - +
479A MET* 3.7 58.1 - - + +
482A PRO* 3.3 23.1 - - - +
483A LEU* 3.9 14.0 - - + +
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Residues in contact with ARG 408 (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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199A PRO 3.6 20.2 + - - +
201A PHE 3.7 7.1 + - - -
203A VAL* 3.4 22.2 - - - +
259A CYS* 2.9 45.0 + - - +
262A GLN* 2.9 27.9 + - - -
263A MET* 3.7 26.6 - - + +
404A SER* 4.3 3.8 + - - +
405A ASN* 3.0 25.7 + - - +
406A GLU 3.7 7.3 - - - +
407A VAL* 1.3 83.0 - - - +
409A PRO* 1.3 79.5 - - + +
410A MET* 3.4 1.6 + - - -
412A VAL* 3.8 23.6 - - + -
413A ALA* 3.9 6.7 - - + +
416A TRP* 5.5 1.8 - - - +
482A PRO* 4.7 4.0 - - - +
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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