Contacts of the helix formed by residues 726 - 731 (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 PRO 726 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B ASP* 3.4 24.7 - - - +
453B TYR* 3.7 10.5 - - + +
458B ARG* 4.5 0.4 - - - -
495B VAL* 3.9 19.3 - - + -
681B PHE* 4.5 4.7 - - + -
720B VAL* 3.5 29.2 - - + -
724B PHE 3.7 5.2 - - - +
725B GLU* 1.3 88.2 - - + +
727B PRO* 1.3 73.6 - - + +
728B SER* 4.2 5.6 - - - +
729B PHE* 3.0 23.7 + - + +
730B VAL* 3.1 12.6 + - - +
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Residues in contact with PRO 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B THR* 3.6 7.2 - - + +
407B ALA* 3.8 18.8 - - + -
413B ASP* 3.6 12.3 - - - +
453B TYR* 3.6 20.4 - - + +
455B HIS* 3.6 43.7 - - + +
457B SER* 4.3 2.7 - - - +
458B ARG* 4.2 11.4 - - + +
726B PRO* 1.3 87.4 - - + +
728B SER* 1.3 55.7 + - - +
729B PHE 3.0 0.2 + - - -
730B VAL* 3.6 10.8 - - + +
731B GLY* 3.0 30.1 + - - -
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Residues in contact with SER 728 (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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407B ALA* 3.5 18.0 - - - +
408B ALA* 3.4 27.5 - - - +
411B GLY* 4.2 13.7 - - - -
412B MET 4.3 2.0 - - - -
413B ASP* 2.5 32.3 + - - -
679B GLN* 5.2 0.9 + - - -
681B PHE* 3.7 24.7 - - - -
726B PRO* 4.2 2.3 - - - +
727B PRO* 1.3 74.9 - - - +
729B PHE* 1.3 57.1 + - - +
732B TRP* 3.4 13.7 + - - -
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Residues in contact with PHE 729 (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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642B LEU* 5.8 2.5 - - + -
666B LEU* 4.4 4.3 - - + -
674B LEU* 3.6 34.1 - - + -
681B PHE* 3.9 26.2 - + + -
683B TRP* 3.7 31.9 - + + -
720B VAL* 4.7 5.8 - - + -
725B GLU* 3.6 31.2 - - + -
726B PRO* 3.0 24.4 + - + +
728B SER* 1.3 79.9 + - - +
730B VAL* 1.3 70.6 + - - +
731B GLY 3.1 1.3 - - - -
732B TRP* 3.1 24.3 + - - +
733B PHE* 3.6 31.0 - + - -
736B TRP* 4.1 9.6 - + - -
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Residues in contact with VAL 730 (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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404B THR* 4.0 18.5 + - + +
458B ARG* 4.2 16.8 - - - +
725B GLU* 3.5 29.8 - - + +
726B PRO 3.1 13.6 + - - +
727B PRO* 3.6 15.5 - - + +
729B PHE* 1.3 78.9 - - + +
731B GLY* 1.3 59.8 + - - +
732B TRP 2.9 0.2 - - - -
733B PHE* 2.8 37.6 + - - +
736B TRP* 3.8 35.4 - - + +
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Residues in contact with GLY 731 (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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404B THR* 3.3 38.4 - - - -
405B ALA* 3.9 14.9 - - - +
408B ALA* 3.6 9.8 - - - +
409B GLN* 5.9 0.2 + - - -
727B PRO 3.0 11.6 + - - -
729B PHE 3.1 0.4 - - - -
730B VAL* 1.3 77.4 - - - +
732B TRP* 1.3 58.3 + - - +
733B PHE 3.3 4.0 + - - -
734B LEU* 5.0 6.8 - - - +
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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