Contacts of the helix formed by residues 403 - 411 (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 SER 403 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B VAL* 4.8 5.1 - - - +
399B THR 4.3 2.7 - - - -
400B LEU 2.9 14.9 + - - +
401B HIS 3.5 0.6 - - - -
402B THR* 1.3 88.5 - - - +
404B THR* 1.3 61.7 + - - +
405B ALA* 3.3 9.0 + - - +
406B MET* 3.0 33.7 + - - +
407B ALA 3.4 10.7 + - - -
455B HIS* 3.3 9.4 + - - -
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Residues in contact with THR 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B THR 6.1 0.4 - - - -
403B SER* 1.3 71.3 - - - +
405B ALA* 1.3 62.8 + - - +
407B ALA* 3.1 8.0 + - - +
408B ALA 2.9 25.3 + - - -
455B HIS* 3.9 7.6 - - + -
457B SER* 3.9 27.4 - - - +
458B ARG* 5.4 0.9 - - - +
727B PRO* 3.6 3.9 - - + +
730B VAL* 4.0 19.8 + - + +
731B GLY* 3.3 25.9 + - - -
733B PHE 5.8 0.2 + - - -
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Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B GLU 5.4 0.9 - - - +
393B VAL* 4.0 16.2 - - + -
403B SER* 3.7 7.4 - - - +
404B THR* 1.3 83.0 + - - +
406B MET* 1.3 54.4 + - - +
408B ALA* 3.4 1.3 + - - +
409B GLN* 3.0 42.6 + - - +
731B GLY 3.9 15.9 - - - +
734B LEU* 5.8 7.0 - - + -
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Residues in contact with MET 406 (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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393B VAL* 3.8 21.9 - - + +
394B PRO 3.0 23.8 - - - +
395B PHE* 4.0 4.0 - - + -
396B ASP* 3.4 34.1 - - + +
399B THR* 3.8 20.0 - - - +
400B LEU* 3.6 25.7 - - + +
403B SER* 3.0 24.1 + - - +
405B ALA* 1.3 74.0 - - - +
407B ALA* 1.3 66.6 + - - +
410B HIS* 3.0 47.7 + - + +
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Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU* 4.0 4.9 - - + +
403B SER 3.4 11.4 + - - +
404B THR 3.1 9.5 + - - +
406B MET* 1.3 79.3 - - - +
408B ALA* 1.3 53.5 + - - +
411B GLY* 2.7 31.5 + - - -
412B MET 3.0 32.2 + - - +
455B HIS* 4.2 4.3 - - - +
727B PRO* 3.8 29.2 - - + -
728B SER* 3.5 3.9 - - - +
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Residues in contact with ALA 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B THR 2.9 16.3 + - - +
405B ALA 3.8 3.1 - - - +
407B ALA* 1.3 76.4 - - - +
409B GLN* 1.3 62.3 + - + +
410B HIS 3.2 0.9 + - - -
411B GLY* 3.4 8.8 + - - -
676B THR* 5.8 0.7 - - - +
728B SER* 3.4 24.9 - - - +
731B GLY* 3.6 25.6 - - - +
732B TRP* 3.5 30.5 + - + +
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Residues in contact with GLN 409 (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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390B VAL* 3.9 15.4 - - - +
391B GLU 3.0 21.7 + - - -
392B ARG* 3.6 8.6 - - - +
393B VAL* 2.9 40.8 + - - +
405B ALA* 3.0 22.9 + - - +
406B MET* 4.8 0.2 - - - -
408B ALA* 1.3 78.0 - - + +
410B HIS* 1.3 76.4 + - + +
411B GLY 3.6 0.2 - - - -
545B SER* 5.2 0.2 + - - -
634B LYS* 5.9 3.1 + - - +
635B MET* 4.4 11.7 - - - -
678B ASP* 5.6 2.3 - - - +
732B TRP* 4.1 23.5 - - + -
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Residues in contact with HIS 410 (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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393B VAL 3.0 27.8 + - - -
394B PRO* 3.6 3.1 - - + -
395B PHE* 3.2 43.9 + - + +
406B MET* 3.0 32.5 + - + +
409B GLN* 1.3 87.3 + - + +
411B GLY* 1.3 67.7 + - - +
412B MET* 3.3 12.2 + - + +
506B ALA* 4.0 12.1 - - - +
545B SER* 3.0 37.3 + - - +
546B SER* 4.9 1.4 - - - -
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Residues in contact with GLY 411 (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 2.7 11.5 + - - -
408B ALA 3.4 8.8 + - - -
409B GLN 3.6 0.4 - - - -
410B HIS* 1.3 78.3 - - - +
412B MET* 1.3 56.4 + - - +
413B ASP* 4.1 1.1 - - - -
505B PRO* 6.1 0.2 - - - +
506B ALA* 4.2 3.0 + - - +
507B HIS* 3.6 27.2 + - - +
679B GLN* 4.4 17.9 + - - -
728B SER* 4.2 11.0 - - - -
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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