Contacts of the helix formed by residues 360 - 370 (chain H) in PDB entry 1D00
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 ASP 360 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359H SER* 1.3 79.6 - - - +
361H PHE* 1.3 64.7 + - - +
362H ALA 3.5 2.0 - - - -
363H ARG* 2.9 42.8 + - - +
364H LYS* 3.2 29.3 + - - +
488H ASP* 3.3 22.1 + - - +
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Residues in contact with PHE 361 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358H ILE* 4.2 11.7 - - + +
359H SER 2.9 4.9 - - - -
360H ASP* 1.3 75.5 - - - +
362H ALA* 1.3 62.6 + - + +
364H LYS* 3.1 6.0 + - - +
365H ARG* 2.8 52.6 + - + +
396H LEU* 4.2 22.4 - - + -
407H LEU* 5.2 2.5 - - + -
478H MET* 3.9 24.2 - - + -
479H GLU* 4.8 7.0 - - + -
485H VAL* 3.6 32.3 - - + -
488H ASP* 3.2 23.1 + - - +
489H ALA* 4.2 5.6 - - - -
490H ILE* 3.7 34.8 - - + -
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Residues in contact with ALA 362 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360H ASP 3.5 0.4 + - - -
361H PHE* 1.3 81.2 - - + +
363H ARG* 1.3 57.5 + - - +
365H ARG* 3.6 4.6 - - - +
366H GLN* 3.0 28.2 + - - +
488H ASP* 3.0 24.2 + - - +
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Residues in contact with ARG 363 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360H ASP* 2.9 43.0 + - - +
361H PHE 3.2 0.4 - - - -
362H ALA* 1.3 75.8 - - - +
364H LYS* 1.3 86.0 + - - +
366H GLN* 3.2 7.0 + - + +
367H GLU* 2.8 78.3 + - + +
372H ARG* 5.9 1.3 - - - +
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Residues in contact with LYS 364 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358H ILE* 3.9 17.5 - - + +
359H SER* 2.7 39.6 + - - +
360H ASP* 3.2 8.7 + - - +
361H PHE* 3.1 5.5 + - - +
363H ARG* 1.3 101.6 - - - +
365H ARG* 1.3 62.2 + - - +
367H GLU* 3.5 16.3 + - - +
368H ALA* 3.2 18.2 + - - +
373H ILE* 4.5 2.6 - - - +
376H ILE* 4.0 22.6 - - + +
396H LEU* 3.5 22.2 - - + +
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Residues in contact with ARG 365 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361H PHE* 2.8 43.1 + - + +
362H ALA* 3.6 7.6 - - - +
364H LYS* 1.3 77.6 - - - +
366H GLN* 1.3 58.4 + - - +
368H ALA* 3.1 5.2 + - - +
369H VAL* 2.9 53.1 + - - +
396H LEU* 3.2 37.0 + - + +
397H ASN* 2.6 26.7 + - - -
404H GLY 5.2 0.2 + - - -
475H VAL* 3.3 39.4 - - - +
479H GLU* 5.6 7.2 - - + +
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Residues in contact with GLN 366 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362H ALA 3.0 18.2 + - - +
363H ARG* 3.2 7.8 + - + +
365H ARG* 1.3 79.0 - - - +
367H GLU* 1.3 58.0 + - - +
369H VAL* 3.2 19.2 + - - +
370H ALA* 3.0 38.3 + - - +
372H ARG* 4.9 11.3 + - - +
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Residues in contact with GLU 367 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363H ARG* 2.8 57.7 + - + +
364H LYS* 3.5 19.9 - - - +
365H ARG 3.2 0.2 - - - -
366H GLN* 1.3 76.1 - - - +
368H ALA* 1.3 55.7 + - - +
371H GLY 3.5 0.9 + - - -
372H ARG* 3.0 45.2 + - + +
373H ILE* 2.8 63.9 + - + +
376H ILE* 5.7 0.5 - - - +
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Residues in contact with ALA 368 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364H LYS 3.2 10.1 + - - +
365H ARG 3.1 9.5 + - - +
367H GLU* 1.3 74.9 - - - +
369H VAL* 1.3 68.0 + - - +
370H ALA 3.1 1.3 - - - -
371H GLY* 2.8 15.1 + - - -
373H ILE 3.2 20.6 + - - +
374H PRO* 4.2 12.3 - - + +
396H LEU* 3.8 20.4 - - + -
397H ASN* 3.9 18.6 + - + +
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Residues in contact with VAL 369 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365H ARG* 2.9 58.2 + - - +
366H GLN* 3.6 21.3 - - - +
368H ALA* 1.3 78.4 - - - +
370H ALA* 1.3 61.0 + - - +
371H GLY* 3.3 0.5 + - - -
397H ASN* 3.7 21.5 + - + +
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Residues in contact with ALA 370 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366H GLN* 3.0 29.4 + - - +
367H GLU 4.2 4.0 - - - +
369H VAL* 1.3 77.2 - - - +
371H GLY* 1.3 58.0 + - - +
372H ARG* 3.3 25.9 + - + +
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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