Contacts of the helix formed by residues 334 - 348 (chain B) 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 ALA 334 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335B MET* 1.3 58.7 + - - +
336B ALA* 2.6 23.6 + - - +
337B ASP* 2.8 21.8 + - + +
338B LEU* 3.0 11.8 + - - +
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Residues in contact with MET 335 (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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334B ALA* 1.3 77.2 - - - +
336B ALA* 1.3 61.8 + - - +
338B LEU* 3.9 11.1 - - + +
339B GLU* 3.1 26.0 + - - +
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Residues in contact with ALA 336 (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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334B ALA* 2.6 9.8 - - - +
335B MET* 1.3 82.2 - - - +
337B ASP* 1.3 63.8 + - - +
339B GLU* 3.4 3.9 + - - +
340B GLN* 3.1 21.4 + - - +
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Residues in contact with ASP 337 (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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334B ALA* 2.8 18.3 + - + +
336B ALA* 1.3 72.9 - - - +
338B LEU* 1.3 64.1 + - - +
340B GLN* 3.3 8.7 + - - +
341B LYS* 3.0 21.2 + - - +
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Residues in contact with LEU 338 (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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334B ALA 3.0 12.7 + - - +
335B MET* 4.1 8.5 - - - +
337B ASP* 1.3 75.7 - - - +
339B GLU* 1.3 66.0 + - - +
341B LYS* 2.8 24.9 + - + +
342B VAL* 3.0 26.1 + - + +
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Residues in contact with GLU 339 (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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335B MET 3.1 18.9 + - - +
336B ALA* 3.5 5.2 - - - +
338B LEU* 1.3 79.0 - - - +
340B GLN* 1.3 51.2 + - - +
342B VAL* 2.7 27.9 + - - +
343B LEU* 2.6 32.0 + - + +
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Residues in contact with GLN 340 (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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336B ALA 3.1 10.2 + - - +
337B ASP* 3.4 13.0 - - - +
338B LEU 3.2 0.2 - - - -
339B GLU* 1.3 77.8 - - - +
341B LYS* 1.3 63.1 + - - +
343B LEU* 3.2 11.4 + - - +
344B GLU* 3.0 24.7 + - - +
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Residues in contact with LYS 341 (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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337B ASP 3.0 11.7 + - - +
338B LEU* 2.8 27.2 + - + +
340B GLN* 1.3 71.8 - - - +
342B VAL* 1.3 56.6 + - + +
344B GLU* 3.8 5.5 - - - +
345B MET* 3.0 41.0 + - - +
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Residues in contact with VAL 342 (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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338B LEU* 3.4 26.9 - - + +
339B GLU* 2.7 20.1 + - - +
341B LYS* 1.3 70.9 - - + +
343B LEU* 1.3 61.8 + - + +
345B MET* 3.5 10.6 + - - +
346B GLU* 2.9 29.9 + - + +
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Residues in contact with LEU 343 (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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339B GLU* 2.6 43.9 + - + +
340B GLN* 3.2 8.5 + - - +
342B VAL* 1.3 79.1 - - + +
344B GLU* 1.3 66.2 + - - +
346B GLU* 3.2 16.5 + - - +
347B ALA* 3.0 25.5 + - - +
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Residues in contact with GLU 344 (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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340B GLN 3.0 16.8 + - - +
341B LYS* 3.8 7.6 - - - +
343B LEU* 1.3 77.6 - - - +
345B MET* 1.3 62.0 + - + +
347B ALA* 3.4 5.6 + - - +
348B SER* 3.2 24.8 + - - -
379B PRO* 6.0 2.2 - - - -
380B ALA 5.0 1.6 - - - +
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Residues in contact with MET 345 (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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341B LYS* 3.0 32.5 + - + +
342B VAL* 3.8 10.5 - - + +
343B LEU 3.2 0.2 - - - -
344B GLU* 1.3 78.4 - - + +
346B GLU* 1.3 61.3 + - - +
348B SER* 3.2 23.6 + - - +
350B TYR* 5.9 1.1 - - - +
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Residues in contact with GLU 346 (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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342B VAL* 2.9 23.0 + - + +
343B LEU* 3.2 17.5 + - - +
345B MET* 1.3 77.8 - - - +
347B ALA* 1.3 56.8 + - - +
348B SER 4.7 2.0 - - - +
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Residues in contact with ALA 347 (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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343B LEU 3.0 15.3 + - - +
344B GLU* 4.0 4.0 - - - +
346B GLU* 1.3 78.6 - - - +
348B SER* 1.3 64.0 + - - +
349B THR* 3.8 6.6 + - - +
354B PHE* 3.9 17.6 - - + -
379B PRO* 3.6 33.0 - - + -
380B ALA 4.5 1.3 - - - +
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Residues in contact with SER 348 (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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344B GLU 3.2 15.1 + - - -
345B MET* 3.2 18.0 + - - +
346B GLU 4.7 1.9 - - - +
347B ALA* 1.3 80.7 - - - +
349B THR* 1.3 62.9 + - - +
350B TYR* 3.3 32.1 + - - -
380B ALA 3.5 19.5 + - - -
382B TYR* 4.1 11.7 - - - -
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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