Contacts of the helix formed by residues 344 - 355 (chain B) in PDB entry 5ODS
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 ASN 344 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A GLN 3.8 1.1 - - - -
224A ALA* 3.2 38.7 + - - +
225A GLY* 3.7 3.4 - - - +
227A LYS* 4.3 3.4 - - - +
291B THR* 3.9 25.1 + - - +
338B ILE* 2.9 18.6 + - + +
342B LEU* 3.8 20.6 - - + +
343B GLN* 1.3 76.5 - - - +
345B PRO* 1.3 64.3 - - - +
346B ASP* 4.1 0.2 - - - +
347B LEU* 3.1 32.7 + - + +
348B ALA 3.2 8.5 + - - -
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Residues in contact with PRO 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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222A GLY 4.0 3.1 - - - +
223A GLN* 3.2 41.3 - - - +
339B THR* 4.7 7.8 - - + +
343B GLN* 3.4 11.7 - - + +
344B ASN* 1.3 87.0 - - - +
346B ASP* 1.3 56.1 + - - +
348B ALA* 3.1 10.1 + - + +
349B LEU* 2.9 38.1 + - + +
363B LEU* 3.8 27.7 - - + +
367B LYS* 6.1 0.9 - - - -
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Residues in contact with ASP 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLN* 2.9 48.1 + - - +
224A ALA* 3.9 12.4 + - + +
344B ASN* 4.1 2.7 - - - +
345B PRO* 1.3 73.0 - - - +
347B LEU* 1.3 61.8 + - - +
349B LEU* 3.8 9.6 - - - +
350B ARG* 3.3 22.7 + - - +
367B LYS* 4.0 17.5 + - - -
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Residues in contact with LEU 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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286B ASP* 3.5 33.2 - - + +
289B THR* 4.3 7.0 - - + +
291B THR* 3.9 24.7 - - + +
293B ILE* 4.0 23.1 - - + -
338B ILE* 3.9 22.0 - - + -
342B LEU* 4.9 2.7 - - + -
344B ASN* 3.1 25.8 + - + +
346B ASP* 1.3 75.8 - - - +
348B ALA* 1.3 60.3 + - - +
350B ARG* 3.5 6.9 + - + +
351B MET* 2.9 36.4 + - - +
354B ARG* 6.0 0.9 - - - +
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Residues in contact with ALA 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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335B ILE* 4.1 15.8 - - + +
338B ILE* 3.6 18.5 - - + +
339B THR* 3.3 26.0 - - - +
344B ASN 3.2 4.6 + - - +
345B PRO* 3.1 9.5 + - + +
347B LEU* 1.3 79.4 - - - +
349B LEU* 1.3 56.4 + - - +
351B MET* 3.3 6.0 + - - +
352B ALA* 2.9 32.6 + - - +
360B ALA* 5.2 0.4 - - - -
363B LEU* 4.1 9.6 - - + -
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Residues in contact with LEU 349 (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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345B PRO* 2.9 30.9 + - + +
346B ASP* 3.8 9.9 - - - +
348B ALA* 1.3 76.6 - - - +
350B ARG* 1.3 63.1 + - - +
352B ALA* 3.4 3.0 + - - +
353B VAL* 3.3 24.8 + - - +
360B ALA* 5.3 1.1 - - - -
363B LEU* 4.4 23.1 - - + -
364B PHE* 3.7 45.8 - - + +
367B LYS* 3.8 39.5 - - + -
383B VAL* 6.1 0.7 - - + -
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Residues in contact with ARG 350 (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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204B PHE* 4.8 2.0 - - - -
205B LYS 5.0 1.4 + - - -
206B MET 4.8 2.0 - - - -
207B GLU* 3.7 49.1 + - - +
286B ASP* 6.0 0.4 - - - +
288B GLU* 3.1 37.9 + - - +
346B ASP 3.3 14.6 + - - +
347B LEU* 3.9 9.2 - - + +
349B LEU* 1.3 77.8 - - - +
351B MET* 1.3 58.6 + - - +
353B VAL* 3.3 20.3 - - - +
354B ARG* 2.9 78.3 + - - +
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Residues in contact with MET 351 (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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270B HIS* 4.2 10.3 - - + +
272B VAL* 3.5 30.1 - - + -
286B ASP* 5.0 1.8 - - - +
293B ILE* 4.5 6.5 - - + -
334B ILE* 3.8 29.4 - - + -
335B ILE* 4.0 16.6 - - + -
338B ILE* 3.9 15.7 - - + -
347B LEU* 2.9 28.8 + - - +
348B ALA* 3.5 6.1 - - - +
349B LEU 3.2 0.2 - - - -
350B ARG* 1.3 77.9 - - - +
352B ALA* 1.3 60.5 - - - +
354B ARG* 4.0 16.6 - - - +
355B ASN* 3.2 39.4 + - - +
357B LEU* 3.9 9.0 - - + +
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Residues in contact with ALA 352 (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 ILE* 4.4 6.5 - - + -
348B ALA 2.9 16.3 + - - +
349B LEU 3.4 3.8 + - - +
351B MET* 1.3 77.0 - - - +
353B VAL* 1.3 58.5 + - - +
356B ASN* 3.3 8.8 - - - -
357B LEU* 3.2 44.2 + - - +
360B ALA* 3.9 24.2 - - + -
364B PHE* 4.4 6.5 - - + -
388B PRO* 3.6 9.4 - - + +
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Residues in contact with VAL 353 (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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207B GLU* 5.1 5.8 - - - +
349B LEU 3.3 14.0 + - - +
350B ARG* 3.3 31.0 - - - +
352B ALA* 1.3 77.8 - - - +
354B ARG* 1.3 71.0 + - - +
356B ASN* 4.0 8.0 + - - +
364B PHE* 4.9 6.5 - - + -
386B ASN* 3.5 37.2 - - + +
387B ALA 5.4 0.4 - - - -
388B PRO* 5.0 8.3 - - + -
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Residues in contact with ARG 354 (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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204B PHE* 3.9 12.0 - - + -
205B LYS 5.8 1.6 - - - +
270B HIS 3.4 22.0 + - - -
271B ASP* 3.3 27.2 + - - +
286B ASP* 3.3 27.7 + - - -
288B GLU* 2.7 35.2 + - - +
347B LEU* 6.0 0.8 - - - +
350B ARG* 2.9 53.9 + - - +
351B MET* 4.0 20.2 - - - -
353B VAL* 1.3 81.4 - - - +
355B ASN* 1.3 69.8 + - - +
356B ASN* 3.4 2.1 + - - +
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Residues in contact with ASN 355 (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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268B GLU 4.4 0.4 + - - -
269B LYS 2.8 28.8 + - - +
270B HIS* 3.2 20.3 - - + +
271B ASP* 2.9 25.6 + - - -
351B MET* 3.2 18.1 + - - +
354B ARG* 1.3 97.1 + - - +
356B ASN* 1.3 71.1 + - - +
357B LEU* 3.3 18.6 + - + +
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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