Contacts of the helix formed by residues 333 - 341 (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 333 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B ILE* 4.0 29.1 - - + +
5B LEU* 3.4 25.5 + - - +
6B PRO* 4.6 0.4 - - - -
330B GLU* 3.0 23.2 + - + +
332B GLU* 1.3 92.2 - - - +
334B ILE* 1.3 64.9 + - - +
335B ILE 3.4 2.0 - - - -
336B PRO* 3.2 9.7 - - - +
337B TYR* 3.0 23.8 + - - +
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Residues in contact with ILE 334 (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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6B PRO* 3.6 27.6 - - + +
284B LEU* 4.8 9.6 - - + -
293B ILE* 4.5 7.4 - - + -
329B VAL* 3.9 22.2 - - + -
330B GLU 2.9 14.3 + - - +
331B GLU* 3.7 20.2 - - - +
333B ASN* 1.3 76.2 - - - +
335B ILE* 1.3 81.3 + - + +
337B TYR* 3.5 1.9 + - - +
338B ILE* 3.1 34.6 + - + +
351B MET* 3.8 29.6 - - + -
357B LEU* 4.0 16.4 - - + -
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Residues in contact with ILE 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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331B GLU 5.3 0.2 - - - +
334B ILE* 1.3 78.4 - - + +
336B PRO* 1.4 69.3 - - + +
338B ILE* 3.4 5.0 + - + +
339B THR* 2.7 40.8 + - - +
348B ALA* 4.1 14.8 - - + +
351B MET* 4.0 30.1 - - + -
352B ALA* 4.2 3.4 - - + +
357B LEU* 3.9 33.2 - - + -
358B ALA 3.8 17.9 - - - +
359B GLY 3.9 21.1 - - - -
360B ALA* 3.9 15.0 - - + +
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Residues in contact with PRO 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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4B ILE* 4.0 14.4 - - + -
332B GLU 3.7 17.5 - - - +
333B ASN* 3.2 16.6 - - - +
335B ILE* 1.4 94.4 - - + +
337B TYR* 1.3 51.4 + - - +
339B THR* 3.2 3.2 + - - +
340B ASN* 2.7 51.2 + - - +
358B ALA 4.6 3.8 - - - +
359B GLY* 4.9 14.1 - - - +
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Residues in contact with TYR 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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254A PRO* 5.1 8.4 - - + +
4B ILE* 3.5 34.6 - - + +
5B LEU* 3.9 1.6 - - + -
6B PRO* 3.5 41.5 - - + -
293B ILE* 3.2 29.0 + - + -
294B TYR* 3.4 18.4 - + - -
333B ASN 3.0 18.3 + - - +
334B ILE 3.8 2.9 - - - +
336B PRO* 1.3 72.9 - - - +
338B ILE* 1.3 66.2 + - - +
341B VAL* 2.9 42.4 + - + +
342B LEU* 2.8 35.9 + - + -
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Residues in contact with ILE 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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293B ILE* 3.8 23.1 - - + -
334B ILE* 3.1 37.1 + - + +
335B ILE* 3.8 5.6 - - - +
337B TYR* 1.3 76.2 - - + +
339B THR* 1.3 57.5 + - - +
342B LEU* 3.5 11.1 - - + +
343B GLN 3.1 6.4 + - - -
344B ASN* 2.9 48.6 + - + +
347B LEU* 3.9 20.4 - - + -
348B ALA* 3.6 16.6 - - + +
351B MET* 3.9 28.5 - - + -
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Residues in contact with THR 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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176A ARG* 4.7 4.1 + - - +
335B ILE* 2.7 25.7 + - - +
336B PRO* 3.5 5.6 - - - +
338B ILE* 1.3 77.0 - - - +
340B ASN* 1.3 74.4 + - - +
343B GLN* 3.1 23.1 - - - +
344B ASN 4.0 4.2 + - - +
345B PRO* 4.7 5.3 - - + +
348B ALA* 3.3 18.4 - - - +
359B GLY 5.0 3.5 + - - +
363B LEU* 3.6 34.9 - - + +
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Residues in contact with ASN 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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176A ARG* 3.6 29.0 + - - +
257A GLN* 3.3 9.9 - - - +
3B GLN* 6.2 0.7 - - - +
4B ILE* 6.3 0.4 - - + -
336B PRO* 2.7 37.7 + - - +
339B THR* 1.3 89.6 - - - +
341B VAL* 1.3 63.9 + - + +
343B GLN* 3.2 23.2 + - - +
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Residues in contact with VAL 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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221A ARG* 4.0 6.2 + - - -
254A PRO* 4.7 17.2 - - + +
257A GLN* 3.6 25.6 - - + +
3B GLN* 3.7 31.4 - - - +
4B ILE* 4.4 4.7 - - + +
337B TYR* 2.9 58.2 + - + +
340B ASN* 1.3 76.3 - - + +
342B LEU* 1.3 64.3 + - - +
343B GLN* 3.3 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