Contacts of the helix formed by residues 330 - 340 (chain B) in PDB entry 1UN0
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 330 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289B GLN* 2.8 33.7 + - - +
293B GLN* 5.0 1.2 + - - -
329B GLY* 1.3 71.1 - - - +
331B ASP* 1.3 62.4 + - - +
332B LEU* 3.0 18.4 + - - +
333B GLN* 2.9 57.5 + - - +
334B THR* 2.9 33.6 + - - -
36D MET* 4.5 0.9 - - - -
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Residues in contact with ASP 331 (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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330B ASN* 1.3 73.9 - - - +
332B LEU* 1.3 68.2 + - + +
334B THR* 3.3 2.9 + - - -
335B GLN* 2.9 21.5 + - - +
371B GLY* 4.5 6.1 - - - -
372B ASN* 3.9 32.6 + - - +
375B GLN* 3.2 16.9 + - - +
36D MET* 4.2 13.2 + - - +
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Residues in contact with LEU 332 (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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330B ASN* 3.0 12.1 + - - +
331B ASP* 1.3 77.4 - - + +
333B GLN* 1.3 63.3 + - + +
335B GLN* 3.3 10.2 + - + +
336B VAL* 3.2 26.3 + - - +
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Residues in contact with GLN 333 (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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289B GLN* 2.9 33.8 + - - +
292B ILE* 3.5 13.6 - - + +
293B GLN* 3.3 34.7 + - - +
296B ILE* 3.6 17.7 - - + +
326B ILE* 3.9 16.8 - - - +
329B GLY* 3.2 10.6 - - - -
330B ASN* 2.9 51.7 + - - +
332B LEU* 1.3 75.2 - - + +
334B THR* 1.3 64.2 + - - +
336B VAL* 3.3 17.5 + - - +
337B VAL 3.6 3.5 + - - -
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Residues in contact with THR 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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327B VAL* 3.6 25.7 - - + +
330B ASN 2.9 14.4 + - - -
331B ASP 3.3 4.9 + - - -
333B GLN* 1.3 76.1 - - - +
335B GLN* 1.3 63.0 + - - +
337B VAL* 3.1 6.6 + - - +
338B ILE* 3.1 24.0 + - + +
368B ILE* 4.0 9.0 - - + -
375B GLN* 3.9 9.6 - - - +
36D MET* 2.3 60.3 - - + -
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Residues in contact with GLN 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 ASP 2.9 17.2 + - - +
332B LEU* 3.3 11.0 + - + +
334B THR* 1.3 73.7 - - - +
336B VAL* 1.3 63.3 + - - +
338B ILE* 3.8 19.7 - - - +
339B ASN* 3.0 54.5 + - - +
372B ASN* 5.1 1.6 + - - +
374B GLU* 5.3 5.1 - - - +
375B GLN* 3.0 31.3 + - - +
378B ALA* 6.1 0.6 - - - +
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Residues in contact with VAL 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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296B ILE* 4.0 36.1 - - + -
301B PRO* 4.1 20.6 - - + -
332B LEU 3.2 16.0 + - - +
333B GLN 3.6 8.7 - - - +
334B THR 3.3 0.4 - - - -
335B GLN* 1.3 75.7 - - - +
337B VAL* 1.3 58.5 + - + +
339B ASN* 3.3 8.1 + - - +
340B ALA* 3.0 27.3 + - + +
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Residues in contact with VAL 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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301B PRO* 4.5 12.6 - - + -
305B VAL* 4.6 5.2 - - + -
323B VAL* 3.9 14.6 - - + +
326B ILE* 3.4 43.5 - - + -
327B VAL* 4.2 13.0 - - + -
333B GLN 3.6 2.7 + - - +
334B THR 3.1 7.9 + - - +
336B VAL* 1.3 75.5 - - + +
338B ILE* 1.3 66.3 + - - +
340B ALA* 3.3 11.9 + - - +
341B GLY 3.4 0.5 + - - -
342B VAL* 3.2 53.0 + - + +
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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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334B THR* 3.1 17.0 + - + +
335B GLN* 3.7 24.9 - - - +
336B VAL 3.4 0.2 - - - -
337B VAL* 1.3 76.7 - - - +
339B ASN* 1.3 61.5 + - - +
341B GLY* 3.2 14.0 + - - -
342B VAL* 3.8 15.6 + - + -
343B LEU* 4.1 21.5 + - + +
344B PRO* 5.8 0.3 - - - +
368B ILE* 3.7 31.9 - - + -
375B GLN* 3.7 29.4 - - + -
378B ALA* 4.4 12.8 - - + -
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Residues in contact with ASN 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 GLN* 3.0 49.6 + - - +
336B VAL* 3.6 7.2 - - - +
338B ILE* 1.3 77.5 - - - +
340B ALA* 1.3 58.3 + - - +
341B GLY 3.3 1.6 + - - -
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Residues in contact with ALA 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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301B PRO* 4.4 2.5 - - + +
302B LYS* 4.0 34.3 - - + +
305B VAL* 3.4 23.1 - - + +
336B VAL* 3.0 18.2 + - + +
337B VAL* 3.8 7.4 - - - +
338B ILE 3.2 0.4 - - - -
339B ASN* 1.3 76.1 - - - +
341B GLY* 1.3 56.7 + - - +
342B VAL 3.6 1.1 - - - -
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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