Contacts of the helix formed by residues 325 - 334 (chain B) in PDB entry 1B3U
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 ILE 325 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283B VAL* 6.3 3.6 - - + -
286B PHE* 5.3 4.7 - - + -
287B GLN* 5.8 2.9 - - + -
290B MET* 4.7 14.8 - - + -
305B VAL* 4.4 5.8 - - + -
308B PHE* 4.5 19.7 - - + -
309B CYS* 3.2 35.9 - - - -
312B LEU* 4.9 7.0 - - + -
320B VAL* 3.3 11.4 + - + +
321B ILE* 3.5 20.0 - - + +
324B GLN* 1.3 76.5 - - + +
326B LEU* 1.3 59.9 + - - +
328B CYS* 2.6 28.8 + - - +
329B ILE* 2.7 37.6 + - + +
351B LEU* 5.3 2.2 - - + -
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Residues in contact with LEU 326 (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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321B ILE 3.0 17.2 + - - +
322B MET* 3.8 27.4 - - + +
325B ILE* 1.3 72.2 - - - +
327B PRO* 1.3 66.4 - - + +
329B ILE* 3.2 10.2 + - + +
330B LYS* 2.9 41.7 + - - +
355B LEU* 6.2 2.9 - - + -
363B HIS* 4.0 41.3 - - + +
364B LEU* 5.2 7.2 - - + -
367B LEU* 3.9 25.1 - - + -
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Residues in contact with PRO 327 (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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291B LYS* 5.6 0.2 - - - -
322B MET 4.1 2.0 - - - +
323B SER 3.2 24.5 - - - +
324B GLN* 2.9 24.2 - - - +
325B ILE 3.2 1.6 - - - -
326B LEU* 1.3 99.2 - - + +
328B CYS* 1.3 61.3 + - - +
330B LYS* 3.5 22.8 - - + +
331B GLU* 3.5 17.4 + - - +
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Residues in contact with CYS 328 (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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287B GLN* 3.9 18.6 - - - -
290B MET* 3.8 34.3 - - + +
291B LYS* 3.7 37.0 + - + +
324B GLN 3.3 17.5 - - - +
325B ILE 2.6 14.8 + - - +
327B PRO* 1.3 75.3 - - - +
329B ILE* 1.3 66.0 + - - +
331B GLU* 3.2 7.3 + - - +
332B LEU* 3.1 23.4 + - - +
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Residues in contact with ILE 329 (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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290B MET* 4.3 7.9 - - - -
305B VAL* 3.7 33.2 - - + -
325B ILE* 2.7 45.4 + - + +
326B LEU* 3.4 10.5 - - + +
328B CYS* 1.3 71.5 - - - +
330B LYS* 1.3 56.2 + - - +
332B LEU* 2.7 30.4 + - + +
333B VAL* 2.9 12.4 + - + -
344B LEU* 4.1 15.3 - - + -
348B ILE* 3.9 29.8 - - + -
351B LEU* 5.0 7.4 - - + -
364B LEU* 6.0 0.9 - - + -
367B LEU* 4.0 11.9 - - + -
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Residues in contact with LYS 330 (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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326B LEU* 2.9 28.3 + - - +
327B PRO* 3.5 16.2 - - + +
329B ILE* 1.3 75.5 - - - +
331B GLU* 1.3 60.6 + - + +
333B VAL* 2.8 30.9 - - + +
334B SER* 3.8 1.9 + - - -
363B HIS* 5.9 2.0 + - - -
367B LEU* 3.9 28.7 - - + +
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Residues in contact with GLU 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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291B LYS* 2.8 30.7 + - - +
327B PRO* 3.6 15.6 - - - +
328B CYS* 3.2 6.3 + - - +
329B ILE 3.1 0.6 - - - -
330B LYS* 1.3 77.6 - - + +
332B LEU* 1.3 64.9 + - + +
334B SER* 2.9 23.7 + - - -
335B ASP* 3.3 7.3 + - - -
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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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290B MET* 3.9 49.6 - - + +
298B ARG* 4.7 4.0 - - + -
302B SER* 3.3 23.3 - - - +
328B CYS 3.1 12.0 + - - +
329B ILE* 2.7 21.4 + - + +
331B GLU* 1.3 76.0 - - + +
333B VAL* 1.3 61.9 + - - +
335B ASP* 2.8 33.3 + - - +
340B VAL* 3.7 25.7 - - + +
341B LYS* 4.1 7.1 + - - +
344B LEU* 3.8 20.8 - - + +
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Residues in contact with VAL 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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329B ILE* 2.9 10.4 + - + +
330B LYS* 2.8 24.2 - - + +
331B GLU 3.2 0.4 - - - -
332B LEU* 1.3 75.7 - - - +
334B SER* 1.3 64.9 - - - +
335B ASP 3.8 0.3 + - - -
341B LYS* 4.0 18.9 + - - +
344B LEU* 3.7 12.2 - - + +
348B ILE* 5.1 0.7 - - + -
367B LEU* 3.8 35.9 - - + +
370B ALA* 4.0 16.8 - - + +
371B GLN* 3.3 38.6 + - + +
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Residues in contact with SER 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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330B LYS 4.0 3.6 + - - -
331B GLU* 2.9 19.0 + - - -
333B VAL* 1.3 86.3 - - - +
335B ASP* 1.3 64.7 + - - +
336B ALA* 3.6 1.6 + - - -
341B LYS* 4.7 3.1 - - - +
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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