Contacts of the helix formed by residues 326 - 340 (chain B) in PDB entry 5ULM
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 ASP 326 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ALA* 5.9 1.2 - - - +
321B TYR* 2.9 36.3 + - + +
324B ILE* 3.1 15.7 + - + +
325B GLN* 1.3 70.1 - - - +
327B TYR* 1.3 63.0 + - - +
328B ASP* 3.7 8.0 + - - +
329B SER* 2.6 36.9 + - - -
330B ILE* 3.3 20.5 + - - +
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Residues in contact with TYR 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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322B ARG* 3.8 14.4 - - + +
325B GLN* 3.3 43.4 + - + +
326B ASP* 1.3 70.5 + - - +
328B ASP* 1.3 60.3 + - - +
330B ILE* 3.1 12.9 + - + +
331B VAL* 2.9 34.8 + - - +
357B PHE* 3.8 23.7 - + - -
358B ALA* 3.7 35.6 - - + +
361B ARG* 3.5 30.5 - - + +
362B ARG* 4.3 11.0 - - + +
509B TRP* 3.3 30.3 - - - +
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Residues in contact with ASP 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ASP* 3.3 7.1 + - - +
327B TYR* 1.3 77.0 - - - +
329B SER* 1.3 56.1 + - - +
331B VAL* 3.3 1.3 + - - +
332B LYS* 3.0 63.4 + - - +
362B ARG* 2.9 46.3 + - + +
364B LEU* 5.0 2.6 - - - +
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Residues in contact with SER 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ARG* 4.7 4.9 + - - -
321B TYR* 3.8 27.8 - - - -
326B ASP* 2.6 36.6 + - - -
327B TYR 3.4 0.2 - - - -
328B ASP* 1.3 76.5 + - - +
330B ILE* 1.3 63.1 + - - +
332B LYS* 4.1 4.8 - - - +
333B LEU* 3.0 26.7 + - - +
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Residues in contact with ILE 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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318B LEU* 3.7 49.6 - - + +
321B TYR* 3.6 19.1 - - + -
322B ARG* 4.0 11.2 - - + +
326B ASP 3.3 10.9 + - - +
327B TYR* 3.1 34.2 + - + +
329B SER* 1.3 77.5 - - - +
331B VAL* 1.3 62.9 + - - +
333B LEU* 3.9 1.0 - - - +
334B VAL* 3.1 28.4 + - + +
354B HIS* 4.0 12.6 - - + +
355B TYR* 4.6 0.9 - - - -
357B PHE* 6.3 0.2 - - + -
358B ALA* 3.6 17.7 - - + -
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B TYR 2.9 20.4 + - - +
328B ASP 3.8 4.0 - - - +
330B ILE* 1.3 76.0 - - - +
332B LYS* 1.3 57.2 + - - +
334B VAL* 3.3 1.4 + - - +
335B GLU* 2.9 49.4 + - - +
355B TYR* 4.1 11.3 - - + +
358B ALA* 3.9 7.2 - - + +
359B LEU* 3.8 44.6 - - + +
362B ARG* 3.6 37.5 - - - +
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Residues in contact with LYS 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ASP* 3.0 49.3 + - - +
329B SER* 4.1 4.5 - - - +
331B VAL* 1.3 76.6 - - - +
333B LEU* 1.3 61.3 + - - +
335B GLU* 3.8 16.8 - - - +
336B THR* 3.1 30.6 + - + +
362B ARG* 4.5 8.3 - - - +
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ARG* 4.1 30.2 - - - +
303B VAL* 5.5 0.7 - - + -
304B ASP* 5.6 0.9 - - - +
309B LEU* 4.7 12.3 - - + -
314B VAL* 4.8 7.0 - - + +
317B LEU* 3.7 31.4 - - + -
318B LEU* 3.6 25.4 - - + -
321B TYR* 4.6 3.4 - - + -
329B SER 3.0 18.5 + - - +
330B ILE 3.9 2.9 - - - +
332B LYS* 1.3 76.8 - - - +
334B VAL* 1.3 63.7 + - + +
336B THR* 2.6 29.9 + - - +
337B LEU* 3.2 26.3 + - + +
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Residues in contact with VAL 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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318B LEU* 3.9 31.0 - - + -
330B ILE* 3.1 21.2 + - + +
333B LEU* 1.3 76.4 - - + +
335B GLU* 1.3 61.2 + - - +
337B LEU* 3.2 12.3 + - + +
338B GLU* 3.1 19.8 + - - +
345B LEU* 3.9 24.2 - - + +
351B VAL* 4.2 7.6 - - + -
355B TYR* 3.5 47.6 - - + -
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Residues in contact with GLU 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 VAL* 2.9 36.9 + - + +
332B LYS* 3.8 19.3 - - - +
334B VAL* 1.3 77.1 - - - +
336B THR* 1.3 63.0 + - + +
338B GLU* 3.3 17.3 + - - +
339B LYS* 3.4 26.2 + - - +
355B TYR* 3.6 22.4 + - - +
359B LEU* 5.5 0.9 - - - +
362B ARG* 4.6 6.9 + - - -
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Residues in contact with THR 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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300B ARG* 5.5 1.8 + - - +
332B LYS* 3.1 16.0 + - + +
333B LEU* 2.6 30.5 + - - +
335B GLU* 1.3 78.0 - - + +
337B LEU* 1.3 58.9 + - - +
339B LYS* 3.4 9.1 + - - +
340B LEU* 3.1 26.2 + - - +
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Residues in contact with LEU 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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309B LEU* 4.1 28.5 - - + -
314B VAL* 3.5 36.1 - - + -
333B LEU* 3.2 20.5 + - + +
334B VAL* 3.2 15.7 + - + +
336B THR* 1.3 77.1 + - - +
338B GLU* 1.3 64.8 + - - +
340B LEU* 3.1 25.7 - - + +
343B PHE* 3.8 52.9 - - + +
345B LEU* 5.3 2.9 - - + +
351B VAL* 4.8 4.3 - - + -
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Residues in contact with GLU 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 VAL 3.1 12.3 + - - +
335B GLU* 3.3 13.2 + - - +
337B LEU* 1.3 77.3 - - - +
339B LYS* 1.3 76.0 + - - +
340B LEU 4.2 2.4 - - - +
343B PHE 5.2 2.3 - - - +
345B LEU* 3.0 41.4 - - + +
346B ALA 5.1 0.2 + - - -
355B TYR* 6.1 2.7 - - + +
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Residues in contact with LYS 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 GLU* 3.4 27.4 + - - +
336B THR* 3.4 8.3 + - - +
337B LEU 3.2 0.2 - - - -
338B GLU* 1.3 92.7 - - - +
340B LEU* 1.3 65.8 + - - +
342B THR* 5.1 0.9 - - - +
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Residues in contact with LEU 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 THR 3.1 17.5 + - - +
337B LEU* 3.1 25.1 + - + +
338B GLU 4.2 2.4 - - - +
339B LYS* 1.3 81.7 - - - +
342B THR* 3.2 44.2 - - - -
343B PHE* 3.3 17.2 + - + +
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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