Contacts of the helix formed by residues 326 - 344 (chain B) in PDB entry 7CAL
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 PRO 326 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A TYR* 3.7 43.7 - - + +
324B GLN 3.8 0.2 - - - -
325B LEU* 1.3 93.2 - - + +
327B HIS* 1.3 64.2 + - - +
328B ASP* 3.2 11.9 + - + +
329B ILE* 3.4 21.0 + - + +
330B GLN* 3.3 19.5 + - - +
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Residues in contact with HIS 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU 3.9 0.4 + - - -
326B PRO* 1.3 74.4 - - - +
328B ASP* 1.3 65.6 + - - +
329B ILE 3.3 0.2 - - - -
330B GLN* 4.0 18.3 + - - -
331B ASP* 3.1 68.3 + - - +
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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 PRO* 3.1 9.8 - - + +
327B HIS* 1.3 89.7 + - - +
329B ILE* 1.3 57.0 + - - +
331B ASP* 4.4 5.0 - - - +
332B GLN* 3.9 23.0 + - - +
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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
----------------------------------------------------------
359A ILE* 4.5 11.9 - - + +
362A SER* 3.9 35.4 - - - +
363A ILE* 4.5 16.4 - - + -
366A TYR* 5.7 1.6 - - + -
325B LEU* 4.0 18.8 - - + -
326B PRO* 3.5 34.9 - - + +
328B ASP* 1.3 77.0 - - - +
330B GLN* 1.3 67.4 + - - +
331B ASP 3.3 1.8 - - - -
332B GLN* 3.3 36.9 + - + +
333B MET* 3.4 15.2 + - - +
403B ASP* 6.0 0.2 - - - +
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Residues in contact with GLN 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ALA 5.4 0.2 - - - +
317B SER* 4.6 18.4 + - - -
320B ALA* 3.4 41.5 + - + +
321B SER* 5.4 2.0 - - - +
325B LEU* 4.6 7.5 - - + +
326B PRO 3.3 17.8 + - - +
327B HIS* 3.7 20.6 + - - +
329B ILE* 1.3 79.3 - - - +
331B ASP* 1.3 63.5 + - - +
333B MET* 3.4 11.0 - - + +
334B LEU* 3.2 37.2 + - + +
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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
----------------------------------------------------------
327B HIS* 3.1 50.4 + - - +
328B ASP* 5.0 4.7 - - - +
329B ILE 3.3 0.4 - - - -
330B GLN* 1.3 79.6 - - - +
332B GLN* 1.3 60.5 + - + +
334B LEU* 3.9 6.6 - - - +
335B SER* 2.6 37.7 + - - +
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Residues in contact with GLN 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ALA 5.3 1.7 - - - +
359A ILE* 3.4 32.7 - - + +
362A SER* 5.6 0.7 - - - -
328B ASP 3.9 16.6 + - - +
329B ILE* 3.3 27.9 + - + +
330B GLN 3.2 0.8 - - - -
331B ASP* 1.3 81.5 - - + +
333B MET* 1.3 59.2 + - - +
334B LEU 3.4 0.2 - - - -
335B SER* 4.5 2.0 - - - -
336B HIS* 3.5 21.8 + - - +
399B PRO* 5.3 2.3 - - - +
401B LYS 3.7 24.4 + - - +
402B GLU* 4.5 6.2 - - + +
403B ASP* 3.6 33.0 + - - +
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Residues in contact with MET 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A THR* 5.2 3.4 - - + -
355A LEU* 3.8 32.5 - - + +
359A ILE* 3.7 19.7 - - + +
363A ILE* 4.0 11.9 - - + -
316B ALA* 4.0 30.7 - - + +
319B PHE* 4.2 14.8 - - + -
320B ALA* 4.1 17.9 - - - -
325B LEU* 4.5 10.1 - - - -
329B ILE 3.4 9.9 + - - +
330B GLN* 3.4 12.8 - - + +
332B GLN* 1.3 78.3 - - - +
334B LEU* 1.3 67.8 + - + +
336B HIS* 4.1 3.1 - - - +
337B ILE* 3.3 30.5 + - - +
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE* 4.6 17.9 - - + -
313B VAL* 4.1 28.0 - - + +
316B ALA* 4.7 7.0 - - + +
317B SER* 3.8 25.4 - - - +
330B GLN* 3.2 34.7 + - + +
331B ASP* 4.5 6.1 - - - +
333B MET* 1.3 85.3 - - + +
335B SER* 1.3 62.8 + - - +
336B HIS 3.2 1.8 - - - -
337B ILE* 3.6 12.4 + - + +
338B CYS* 3.3 28.8 + - - -
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE* 6.1 0.2 - - - -
331B ASP* 2.6 28.5 + - - +
332B GLN* 4.7 1.8 - - - -
334B LEU* 1.3 76.5 - - - +
336B HIS* 1.3 62.2 + - - +
338B CYS* 3.8 6.8 + - - +
339B LEU* 3.3 23.0 + - - +
399B PRO* 4.0 22.3 - - - +
400B PRO 6.0 0.9 - - - -
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Residues in contact with HIS 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ASN 4.2 12.6 + - - -
355A LEU* 4.9 8.7 - - + -
356A PRO* 3.9 36.7 - - + +
359A ILE* 5.4 3.8 - - + +
332B GLN 3.5 18.7 + - - +
333B MET* 4.3 5.8 - - - +
334B LEU 3.2 0.8 - - - -
335B SER* 1.3 78.0 - - - +
337B ILE* 1.3 64.6 + - + +
339B LEU* 3.4 1.7 + - - +
340B LYS* 2.9 47.9 + - + +
396B GLU 4.5 16.8 - - - -
397B TYR 5.1 1.3 + - - -
398B PHE* 5.2 10.3 - + - -
399B PRO* 4.3 23.5 - - + +
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Residues in contact with ILE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A THR* 6.1 0.7 - - + -
355A LEU* 5.2 8.3 - - + -
309B PHE* 4.0 5.6 - - + -
312B SER* 3.7 31.4 - - - +
313B VAL* 3.9 16.8 - - + -
316B ALA* 3.7 28.5 - - + -
333B MET 3.3 20.6 - - - +
334B LEU* 3.6 11.5 + - + +
335B SER 3.5 0.2 - - - -
336B HIS* 1.3 83.7 - - + +
338B CYS* 1.3 61.7 + - - +
340B LYS* 3.5 6.9 + - - +
341B PHE* 3.1 23.4 + - - +
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Residues in contact with CYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LYS 5.4 1.6 - - - -
189A ILE* 3.7 40.4 - - - -
309B PHE* 4.2 17.0 - - + -
313B VAL* 4.9 3.4 - - - -
334B LEU 3.3 19.0 + - - +
335B SER* 4.1 6.7 - - - +
336B HIS 3.3 0.6 - - - -
337B ILE* 1.3 78.6 - - - +
339B LEU* 1.3 59.0 + - - +
341B PHE* 3.6 3.8 + - - +
342B LYS* 3.3 30.4 + - + +
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Residues in contact with LEU 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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120A TYR* 5.4 5.4 - - + -
335B SER 3.3 15.3 + - - +
336B HIS 4.1 2.9 - - - +
337B ILE 3.3 0.2 - - - -
338B CYS* 1.3 77.4 - - - +
340B LYS* 1.3 63.0 + - - +
341B PHE 3.2 0.4 - - - -
342B LYS* 4.1 24.7 - - - +
343B THR* 2.8 47.3 + - + -
397B TYR* 3.3 30.1 - - + +
398B PHE 3.9 3.4 - - - +
399B PRO* 3.6 30.5 - - + -
400B PRO* 5.4 1.6 - - + -
461B THR* 4.8 11.2 - - + +
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Residues in contact with LYS 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ASN* 3.5 42.7 + - + +
336B HIS* 2.9 40.0 + - + +
337B ILE* 3.9 7.9 - - + +
338B CYS 3.4 0.2 - - - -
339B LEU* 1.3 77.6 - - - +
341B PHE* 1.3 57.3 + - - +
343B THR* 4.1 4.0 - - - -
344B GLU* 3.0 41.1 + - + +
345B GLY 3.3 6.4 - - - +
346B LEU 6.0 1.6 - - - -
396B GLU 6.1 1.3 - - - +
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Residues in contact with PHE 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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187A LYS* 4.3 23.3 - - + -
305B ARG* 3.5 62.1 + - - -
306B THR* 4.6 6.3 - - + -
309B PHE* 3.8 44.4 - + + -
337B ILE 3.1 16.3 + - - +
338B CYS 3.9 5.6 - - - +
339B LEU 3.2 0.2 - - - -
340B LYS* 1.3 78.4 - - - +
342B LYS* 1.3 70.6 + - + +
343B THR 3.5 0.2 + - - -
345B GLY* 3.5 25.7 + - - +
346B LEU* 4.1 11.9 - - + -
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Residues in contact with LYS 342 (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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115A LEU* 5.0 18.3 - - - +
120A TYR* 3.7 32.4 + - + +
187A LYS* 6.5 1.1 - - - -
338B CYS* 3.3 20.1 + - + +
339B LEU* 4.0 23.4 - - + +
340B LYS 3.4 0.4 - - - -
341B PHE* 1.3 85.4 - - + +
343B THR* 1.3 62.9 + - + +
345B GLY 4.8 0.2 - - - -
322C ARG* 4.8 6.2 + - - -
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Residues in contact with THR 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A TYR* 3.6 36.4 + - + -
339B LEU* 2.8 38.8 + - + +
340B LYS* 4.1 2.4 + - - -
342B LYS* 1.3 81.4 - - - +
344B GLU* 1.3 68.3 + - - +
345B GLY 3.2 4.7 - - - -
348B GLN* 4.6 1.0 - - - +
397B TYR* 3.8 33.8 - - + +
322C ARG* 3.0 29.1 + - - -
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B LYS* 3.0 31.3 + - + +
343B THR* 1.3 82.4 + - - +
345B GLY* 1.3 64.4 + - - +
346B LEU* 3.6 1.0 + - - -
347B LYS 4.9 0.2 - - - -
348B GLN* 3.3 45.6 + - + +
395B ALA* 4.9 10.8 - - + +
322C ARG* 3.7 5.0 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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