Contacts of the helix formed by residues 319 - 337 (chain B) in PDB entry 2VZI
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 SER 319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B PRO 3.6 0.2 - - - -
318B ASP* 1.3 89.5 + - - +
320B PHE* 1.3 62.8 + - - +
321B GLU* 3.3 8.9 + - - +
322B GLN* 3.1 27.6 + - - +
323B LYS* 3.2 23.6 + - - +
1373B PG4 3.6 11.4 - - - -
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Residues in contact with PHE 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B SER* 1.3 73.6 - - - +
321B GLU* 1.3 66.0 + - + +
323B LYS* 3.2 5.6 + - - +
324B VAL* 2.9 44.5 + - + +
347B GLU* 3.7 29.4 - - + -
350B VAL* 3.4 31.2 - - + -
351B ASN* 3.9 21.8 - - - -
1373B PG4 3.4 30.2 - - - -
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Residues in contact with GLU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B SER* 3.2 8.3 + - - +
320B PHE* 1.3 87.6 - - + +
322B GLN* 1.3 58.6 + - + +
324B VAL* 3.4 18.9 + - - +
325B LEU* 3.0 54.6 + - + +
347B GLU* 5.7 0.3 - - - +
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Residues in contact with GLN 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B PHE* 3.6 49.6 - - + -
316B THR 4.1 2.9 - - - +
317B PRO* 3.4 15.7 - - + +
318B ASP* 3.1 41.5 + - - +
319B SER* 3.1 19.3 + - - +
321B GLU* 1.3 77.0 - - + +
323B LYS* 1.3 58.1 + - - +
325B LEU* 3.4 2.9 + - + -
326B ASN* 3.1 31.7 + - - +
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Residues in contact with LYS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ASP* 3.7 30.8 - - + +
317B PRO* 3.6 21.5 - - + -
319B SER 3.2 10.8 + - - +
320B PHE 3.5 7.2 - - - +
322B GLN* 1.3 73.9 - - - +
324B VAL* 1.3 64.0 + - - +
326B ASN* 3.2 4.3 + - - +
327B VAL* 3.1 26.0 + - - +
350B VAL* 3.7 15.5 - - + -
1373B PG4 2.9 103.7 + - - +
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B PHE* 2.9 48.9 + - + +
321B GLU* 3.5 23.3 - - - +
323B LYS* 1.3 76.0 - - - +
325B LEU* 1.3 59.2 + - + +
327B VAL* 3.1 4.6 + - - +
328B SER* 2.8 31.3 + - - +
346B PRO* 3.9 16.1 - - + +
347B GLU* 4.0 24.2 - - + +
350B VAL* 3.9 15.9 - - + -
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Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B PHE* 3.9 28.0 - - + -
321B GLU* 3.0 45.9 + - + +
322B GLN* 3.7 7.0 - - + +
323B LYS 3.3 0.2 - - - -
324B VAL* 1.3 78.0 - - + +
326B ASN* 1.3 59.1 + - - +
328B SER* 3.7 8.6 - - - -
329B PHE* 3.0 29.5 + - - +
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Residues in contact with ASN 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ASP 3.2 22.6 + - - +
293B GLY* 3.7 11.9 - - - +
294B VAL* 4.0 4.8 - - - +
297B VAL* 3.3 13.6 - - + +
313B PHE* 3.3 13.8 - - - +
314B PHE* 2.7 58.0 + - - +
317B PRO* 3.8 4.9 - - - +
322B GLN 3.1 12.3 + - - +
323B LYS 3.2 8.0 + - - +
325B LEU* 1.3 77.0 - - - +
327B VAL* 1.3 57.7 + - - +
329B PHE* 3.2 5.8 + - - +
330B ALA 2.9 24.1 + - - -
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Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B GLY* 3.7 20.6 - - - +
296B LEU* 4.5 4.9 - - + -
323B LYS 3.1 15.7 + - - +
324B VAL 3.1 5.8 + - - +
326B ASN* 1.3 72.5 - - - +
328B SER* 1.3 60.3 + - - +
330B ALA* 3.2 6.1 + - - +
331B PHE* 2.9 58.2 + - + -
346B PRO* 3.7 18.4 - - + +
349B ILE* 3.8 25.4 - - + -
350B VAL* 3.9 16.6 - - + -
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Residues in contact with SER 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B VAL* 2.8 20.9 + - - +
325B LEU* 3.7 13.2 - - - -
327B VAL* 1.3 71.5 - - - +
329B PHE* 1.3 58.2 + - - +
331B PHE* 3.4 9.2 + - - +
332B GLU* 3.0 29.4 + - - +
346B PRO* 3.5 24.7 - - - +
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Residues in contact with PHE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B VAL* 4.0 11.2 - - + -
308B VAL* 3.8 27.1 - - + -
309B PRO* 6.2 0.2 - - + -
312B SER* 3.6 38.6 - - - +
313B PHE* 3.9 12.1 - - + -
325B LEU 3.0 19.2 + - - +
326B ASN* 3.5 5.2 - - - +
328B SER* 1.3 75.6 - - - +
330B ALA* 1.3 58.9 + - - +
332B GLU* 3.4 26.8 + - - +
333B LEU* 3.0 55.1 + - + +
1377B PGE 5.2 6.7 - - - -
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU* 3.8 42.8 - - + +
297B VAL* 3.8 7.7 - - + +
300B MET* 3.9 1.9 - - - +
326B ASN 2.9 16.4 + - - +
327B VAL* 3.6 8.3 - - - +
329B PHE* 1.3 73.3 - - - +
331B PHE* 1.3 56.9 + - - +
333B LEU* 3.3 10.0 + - - +
334B MET* 2.9 42.1 + - + +
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Residues in contact with PHE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU* 4.4 3.6 - - + -
327B VAL* 2.9 38.0 + - + +
328B SER* 3.5 7.9 - - - +
330B ALA* 1.3 73.6 - - + +
332B GLU* 1.3 61.1 + - - +
334B MET* 3.3 23.0 + - + +
335B GLN* 3.0 37.7 + - - +
342B PRO* 3.6 28.1 - - + +
344B PRO* 3.5 25.1 - - + -
346B PRO* 3.9 24.7 - - + -
349B ILE* 3.9 9.9 - - + -
360B VAL* 3.8 32.3 - - + -
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Residues in contact with GLU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B SER 3.0 14.5 + - - +
329B PHE* 3.4 32.5 - - + +
331B PHE* 1.3 77.2 - - - +
333B LEU* 1.3 57.3 + - - +
335B GLN* 3.3 10.0 + - - +
336B ASP* 2.9 46.4 + - - +
1377B PGE 5.1 8.7 + - - -
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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
----------------------------------------------------------
297B VAL* 4.3 14.1 - - + +
300B MET* 3.8 26.5 - - + +
304B GLU* 5.1 0.9 - - - +
306B TYR* 3.4 32.5 + - + +
308B VAL* 4.6 2.7 - - + -
329B PHE* 3.0 56.2 + - + +
330B ALA* 3.3 8.5 + - - +
332B GLU* 1.3 73.0 - - - +
334B MET* 1.3 64.2 + - - +
336B ASP* 3.3 14.9 + - + +
337B GLY* 3.1 16.8 + - - -
1377B PGE 4.0 26.0 - - - +
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Residues in contact with MET 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU* 3.9 21.5 - - + -
300B MET* 3.5 30.7 - - + +
330B ALA* 2.9 27.9 + - + +
331B PHE* 3.3 25.3 + - + +
333B LEU* 1.3 75.5 - - - +
335B GLN* 1.3 62.6 + - + +
337B GLY* 3.1 12.3 + - - -
338B GLY 3.3 0.2 + - - -
339B LEU* 3.2 34.6 + - + +
342B PRO* 4.2 3.6 - - + -
360B VAL* 3.8 21.8 - - + -
364B LEU* 4.0 10.5 - - + -
1376B EDO 3.5 28.0 - - - -
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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 PHE* 3.0 25.9 + - - +
332B GLU* 3.3 8.1 + - - +
334B MET* 1.3 75.5 - - - +
336B ASP* 1.3 63.4 + - - +
338B GLY* 3.1 13.5 + - - -
339B LEU 3.3 20.0 - - - +
340B GLU* 4.1 3.0 - - - +
341B LYS* 3.5 46.1 + - - +
342B PRO* 4.1 5.6 - - + +
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Residues in contact with ASP 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLU* 5.4 0.2 - - - +
306B TYR* 5.6 1.8 - - + +
332B GLU* 2.9 37.2 + - - +
333B LEU* 3.5 20.6 - - + +
335B GLN* 1.3 77.0 - - - +
337B GLY* 1.3 58.5 + - - +
338B GLY 3.3 0.6 + - - -
1377B PGE 3.6 45.8 - - - +
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Residues in contact with GLY 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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304B GLU* 3.7 30.0 - - - +
333B LEU 3.1 8.6 + - - -
334B MET 3.1 9.2 + - - -
336B ASP* 1.3 74.9 - - - +
338B GLY* 1.3 58.2 + - - +
339B LEU 3.5 2.5 - - - -
367B LYS* 2.8 24.8 + - - -
368B TYR* 4.1 3.4 - - - -
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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