Contacts of the helix formed by residues 353 - 368 (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 ASP 353 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B ASP* 2.9 24.2 + - + +
351B ASN* 3.3 4.7 - - + +
352B CYS* 1.3 74.8 - - - +
354B LEU* 1.3 60.6 + - - +
355B LYS* 3.8 12.3 + - - +
356B SER* 2.5 37.0 + - - +
357B THR* 2.9 28.6 + - - -
359B ARG* 5.0 1.2 + - - -
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B PHE* 4.0 26.2 - - + -
261B LEU* 4.9 8.5 - - + -
265B LYS* 5.5 7.9 - - + -
286B LEU* 4.5 8.7 - - + +
287B GLU* 3.8 48.2 - - + +
352B CYS 3.2 8.4 + - - +
353B ASP* 1.3 70.4 + - - +
355B LYS* 1.3 56.8 + - - +
357B THR* 3.2 5.0 + - - -
358B LEU* 2.7 60.2 + - + +
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Residues in contact with LYS 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ARG* 4.7 5.5 - - - +
250B PHE* 3.6 16.4 - - + +
251B ASP* 3.2 26.9 + - - +
254B PHE* 3.6 52.8 - - + +
255B ASP* 3.8 18.2 + - - -
353B ASP* 3.4 10.9 - - - +
354B LEU* 1.3 75.4 - - - +
356B SER* 1.3 57.8 + - - +
358B LEU* 3.2 4.7 + - - +
359B ARG* 2.9 52.1 + - - +
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Residues in contact with SER 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B PRO* 3.6 26.5 - - - +
348B ASP* 3.5 21.9 + - - +
349B ILE* 3.5 14.4 - - - +
353B ASP* 2.5 29.3 + - - -
354B LEU 3.3 0.2 - - - -
355B LYS* 1.3 74.2 - - - +
357B THR* 1.3 65.8 + - - +
359B ARG* 3.5 13.3 + - - +
360B VAL* 3.2 22.5 + - - +
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Residues in contact with THR 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 3.4 28.7 + - + +
287B GLU* 5.3 1.6 + - - -
290B PHE* 4.2 17.3 - - + -
349B ILE* 3.6 26.6 + - + +
352B CYS* 4.7 2.8 - - - -
353B ASP 2.9 21.0 + - - -
354B LEU* 3.2 9.2 + - + -
356B SER* 1.3 74.9 - - - +
358B LEU* 1.3 63.2 + - + +
360B VAL* 3.5 1.7 + - - +
361B LEU* 3.1 46.7 + - + +
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Residues in contact with LEU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B PHE* 3.8 18.4 - - + -
254B PHE* 3.7 21.8 - - + -
261B LEU* 3.5 32.1 - - + -
264B VAL* 4.5 11.2 - - + -
265B LYS* 4.9 5.8 - - + -
268B LEU* 4.0 15.5 - - + +
286B LEU* 3.9 28.9 - - + -
354B LEU* 2.7 37.8 + - + +
355B LYS 3.6 4.5 - - - +
357B THR* 1.3 75.6 - - - +
359B ARG* 1.3 55.4 + - - +
361B LEU* 3.5 1.7 + - + +
362B TYR* 2.9 33.3 + - - +
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Residues in contact with ARG 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ASP* 2.7 40.8 + - - +
250B PHE* 3.5 34.4 - - + +
251B ASP* 3.2 24.4 + - - -
343B LYS* 4.5 25.1 - - + +
344B PRO* 4.9 8.7 - - + +
353B ASP* 5.0 0.8 + - - -
355B LYS* 2.9 40.7 + - - +
356B SER* 3.8 14.3 + - - +
358B LEU* 1.3 72.0 - - - +
360B VAL* 1.3 67.3 + - - +
362B TYR* 3.4 0.9 + - - +
363B ASN* 3.1 36.3 + - - +
1376B EDO 4.7 0.7 - - - +
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU* 4.0 23.6 - - + -
331B PHE* 3.8 21.1 - - + -
334B MET* 3.8 25.1 - - + -
344B PRO* 3.8 18.6 - - + -
349B ILE* 4.1 6.5 - - + -
356B SER 3.2 16.6 + - - +
357B THR 4.0 3.1 - - - +
359B ARG* 1.3 81.0 - - - +
361B LEU* 1.3 63.2 + - + +
364B LEU* 3.2 10.2 + - + +
1376B EDO 2.4 42.2 + - - +
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B LEU* 3.6 18.0 - - + +
271B PHE* 4.1 3.2 - - + -
272B VAL* 4.0 21.8 - - + -
286B LEU* 3.6 35.7 - - + -
290B PHE* 3.6 20.9 - - + -
296B LEU* 3.8 28.0 - - + -
299B LEU* 4.4 0.7 - - + -
357B THR* 3.1 29.5 + - + +
358B LEU* 4.1 2.9 - - - +
360B VAL* 1.3 75.8 - - + +
362B TYR* 1.3 57.1 + - - +
364B LEU* 3.3 14.4 + - + +
365B PHE* 2.9 26.9 + - - +
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Residues in contact with TYR 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.0 26.5 - - + -
6A ASP* 4.1 11.2 + - - -
9A MET* 3.7 37.8 - - + +
250B PHE* 3.6 26.2 - + + -
268B LEU* 3.8 12.0 - - + +
358B LEU 2.9 19.3 + - - +
359B ARG 3.9 2.0 - - - +
360B VAL 3.3 0.2 - - - -
361B LEU* 1.3 76.2 - - - +
363B ASN* 1.3 69.7 + - - +
365B PHE* 3.1 14.1 + + - +
366B THR* 2.9 56.7 + - + +
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Residues in contact with ASN 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B PHE* 5.8 0.3 - - - -
339B LEU* 4.0 14.8 - - + +
343B LYS* 5.9 4.2 - - - +
359B ARG* 3.1 20.3 + - - +
362B TYR* 1.3 86.9 - - - +
364B LEU* 1.3 60.3 + - - +
366B THR* 3.3 9.9 + - - -
367B LYS* 3.2 28.1 + - - +
1376B EDO 2.6 41.7 + - - +
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Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PHE* 3.8 12.7 - - + -
296B LEU* 4.4 3.1 - - + -
299B LEU* 3.9 28.0 - - + -
300B MET* 3.6 32.5 - - - -
303B LEU* 4.2 4.9 - - + -
334B MET* 4.0 14.4 - - + -
339B LEU* 3.7 22.4 - - + -
360B VAL* 3.2 14.5 + - + +
361B LEU* 3.5 17.7 - - + +
363B ASN* 1.3 73.5 - - - +
365B PHE* 1.3 57.8 + - - +
367B LYS* 4.7 0.2 - - - -
368B TYR* 2.8 49.9 + - + +
1376B EDO 3.6 4.9 - - - +
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Residues in contact with PHE 365 (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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2A THR* 3.8 22.0 - - + -
5A LEU* 4.0 14.6 - - + -
6A ASP* 3.8 9.6 - - - -
267B THR* 3.9 19.5 - - + -
268B LEU* 3.7 18.8 - - + -
271B PHE* 3.7 37.8 - + + -
361B LEU 2.9 13.9 + - - +
362B TYR* 3.2 15.5 - + - +
364B LEU* 1.3 77.9 - - - +
366B THR* 1.3 67.9 + - + +
369B ARG* 3.1 68.5 + - + +
1374B EDO 4.6 7.9 - - - -
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Residues in contact with THR 366 (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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362B TYR* 2.9 56.1 + - + +
363B ASN* 3.3 15.8 + - - -
364B LEU 3.3 0.2 - - - -
365B PHE* 1.3 73.4 - - + +
367B LYS* 1.3 67.5 + - - +
369B ARG* 3.9 32.5 + - - +
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Residues in contact with LYS 367 (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* 4.7 0.9 - - - -
337B GLY 2.8 29.0 + - - -
338B GLY* 3.7 16.4 + - - -
339B LEU* 3.9 25.1 - - + +
363B ASN 3.2 15.7 + - - +
366B THR* 1.3 85.7 + - - +
368B TYR* 1.3 93.1 + - + +
369B ARG* 3.7 0.9 + - - +
370B ASN 5.2 0.7 + - - -
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Residues in contact with TYR 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PHE* 4.1 3.3 - - + -
300B MET* 3.7 10.3 - - + +
303B LEU* 3.6 59.7 - - + -
304B GLU* 2.6 40.6 + - + +
337B GLY* 4.1 8.3 - - - -
339B LEU* 4.4 3.8 - - + +
364B LEU* 2.8 47.9 + - + +
365B PHE 3.8 2.5 - - - -
367B LYS* 1.3 102.1 - - + +
369B ARG* 1.3 55.3 + - - +
370B ASN 3.1 5.2 + - - +
371B VAL* 3.2 17.3 + - + +
1374B EDO 2.7 27.3 + - - -
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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