Contacts of the helix formed by residues 342 - 354 (chain A) in PDB entry 2VZE
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 LEU 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A PRO* 5.7 0.2 - - - +
316A ARG* 3.6 32.1 - - - +
340A SER* 3.5 22.1 + - - +
341A LEU* 1.3 75.8 - - - +
343A PRO* 1.4 76.0 - - + +
344A GLU* 3.6 21.3 - - + +
345A THR* 3.0 24.8 + - - +
346A LEU* 3.2 11.3 + - - +
502A GLY* 5.3 5.6 - - - -
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Residues in contact with PRO 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A LEU 3.6 5.4 - - - +
342A LEU* 1.4 86.7 - - + +
344A GLU* 1.3 67.6 + - - +
346A LEU* 3.4 9.5 + - + +
347A GLU* 2.8 33.9 + - - +
380A PRO* 4.1 19.4 - - + +
381A GLY* 3.9 26.9 - - - +
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Residues in contact with GLU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A LEU* 3.6 19.4 - - + +
343A PRO* 1.3 98.0 - - - +
345A THR* 1.3 56.7 + - - +
347A GLU* 3.5 10.0 + - - +
348A ASN* 3.1 29.8 + - - +
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Residues in contact with THR 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A PRO* 4.8 1.7 - - + +
315A TYR* 4.1 14.8 - - + -
316A ARG* 3.7 34.6 + - + +
319A LEU* 3.8 22.2 - - + +
341A LEU* 3.9 20.2 - - + -
342A LEU* 3.0 22.2 + - - +
344A GLU* 1.3 74.1 - - - +
346A LEU* 1.3 61.5 + - - +
348A ASN* 3.3 2.5 + - - +
349A TRP* 2.9 30.3 + - - +
357A ILE* 4.4 1.6 - - + -
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A LEU* 4.4 12.0 - - + +
342A LEU 3.2 8.3 + - - +
343A PRO* 3.5 9.6 - - + +
345A THR* 1.3 79.7 - - - +
347A GLU* 1.3 62.0 + - - +
349A TRP* 3.4 1.6 + - - +
350A ARG* 3.0 49.8 + - - +
356A ASP* 4.8 0.2 - - - -
357A ILE* 3.5 50.3 - - + +
378A ILE* 3.7 26.0 - - + -
380A PRO* 4.0 26.0 - - + -
381A GLY 5.3 0.4 - - - +
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Residues in contact with GLU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A PRO 2.8 20.9 + - - +
344A GLU* 3.6 10.3 - - - +
346A LEU* 1.3 73.0 - - - +
348A ASN* 1.3 58.5 + - - +
350A ARG* 3.3 13.1 + - + +
351A ALA* 3.0 29.2 + - + +
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Residues in contact with ASN 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A LEU* 3.3 32.9 + - + +
320A GLN* 5.4 3.6 + - - -
344A GLU 3.1 17.6 + - - +
345A THR* 3.3 3.1 + - - +
347A GLU* 1.3 74.9 - - - +
349A TRP* 1.3 65.6 + - - +
351A ALA* 3.3 5.9 + - - +
352A GLN* 2.9 46.9 + - - +
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Residues in contact with TRP 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A LEU* 5.0 0.4 - - + -
308A MET* 4.5 5.6 - - - -
315A TYR* 3.8 32.3 - + + -
318A LEU* 3.7 39.7 - - + -
319A LEU* 3.8 21.9 - - + +
323A LEU* 4.5 7.2 - - + -
328A PHE* 4.2 19.1 - + - -
334A CYS* 3.6 27.5 - - - +
345A THR 2.9 17.2 + - - +
346A LEU 3.8 2.2 - - - +
348A ASN* 1.3 75.8 - - - +
350A ARG* 1.3 55.0 + - - +
353A THR* 2.6 77.3 + - + -
355A LEU* 3.4 18.6 - - - +
356A ASP 4.4 0.2 - - - -
357A ILE* 3.4 28.9 - - + -
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Residues in contact with ARG 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A LEU* 3.0 44.2 + - - +
347A GLU* 3.4 12.0 - - - +
349A TRP* 1.3 73.0 - - - +
351A ALA* 1.3 62.6 + - - +
354A GLY* 2.8 30.3 + - - +
355A LEU 3.3 21.7 + - - +
356A ASP* 2.9 26.6 + - - +
378A ILE* 3.5 29.6 + - - +
380A PRO* 4.7 12.1 - - - +
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Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A GLU* 3.0 13.9 + - + +
348A ASN* 3.3 8.9 + - - +
350A ARG* 1.3 82.0 - - - +
352A GLN* 1.3 64.7 + - + +
354A GLY 4.6 0.9 + - - -
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Residues in contact with GLN 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A LEU* 3.7 23.4 + - + +
321A GLN 5.5 1.4 + - - -
323A LEU* 3.8 39.8 - - + +
324A SER* 5.3 3.0 - - - +
327A LYS* 4.3 16.8 + - - -
348A ASN* 2.9 39.1 + - - +
349A TRP 4.4 0.7 - - - +
351A ALA* 1.3 82.4 - - + +
353A THR* 1.3 60.2 + - - +
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Residues in contact with THR 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A LEU* 3.9 20.0 - - + -
328A PHE* 4.0 27.7 - - + -
349A TRP* 2.6 54.5 + - + +
352A GLN* 1.3 80.7 - - + +
354A GLY* 1.3 60.8 + - - +
355A LEU* 3.1 23.7 + - - +
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Residues in contact with GLY 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ARG* 2.8 21.7 + - - +
351A ALA 4.6 1.0 + - - -
352A GLN 3.8 0.8 - - - -
353A THR* 1.3 75.5 - - - +
355A LEU* 1.3 63.7 + - - +
356A ASP* 4.3 0.5 + - - -
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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