Contacts of the helix formed by residues 345 - 357 (chain A) in PDB entry 5VZH
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 GLY 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A GLU 3.3 1.0 + - - -
344A ALA* 1.3 73.2 - - - +
346A LEU* 1.3 63.5 + - - +
347A LEU 3.5 2.0 - - - -
348A PRO* 3.5 17.8 - - - +
349A ARG* 3.7 19.9 - - - +
384A ALA* 6.1 4.7 - - - -
385A PHE 5.7 1.8 - - - -
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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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306A VAL* 5.0 2.5 - - + +
309A ALA* 3.8 12.1 - - + +
310A LEU* 3.6 41.1 - - + +
313A ALA* 4.3 7.9 - - + -
335A ILE* 3.6 30.1 - - + -
336A THR 5.1 1.1 - - - +
343A GLU* 3.1 25.7 + - + +
344A ALA 3.2 1.5 - - - +
345A GLY* 1.3 78.1 - - - +
347A LEU* 1.3 66.9 + - - +
349A ARG* 3.0 18.5 + - + +
350A VAL* 3.0 28.3 + - + +
385A PHE 5.6 0.2 + - - -
421A VAL* 4.5 13.0 - - + +
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Residues in contact with LEU 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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335A ILE* 4.7 3.4 - - + -
346A LEU* 1.3 79.4 - - - +
348A PRO* 1.3 64.6 - - + +
350A VAL* 3.1 11.8 + - + +
351A MET* 2.8 35.5 + - + +
385A PHE* 3.6 31.8 + - + +
386A GLU 3.4 32.3 - - - +
387A ARG* 3.5 14.4 - - - +
388A SER* 3.7 5.2 - - - +
419A LEU* 4.0 35.2 - - + +
421A VAL* 4.0 21.1 - - + +
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Residues in contact with PRO 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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345A GLY* 3.5 19.7 - - - +
347A LEU* 1.3 93.4 - - + +
349A ARG* 1.3 57.2 + - + +
351A MET* 3.9 1.8 - - + +
352A CYS* 3.0 38.6 + - - +
384A ALA* 4.5 8.1 - - - +
385A PHE* 3.5 45.7 - - + +
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Residues in contact with ARG 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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308A GLN 4.1 3.8 + - - -
309A ALA* 2.8 38.7 + - + +
345A GLY 3.7 19.5 - - - +
346A LEU* 3.0 11.3 + - - +
348A PRO* 1.3 75.3 - - + +
350A VAL* 1.3 64.8 + - - +
352A CYS* 3.7 2.4 + - - +
353A ARG* 3.0 67.7 + - - +
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Residues in contact with VAL 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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302A VAL* 5.2 1.1 - - + +
305A ALA* 4.4 6.4 - - + +
306A VAL* 3.9 30.1 - - + -
309A ALA* 3.9 10.5 - - + -
335A ILE* 5.0 2.7 - - + -
346A LEU* 3.0 35.2 + - + +
347A LEU* 3.1 14.3 + - + +
349A ARG* 1.3 75.2 - - - +
351A MET* 1.3 65.8 + - - +
353A ARG* 3.2 5.8 + - - +
354A LEU* 3.0 42.1 + - + +
419A LEU* 4.1 16.4 - - + -
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Residues in contact with MET 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 LEU* 2.8 21.8 + - + +
348A PRO 4.0 2.9 - - - +
350A VAL* 1.3 76.2 - - - +
352A CYS* 1.3 58.0 + - - +
354A LEU* 3.3 7.3 + - + +
355A GLN* 2.8 31.8 + - - +
360A ILE* 4.0 20.4 - - + -
363A HIS* 3.7 39.2 + - + +
385A PHE* 4.0 23.3 - - + -
388A SER* 3.6 18.4 - - - +
390A CYS* 3.5 23.1 - - - -
419A LEU* 3.6 22.7 - - - -
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Residues in contact with CYS 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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348A PRO* 3.0 23.6 + - - +
349A ARG* 4.2 5.6 - - - +
350A VAL 3.2 0.2 - - - -
351A MET* 1.3 78.7 - - - +
353A ARG* 1.3 60.1 + - - +
355A GLN* 3.4 6.4 + - - +
356A ASP* 2.9 38.9 + - - +
363A HIS* 6.2 3.1 - - - -
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Residues in contact with ARG 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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305A ALA* 4.0 18.2 - - + -
308A GLN* 4.0 24.0 + - - +
309A ALA* 4.0 24.8 - - - +
349A ARG* 3.0 70.6 + - - +
350A VAL 3.2 4.3 + - - +
352A CYS* 1.3 80.2 - - + +
354A LEU* 1.3 65.7 + - - +
356A ASP* 3.2 11.0 + - - +
357A GLN* 3.0 29.0 + - - +
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Residues in contact with LEU 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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301A VAL 4.0 13.5 - - - +
302A VAL* 4.7 4.3 - - + -
305A ALA* 3.6 21.5 - - + -
350A VAL* 3.0 36.3 + - + +
351A MET* 3.7 12.8 - - - +
353A ARG* 1.3 75.4 - - - +
355A GLN* 1.3 64.1 + - - +
357A GLN* 3.1 16.5 + - - +
359A LEU* 3.2 34.2 + - + +
360A ILE* 3.6 20.0 - - + -
392A PHE* 3.4 38.1 - - + -
419A LEU* 4.2 4.0 - - + -
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Residues in contact with GLN 355 (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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351A MET 2.8 18.0 + - - +
352A CYS* 3.7 7.9 - - - +
354A LEU* 1.3 76.8 - - - +
356A ASP* 1.3 64.4 + - - +
358A GLY* 3.0 14.7 + - - -
360A ILE* 3.7 19.9 - - + +
363A HIS* 4.8 12.1 - - + +
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Residues in contact with ASP 356 (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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352A CYS* 2.9 26.7 + - - +
353A ARG* 3.2 10.9 + - - +
355A GLN* 1.3 81.0 - - - +
357A GLN* 1.4 58.3 + - + +
358A GLY 3.1 3.7 + - - -
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Residues in contact with GLN 357 (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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301A VAL* 5.6 3.4 - - - -
304A GLU* 5.9 5.4 - - - -
305A ALA* 5.4 8.3 - - - -
308A GLN* 5.8 6.7 - - - -
353A ARG* 3.0 19.8 + - - +
354A LEU* 3.1 14.5 + - - +
356A ASP* 1.4 76.4 - - + +
358A GLY* 1.3 60.6 + - - +
359A LEU* 3.3 28.9 + - + +
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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