Contacts of the helix formed by residues 352 - 368 (chain A) in PDB entry 3DVA
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 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A PHE* 3.6 38.1 - - + -
350A GLU 3.5 4.2 - - - +
351A LEU* 1.3 89.8 - - + +
353A PHE* 1.3 68.1 + - - +
354A ASN* 3.3 20.0 - - - +
355A LEU* 3.2 12.4 + - + -
356A LYS* 3.1 17.2 + - - +
143B LYS* 4.9 8.3 - - - -
239B GLN* 6.0 0.2 - - - +
240B PRO* 3.5 26.0 - - + -
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Residues in contact with PHE 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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352A PRO* 1.3 72.9 - - - +
354A ASN* 1.3 67.3 + - - +
356A LYS* 3.2 27.0 + - + +
357A GLU* 3.2 49.2 + - + +
193B GLY 6.1 0.7 - - - +
240B PRO* 4.4 7.3 - - + +
241B LEU 4.4 13.2 - - - +
242B ASP* 6.1 0.9 - - - -
243B ILE* 3.6 43.5 - - + -
244B GLU* 5.0 12.1 - - + -
279B ARG* 4.9 0.2 - - - -
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Residues in contact with ASN 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PRO* 3.3 24.0 - - - +
353A PHE* 1.3 78.4 - - + +
355A LEU* 1.3 72.5 + - - +
357A GLU* 3.5 12.4 + - - +
358A GLN* 3.2 44.9 + - - +
239B GLN* 4.2 16.4 + - - +
240B PRO* 3.9 9.6 - - + +
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Residues in contact with LEU 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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344A ILE* 3.9 29.5 - - + +
347A MET* 3.7 33.4 - - + -
348A PHE* 3.8 22.7 - - + -
351A LEU* 4.1 17.5 - - + -
352A PRO* 3.2 15.6 + - + +
354A ASN* 1.3 88.4 + - - +
356A LYS* 1.3 56.1 + - - +
358A GLN* 4.0 17.7 - - - +
359A TYR* 2.7 37.4 + - - +
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Residues in contact with LYS 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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350A GLU* 4.6 12.6 + - - -
351A LEU* 3.3 35.0 + - + +
352A PRO 3.1 17.3 + - - +
353A PHE* 3.2 19.7 + - + +
355A LEU* 1.3 75.4 - - - +
357A GLU* 1.3 64.1 + - + +
359A TYR* 3.4 6.7 + - - +
360A GLU* 3.2 28.4 + - - +
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Residues in contact with GLU 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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353A PHE* 3.2 41.0 + - + +
354A ASN* 3.6 12.7 - - - +
356A LYS* 1.3 79.6 - - + +
358A GLN* 1.3 61.6 + - + +
360A GLU* 3.1 10.6 + - - +
361A ILE* 3.0 31.9 + - + +
279B ARG* 2.7 45.3 + - - -
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Residues in contact with GLN 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ILE* 3.9 11.8 - - + +
354A ASN* 3.2 36.4 + - - +
355A LEU* 4.0 17.2 - - - +
357A GLU* 1.3 75.5 + - + +
359A TYR* 1.3 65.2 + - - +
361A ILE* 3.2 10.3 + - + -
362A TYR* 2.9 43.2 + - + +
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Residues in contact with TYR 359 (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 THR* 3.6 28.9 - - + +
344A ILE* 3.7 28.6 - - + +
345A SER* 3.2 26.1 + - - -
351A LEU* 4.5 9.9 - - + -
355A LEU 2.7 23.0 + - - +
356A LYS* 3.6 7.6 - - - +
358A GLN* 1.3 74.3 - - - +
360A GLU* 1.3 71.5 + - - +
362A TYR 3.4 0.2 + - - -
363A LYS* 2.9 61.7 + - + +
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Residues in contact with GLU 360 (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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356A LYS 3.3 13.8 - - - +
357A GLU* 3.1 10.2 + - - +
359A TYR* 1.3 87.6 - - - +
361A ILE* 1.3 65.4 + - + +
363A LYS* 3.4 13.3 + - - +
364A GLU* 3.2 23.2 + - - +
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Residues in contact with ILE 361 (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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357A GLU* 3.0 22.8 + - + +
358A GLN* 3.2 15.2 + - + +
360A GLU* 1.3 79.5 - - + +
362A TYR* 1.3 71.0 + - + +
364A GLU* 3.3 7.3 + - - +
365A LYS* 3.3 46.0 + - - +
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Residues in contact with TYR 362 (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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340A VAL* 3.6 51.1 - - + -
341A THR* 3.9 9.0 - - + -
344A ILE* 4.6 1.3 - - + -
358A GLN* 2.9 42.9 + - + +
361A ILE* 1.3 85.7 - - + +
363A LYS* 1.3 59.7 - - - +
365A LYS* 3.8 34.0 + - + +
366A GLU* 2.9 39.7 + - + +
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Residues in contact with LYS 363 (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 THR* 3.8 10.7 - - + +
359A TYR* 2.9 50.0 + - + +
360A GLU* 3.9 15.7 - - - +
361A ILE 3.3 0.4 - - - -
362A TYR* 1.3 76.0 - - - +
364A GLU* 1.3 66.7 + - - +
366A GLU* 3.3 6.0 + - + +
367A SER* 3.1 26.7 + - - -
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Residues in contact with GLU 364 (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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360A GLU 3.2 13.2 + - - +
361A ILE* 3.5 10.7 - - - +
362A TYR 3.3 0.2 - - - -
363A LYS* 1.3 79.1 - - - +
365A LYS* 1.3 71.9 + - - +
367A SER* 3.2 18.8 + - - +
368A LYS* 3.4 26.4 + - - +
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Residues in contact with LYS 365 (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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361A ILE* 3.3 34.0 + - - +
362A TYR* 3.9 39.8 + - + +
363A LYS 3.2 0.6 - - - -
364A GLU* 1.3 87.7 - - - +
366A GLU* 1.3 61.3 + - + +
367A SER 3.4 0.6 + - - -
368A LYS* 3.9 14.7 - - - +
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Residues in contact with GLU 366 (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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339A LYS* 3.2 31.6 - - + +
340A VAL* 3.2 16.8 + - - +
341A THR* 2.6 48.8 + - - +
362A TYR* 2.9 25.0 + - + +
363A LYS* 3.3 7.1 + - - +
365A LYS* 1.3 80.1 - - + +
367A SER* 1.3 59.7 + - - +
368A LYS 3.7 1.5 - - - +
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Residues in contact with SER 367 (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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363A LYS* 3.1 15.5 + - - +
364A GLU* 3.2 15.6 + - - +
365A LYS 3.4 0.2 - - - -
366A GLU* 1.3 80.0 - - - +
368A LYS* 1.3 64.7 + - - +
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Residues in contact with LYS 368 (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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364A GLU* 3.4 27.6 + - - +
365A LYS* 3.9 13.1 + - - +
366A GLU 4.9 1.1 - - - -
367A SER* 1.3 86.4 + - - +
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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
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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