Contacts of the helix formed by residues 399 - 410 (chain A) in PDB entry 2VWR
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 THR 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A ARG* 6.3 2.7 - - - +
364A VAL* 3.5 10.3 - - - +
395A LEU* 4.3 0.7 - - - +
397A TYR 5.2 1.8 - - - +
398A GLY* 1.3 78.8 - - - +
400A PRO* 1.3 77.1 - - + +
401A GLU* 3.4 15.0 + - - +
402A LEU* 2.9 28.5 + - + +
403A ALA* 3.0 16.5 + - - +
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Residues in contact with PRO 400 (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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355A LEU* 4.2 18.2 - - + +
356A VAL* 3.9 11.4 - - - +
357A ARG* 3.8 44.2 - - + +
364A VAL* 4.1 11.2 - - + -
399A THR* 1.3 88.0 - - + +
401A GLU* 1.3 69.9 + - - +
403A ALA* 3.3 7.7 + - + +
404A ALA* 2.9 29.7 + - - +
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Residues in contact with GLU 401 (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 ARG* 4.9 10.1 + - - -
399A THR* 3.1 18.0 - - - +
400A PRO* 1.3 90.5 - - - +
402A LEU* 1.3 57.4 + - - +
404A ALA* 3.2 7.6 + - - +
405A GLN* 3.0 36.8 + - - +
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Residues in contact with LEU 402 (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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394A ASP 4.4 9.9 - - - +
395A LEU* 3.8 20.2 - - + -
398A GLY* 4.4 11.7 - - - -
399A THR* 2.9 21.2 + - + +
401A GLU* 1.3 72.5 - - - +
403A ALA* 1.3 66.5 + - - +
405A GLN* 3.2 22.7 + - + +
406A ILE* 3.0 40.3 + - + +
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Residues in contact with ALA 403 (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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355A LEU* 3.5 27.4 - - + -
364A VAL* 4.6 4.0 - - + -
387A VAL* 6.0 0.2 - - + -
390A ILE* 4.3 4.5 - - + -
395A LEU* 3.9 27.9 - - + +
399A THR 3.0 11.6 + - - +
400A PRO* 3.5 9.2 - - + +
402A LEU* 1.3 78.1 - - - +
404A ALA* 1.3 56.4 + - - +
406A ILE* 3.2 4.2 + - - +
407A ILE* 2.9 35.6 + - - +
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Residues in contact with ALA 404 (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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355A LEU* 5.3 0.8 - - - +
400A PRO 2.9 14.3 + - - +
401A GLU* 3.4 12.3 - - - +
403A ALA* 1.3 74.9 - - - +
405A GLN* 1.3 58.7 + - + +
407A ILE* 3.9 6.6 - - - +
408A GLN* 2.9 50.5 + - - +
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Residues in contact with GLN 405 (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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401A GLU* 3.0 20.6 + - + +
402A LEU* 3.2 27.9 + - + +
404A ALA* 1.3 76.1 - - + +
406A ILE* 1.3 63.6 + - + +
408A GLN* 3.5 7.7 + - - +
409A ALA* 3.2 25.8 + - - +
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Residues in contact with ILE 406 (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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390A ILE* 3.8 33.2 - - + +
391A ASN* 4.9 5.6 - - + +
393A HIS* 3.7 40.8 - - + +
394A ASP 5.3 0.4 - - - +
395A LEU* 4.2 20.6 - - + -
402A LEU* 3.0 37.9 + - + +
403A ALA* 3.6 5.2 - - - +
405A GLN* 1.3 77.8 - - + +
407A ILE* 1.3 63.0 + - - +
409A ALA* 3.3 5.1 + - - +
410A SER* 3.1 21.7 + - - -
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Residues in contact with ILE 407 (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 LYS* 3.0 15.0 + - + +
349A GLU 5.4 2.5 - - - +
350A GLN* 5.9 1.6 - - - -
351A LEU* 3.7 46.7 - - + +
353A ILE* 5.7 2.0 - - + -
355A LEU* 4.5 14.8 - - + -
390A ILE* 3.7 30.3 - - + -
403A ALA 2.9 24.2 + - - +
404A ALA* 4.0 5.6 - - - +
406A ILE* 1.3 76.7 - - - +
408A GLN* 1.3 62.4 + - + +
410A SER* 2.7 28.8 + - - +
414A VAL* 4.5 2.9 - - + -
416A LEU* 5.6 1.1 - - + -
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Residues in contact with GLN 408 (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 LYS* 3.9 9.3 + - - +
347A SER 4.4 5.9 - - - +
404A ALA* 2.9 34.8 + - - +
405A GLN* 4.1 6.6 - - - +
407A ILE* 1.3 80.4 - - + +
409A ALA* 1.3 58.5 + - - +
410A SER 3.6 1.4 + - - +
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Residues in contact with ALA 409 (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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405A GLN 3.2 18.0 + - - +
406A ILE* 3.7 4.5 - - - +
408A GLN* 1.3 74.5 - - - +
410A SER* 1.3 65.3 + - - +
411A GLY 3.8 0.5 + - - -
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Residues in contact with SER 410 (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 LYS* 2.8 24.3 + - - -
347A SER* 5.0 4.7 - - - +
391A ASN* 3.9 22.0 - - - +
406A ILE 3.1 12.0 + - - -
407A ILE* 2.7 22.7 + - - -
408A GLN 3.3 0.7 - - - +
409A ALA* 1.3 81.7 - - - +
411A GLY* 1.3 69.4 + - - +
414A VAL* 3.5 11.8 - - - +
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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