Contacts of the helix formed by residues 451 - 462 (chain B) in PDB entry 1JVN
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 VAL 451 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403B VAL* 3.5 29.8 - - + -
405B PRO* 4.6 2.0 - - + -
436B TYR* 2.8 30.6 + - + +
438B CYS* 3.5 9.6 - - - -
450B GLY* 1.3 69.2 - - - -
452B TRP* 1.3 58.6 + - - +
454B LEU* 4.1 1.1 - - - -
455B THR* 2.8 49.6 + - + +
468B LEU* 4.1 5.6 - - + -
484B LEU* 4.1 4.3 - - + -
487B HIS* 3.5 27.8 + - + +
488B VAL* 3.8 26.7 - - + -
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Residues in contact with TRP 452 (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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419B LYS* 3.5 49.4 - - + +
450B GLY* 5.4 0.2 - - - -
451B VAL* 1.3 85.8 - - - +
453B GLU* 1.3 77.2 + - + +
455B THR* 3.3 5.4 + - - -
456B ARG* 3.2 64.6 + - - +
487B HIS* 3.4 37.0 + + + +
488B VAL* 6.1 0.2 - - - +
490B ASP* 3.7 28.5 - - + -
491B ALA* 3.5 30.5 - - + -
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Residues in contact with GLU 453 (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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375B TYR* 2.5 49.8 + - + +
417B LYS 4.6 1.4 - - - +
418B ASN* 3.5 19.3 - - - +
419B LYS* 2.7 37.5 + - - +
449B LEU* 3.9 11.7 - - + -
450B GLY* 3.2 25.8 - - - +
452B TRP* 1.3 89.2 - - + +
454B LEU* 1.3 61.0 + - - +
457B ALA 3.1 9.7 + - - -
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Residues in contact with LEU 454 (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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367B ALA* 3.4 30.5 - - + +
368B VAL* 3.6 21.1 - - + -
371B ALA* 3.5 17.0 - - + -
401B ILE* 5.2 1.8 - - + -
402B SER 5.6 0.7 - - - +
403B VAL* 3.9 32.5 - - + -
404B ASP 5.7 0.2 - - - +
438B CYS* 3.3 28.5 - - + -
449B LEU* 3.7 9.1 - - + +
450B GLY 2.8 20.2 + - - +
451B VAL 3.4 2.7 + - - +
453B GLU* 1.3 72.1 - - - +
455B THR* 1.3 64.3 + - - +
457B ALA* 3.3 3.1 + - - +
458B CYS* 3.0 35.1 + - - -
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Residues in contact with THR 455 (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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401B ILE* 6.2 0.4 - - - -
403B VAL* 4.3 7.9 - - + -
451B VAL* 2.8 46.0 + - + +
452B TRP 3.3 5.2 + - - -
454B LEU* 1.3 73.0 - - - +
456B ARG* 1.3 59.2 + - - +
458B CYS* 3.4 5.3 + - - +
459B GLU* 2.8 32.4 + - - +
466B ILE* 4.1 26.2 - - + -
488B VAL* 3.9 18.1 - - + +
491B ALA* 3.7 9.5 - - - +
492B VAL* 3.5 20.4 - - - +
494B ILE* 4.8 2.1 - - - +
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Residues in contact with ARG 456 (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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374B TYR* 5.0 1.2 + - - -
375B TYR* 3.9 11.9 + - - +
452B TRP* 3.2 63.6 + - - +
455B THR* 1.3 80.7 + - - +
457B ALA* 1.3 62.0 + - - +
459B GLU* 3.6 6.6 - - - +
460B ALA* 3.2 22.5 + - - +
490B ASP 4.7 1.8 + - - -
491B ALA* 2.9 46.6 + - + +
492B VAL* 3.8 4.9 - - - -
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Residues in contact with ALA 457 (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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371B ALA* 3.6 18.4 - - + -
374B TYR* 3.5 33.6 - - + -
375B TYR* 3.6 10.0 + - + -
453B GLU 3.1 18.6 + - - +
454B LEU 3.6 4.0 - - - +
455B THR 3.3 0.2 - - - -
456B ARG* 1.3 76.3 - - - +
458B CYS* 1.3 51.4 + - - +
460B ALA* 3.0 8.0 + - - +
461B LEU* 2.8 38.5 + - - +
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Residues in contact with CYS 458 (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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367B ALA* 3.6 31.4 - - - -
371B ALA* 4.5 2.9 - - - -
387B ILE* 3.6 18.2 - - + +
401B ILE* 3.9 24.9 - - + -
454B LEU* 3.0 27.9 + - - +
455B THR* 3.9 5.8 - - - +
457B ALA* 1.3 75.3 - - - +
459B GLU* 1.3 62.4 + - - +
461B LEU* 3.2 11.0 + - - +
462B GLY 3.1 6.4 + - - -
463B ALA* 2.9 26.7 + - + +
466B ILE* 5.1 1.1 - - + -
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Residues in contact with GLU 459 (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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455B THR 2.8 18.4 + - - +
456B ARG* 3.6 8.3 - - - +
458B CYS* 1.3 75.7 - - - +
460B ALA* 1.3 63.0 + - - +
462B GLY* 3.1 13.9 + - - -
463B ALA* 3.9 6.4 + - - +
491B ALA 4.3 2.6 - - - +
492B VAL* 3.3 18.5 - - + +
493B LYS* 2.5 42.3 + - - +
494B ILE* 3.2 40.1 + - + +
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Residues in contact with ALA 460 (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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374B TYR* 3.5 31.0 - - + +
456B ARG 3.2 11.7 + - - +
457B ALA 3.0 12.0 + - - +
459B GLU* 1.3 81.6 - - - +
461B LEU* 1.3 57.6 + - - +
462B GLY* 3.3 1.6 + - - -
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Residues in contact with LEU 461 (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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370B ALA* 3.7 43.5 - - + +
371B ALA 4.4 0.4 - - - +
374B TYR* 4.0 14.6 - - + -
381B GLY* 3.7 18.6 - - - -
385B SER* 4.2 4.5 - - - +
387B ILE* 3.7 13.0 - - + +
388B GLU* 3.4 58.6 - - + +
391B SER* 3.7 1.7 + - - -
392B LYS* 5.6 1.4 - - - -
457B ALA 2.8 22.9 + - - +
458B CYS* 3.2 13.6 + - - +
460B ALA* 1.3 75.3 - - - +
462B GLY* 1.3 56.4 + - - +
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Residues in contact with GLY 462 (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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387B ILE* 3.9 1.8 - - - -
391B SER* 3.2 30.4 - - - -
396B ALA* 3.2 16.0 - - - +
399B VAL* 4.7 0.2 - - - +
459B GLU 3.1 9.6 + - - -
460B ALA 3.1 2.1 - - - -
461B LEU* 1.3 81.7 - - - +
463B ALA* 1.3 66.7 + - - +
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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