Contacts of the helix formed by residues 390 - 403 (chain A) in PDB entry 1PJR
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 LYS 390 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A LEU* 5.6 1.6 - - - +
388A ASP 3.7 1.7 + - - -
389A ARG* 1.3 72.0 - - - +
391A GLU* 1.3 63.0 + - - +
393A LYS* 3.3 4.5 + - - -
394A ASP* 2.8 51.5 + - - +
413A ARG* 3.1 24.3 + - - +
417A VAL* 4.8 9.3 - - - +
493A TYR* 3.1 14.3 + - - -
496A MET* 5.3 6.9 - - - +
497A LEU* 5.7 2.4 - - - +
508A ARG* 4.3 31.6 - - - +
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Residues in contact with GLU 391 (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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389A ARG* 3.7 19.2 - - - +
390A LYS* 1.3 72.7 + - - +
392A ILE* 1.3 72.6 + - + +
394A ASP* 3.7 2.3 - - - +
395A ILE* 3.2 27.5 + - - +
493A TYR* 3.6 26.8 + - + +
507A SER 4.6 0.2 - - - +
508A ARG* 2.7 69.4 + - + +
511A ASN* 3.5 21.6 - - + +
512A LEU* 3.7 14.3 - - + +
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Residues in contact with ILE 392 (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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386A PHE* 3.5 31.2 - - + +
387A TYR* 3.8 39.7 - - + +
389A ARG* 3.3 15.5 + - + +
390A LYS 3.2 0.2 - - - -
391A GLU* 1.3 79.2 - - + +
393A LYS* 1.3 61.8 + - - +
395A ILE* 3.3 6.7 - - - +
396A LEU* 2.9 33.7 + - + +
511A ASN* 3.4 32.1 - - + +
512A LEU* 4.1 10.5 - - + -
515A PHE* 4.0 24.7 - - + -
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Residues in contact with LYS 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A TYR 3.9 11.9 - - - +
388A ASP* 3.6 37.3 + - - +
389A ARG 3.0 12.7 + - - +
390A LYS* 3.4 9.6 - - - +
392A ILE* 1.3 76.8 - - - +
394A ASP* 1.3 54.8 + - - +
396A LEU* 3.9 8.1 - - + +
397A ALA* 3.1 27.7 + - - +
413A ARG* 3.6 30.2 + - - +
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Residues in contact with ASP 394 (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 LYS* 2.8 39.6 + - - +
391A GLU 3.7 2.5 - - - +
392A ILE 3.3 0.4 - - - -
393A LYS* 1.3 71.7 - - - +
395A ILE* 1.3 62.1 + - - +
397A ALA* 3.1 14.0 + - - +
398A TYR* 3.1 19.8 + - - -
413A ARG* 2.7 32.8 + - - +
414A ILE* 3.6 2.1 - - - +
417A VAL* 4.2 18.6 - - + +
493A TYR* 2.6 40.9 + - + +
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Residues in contact with ILE 395 (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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391A GLU 3.2 13.1 + - - +
392A ILE* 3.3 16.4 - - - +
394A ASP* 1.3 78.0 - - - +
396A LEU* 1.3 60.5 + - - +
398A TYR* 3.4 8.3 + - + -
399A LEU* 3.0 37.3 + - + +
484A VAL* 4.2 24.0 - - + -
487A VAL* 3.9 28.0 - - + -
488A LEU* 3.9 30.3 - - + -
493A TYR* 5.2 1.5 - - + -
512A LEU* 4.1 10.5 - - + -
515A PHE* 4.3 20.4 - - + -
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Residues in contact with LEU 396 (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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387A TYR* 4.5 14.6 - - + +
392A ILE* 2.9 33.5 + - + +
393A LYS* 3.9 8.3 - - + +
394A ASP 3.3 0.2 - - - -
395A ILE* 1.3 76.6 - - - +
397A ALA* 1.3 51.6 + - - +
399A LEU* 3.3 13.6 + - + +
400A ARG* 2.8 61.4 + - - +
515A PHE* 4.5 12.1 - - + -
535A LEU* 3.7 23.6 - - + -
538A LEU* 3.4 35.0 - - + -
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Residues in contact with ALA 397 (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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393A LYS 3.1 15.6 + - - +
394A ASP 3.3 9.6 - - - +
396A LEU* 1.3 71.1 - - - +
398A TYR* 1.3 65.4 + - - +
400A ARG* 3.0 6.6 + - - +
401A VAL* 3.0 21.7 + - - +
410A SER* 3.4 32.0 - - - +
413A ARG* 3.9 14.1 - - - -
414A ILE* 3.8 17.5 - - + -
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Residues in contact with TYR 398 (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 3.1 22.2 + - - -
395A ILE* 3.5 11.0 - - + +
397A ALA* 1.3 78.6 - - - +
399A LEU* 1.3 63.4 + - - +
401A VAL* 3.2 4.5 + - + +
402A ILE* 3.1 28.7 + - + +
414A ILE* 3.5 42.3 - - + +
417A VAL* 2.6 27.0 + - + -
418A PRO* 3.6 1.7 - - - +
420A ARG* 3.2 21.9 + - - -
464A PHE* 5.1 1.3 - + - -
471A TRP* 3.8 25.8 - + - -
487A VAL* 3.7 27.8 - - + -
488A LEU* 6.4 0.4 - - + -
491A SER* 3.5 20.5 - - - -
493A TYR* 4.2 17.5 - + - -
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Residues in contact with LEU 399 (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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395A ILE* 3.0 27.9 + - + +
396A LEU* 3.6 13.9 - - + +
398A TYR* 1.3 74.4 - - - +
400A ARG* 1.3 61.3 + - - +
402A ILE* 3.4 11.4 + - + +
403A ALA* 3.2 16.8 + - - +
483A LEU* 4.5 17.5 - - + -
484A VAL* 3.9 32.1 - - + -
487A VAL* 4.9 1.8 - - + -
515A PHE* 4.4 12.3 - - + -
531A LEU* 3.5 33.7 - - + +
534A PHE* 3.9 27.4 - - + -
535A LEU* 4.4 6.5 - - + -
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Residues in contact with ARG 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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396A LEU* 2.8 44.2 + - - +
397A ALA* 3.0 10.4 + - - +
399A LEU* 1.3 74.3 - - - +
401A VAL* 1.3 59.0 + - - +
403A ALA* 3.1 4.2 + - - +
404A ASN* 3.0 28.6 + - - +
407A ASP* 4.0 11.8 - - - +
410A SER* 3.4 22.8 + - - +
535A LEU* 4.2 33.6 + - + +
538A LEU* 5.9 3.6 - - - +
539A ALA* 6.1 2.8 - - - +
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Residues in contact with VAL 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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397A ALA 3.0 6.0 + - - +
398A TYR* 3.3 14.8 - - + +
400A ARG* 1.3 70.4 - - - +
402A ILE* 1.3 66.4 + - + +
404A ASN 3.5 7.6 - - - +
405A PRO* 3.3 30.0 - - + +
407A ASP* 3.7 12.1 - - + +
410A SER* 3.7 7.9 - - - -
411A LEU* 3.3 47.1 - - + +
414A ILE* 3.8 21.3 - - + -
468A LEU* 3.9 22.0 - - + +
471A TRP* 6.3 0.4 - - + -
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Residues in contact with ILE 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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398A TYR* 3.1 19.7 + - + +
399A LEU* 3.7 12.1 - - + +
400A ARG 3.3 0.2 - - - -
401A VAL* 1.3 81.3 - - + +
403A ALA* 1.3 58.7 + - - +
405A PRO* 4.7 0.9 - - - +
468A LEU* 4.7 3.8 - - + -
471A TRP* 3.7 53.6 - - + +
472A THR* 3.8 21.8 - - - +
475A GLN* 3.4 16.8 + - + +
483A LEU* 4.3 21.1 - - + -
487A VAL* 3.5 32.1 - - + -
531A LEU* 4.7 2.7 - - + -
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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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399A LEU 3.2 6.1 + - - +
400A ARG 3.1 8.1 + - - +
402A ILE* 1.3 77.5 - - - +
404A ASN* 1.3 61.3 + - + +
405A PRO* 4.1 3.1 - - - +
475A GLN* 4.2 11.7 + - - +
531A LEU* 3.7 20.6 - - + -
532A ILE* 4.7 21.4 - - + +
535A LEU* 4.1 13.7 - - + -
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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