Contacts of the helix formed by residues 532 - 543 (chain A) 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 THR 532 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A GLN* 3.6 43.1 - - + +
526A PHE* 3.6 10.7 - - - +
529A GLY* 5.5 5.2 - - - +
531A PHE* 1.3 77.2 - - - +
533A VAL* 1.3 64.6 + - - +
534A ASN* 3.4 9.6 + - - +
535A ASP* 2.8 49.0 + - - +
536A VAL* 3.3 5.5 + - - +
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Residues in contact with VAL 533 (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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240A ILE* 3.6 25.8 - - + -
242A ALA* 4.3 6.1 - - + +
286A TYR* 4.5 7.0 - - + +
289A GLN* 3.5 12.4 + - + +
290A GLY 3.1 26.7 - - - +
291A ALA* 3.6 24.9 - - + +
526A PHE* 3.8 34.8 - - + -
532A THR* 1.3 73.7 - - - +
534A ASN* 1.3 58.1 + - - +
536A VAL* 3.2 4.3 + - - +
537A LYS* 2.9 30.0 + - - +
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Residues in contact with ASN 534 (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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288A GLN 4.5 4.0 + - - -
289A GLN* 2.9 34.6 + - - +
290A GLY* 3.3 14.3 - - - +
532A THR* 3.1 7.8 - - - +
533A VAL* 1.3 77.4 - - - +
535A ASP* 1.3 52.7 + - - +
537A LYS* 3.7 13.0 - - - +
538A GLU* 2.8 46.5 + - + +
549A MET* 4.4 14.1 - - - +
551A GLU* 5.6 6.7 + - - +
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Residues in contact with ASP 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A PRO* 4.2 4.5 - - + +
530A GLU 4.6 1.2 - - - +
531A PHE* 3.5 25.6 - - + -
532A THR* 2.8 48.6 + - - +
534A ASN* 1.3 74.2 - - - +
536A VAL* 1.3 66.7 + - - +
538A GLU* 3.9 7.9 - - - +
539A TYR* 3.2 22.9 + - - +
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Residues in contact with VAL 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ILE* 4.1 8.1 - - + -
505A PRO* 4.0 17.0 - - + -
508A PHE* 3.5 44.0 - - + -
525A MET* 3.9 17.9 - - + -
526A PHE* 3.7 30.1 - - + -
531A PHE* 4.8 0.9 - - + -
532A THR 3.8 2.2 - - - +
533A VAL* 3.2 8.5 + - - +
535A ASP* 1.3 77.1 - - - +
537A LYS* 1.3 58.4 + - - +
539A TYR* 3.3 4.3 + - - +
540A LEU* 3.0 41.8 + - + +
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Residues in contact with LYS 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ILE* 4.0 14.8 - - + -
290A GLY* 2.6 31.3 + - - +
292A ASP* 2.7 34.0 + - - -
533A VAL* 2.9 21.7 + - - +
534A ASN* 3.7 14.1 - - - +
536A VAL* 1.3 74.7 - - - +
538A GLU* 1.3 54.4 + - - +
540A LEU* 3.2 7.0 + - - +
541A LEU* 2.8 38.5 + - - +
547A VAL* 3.8 14.4 - - + +
548A ARG* 2.7 40.1 + - - +
549A MET* 3.9 16.4 - - - -
550A ASP 5.7 0.2 - - - +
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Residues in contact with GLU 538 (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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534A ASN* 2.8 33.8 + - + +
535A ASP* 3.9 7.6 - - - +
536A VAL 3.4 0.2 - - - -
537A LYS* 1.3 71.0 - - - +
539A TYR* 1.3 58.1 + - - +
541A LEU* 3.3 13.7 - - - +
542A GLU* 3.0 31.1 + - - +
549A MET* 3.1 27.2 - - - +
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Residues in contact with TYR 539 (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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505A PRO* 3.6 28.3 - - + -
506A GLU* 3.1 38.9 + - + +
509A GLU* 3.0 37.9 + - + -
535A ASP 3.2 12.1 + - - +
536A VAL 3.4 8.3 - - - +
537A LYS 3.2 0.4 - - - -
538A GLU* 1.3 77.2 - - - +
540A LEU* 1.3 68.9 + - + +
542A GLU* 3.3 11.7 + - - +
543A HIS* 2.7 62.1 + + - -
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Residues in contact with LEU 540 (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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238A ARG* 4.5 1.6 - - + -
240A ILE* 3.7 31.2 - - + -
505A PRO 4.4 3.6 - - - +
508A PHE* 4.0 3.4 - - + -
509A GLU* 3.5 42.0 - - + +
512A PHE* 3.8 14.1 - - + -
536A VAL* 3.0 27.2 + - + +
537A LYS 3.7 3.6 - - - +
539A TYR* 1.3 75.0 - - + +
541A LEU* 1.3 62.8 + - - +
543A HIS* 3.0 11.6 + - - +
544A GLY 3.4 0.3 + - - -
545A LEU* 3.0 43.5 + - + +
547A VAL* 4.1 20.0 - - + -
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Residues in contact with LEU 541 (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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226A LEU* 4.6 34.5 - - + +
227A LEU* 6.4 1.8 - - + -
537A LYS 2.8 13.4 + - - +
538A GLU* 3.3 16.8 - - - +
540A LEU* 1.3 77.7 - - - +
542A GLU* 1.3 61.7 + - - +
544A GLY* 3.1 15.1 + - - -
545A LEU 3.6 14.9 + - - +
546A LYS* 4.9 1.1 - - + -
547A VAL* 3.4 26.6 - - + +
549A MET* 3.6 39.3 - - + -
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Residues in contact with GLU 542 (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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538A GLU 3.0 18.4 + - - +
539A TYR* 3.4 12.5 - - - +
540A LEU 3.3 0.2 - - - -
541A LEU* 1.3 75.1 - - - +
543A HIS* 1.3 74.6 + - + +
544A GLY 3.3 2.8 + - - -
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Residues in contact with HIS 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A GLU* 3.7 36.8 - - + +
513A LEU* 5.3 6.7 - - + +
539A TYR* 2.7 59.5 + + - +
540A LEU* 3.0 10.5 + - - +
542A GLU* 1.3 94.7 - - + +
544A GLY* 1.3 59.0 + - - +
545A LEU* 3.4 9.1 + - + +
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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