Contacts of the helix formed by residues 535 - 545 (chain A) in PDB entry 1SJ0
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 535 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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533A VAL 3.4 5.1 - - - +
534A VAL* 1.3 103.1 - - + +
536A LEU* 1.3 64.2 + - - +
537A TYR* 3.9 7.9 - - + +
538A ASP* 2.8 37.2 - - - +
539A LEU* 3.2 7.8 + - - +
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Residues in contact with LEU 536 (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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354A LEU* 4.4 4.0 - - + -
380A GLU* 4.2 17.4 + - + +
383A TRP* 3.3 44.4 - - + +
522A MET* 5.5 1.1 - - + -
534A VAL 3.5 1.9 + - - -
535A PRO* 1.3 72.1 - - - +
537A TYR* 1.3 63.3 + - - +
539A LEU* 4.0 19.1 - - + -
540A LEU* 2.9 51.7 + - + +
600A E4D 3.9 26.2 - - + -
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Residues in contact with TYR 537 (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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373A HIS* 2.7 47.5 + + - +
376A VAL* 3.6 32.0 - - + +
377A HIS* 4.7 6.3 - - + -
380A GLU* 3.5 27.6 + - - +
535A PRO* 3.1 6.0 - - + +
536A LEU* 1.3 79.1 - - - +
538A ASP* 1.3 67.3 + - - +
540A LEU* 3.0 5.8 + - - +
541A LEU* 2.7 54.8 + - + +
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Residues in contact with ASP 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 VAL* 3.4 18.1 - - + +
535A PRO* 2.8 37.6 + - - +
537A TYR* 1.3 87.2 - - - +
539A LEU* 1.3 57.2 + - - +
541A LEU* 3.4 13.6 - - + +
542A GLU* 3.0 27.9 + - - +
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Residues in contact with LEU 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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354A LEU* 4.2 7.2 - - + -
534A VAL* 4.0 11.6 - - + +
535A PRO 3.2 12.4 + - - +
536A LEU* 3.9 23.1 - - + +
537A TYR 3.1 0.6 - - - -
538A ASP* 1.3 77.1 - - - +
540A LEU* 1.3 64.5 + - - +
542A GLU* 3.6 10.0 + - + +
543A MET* 3.2 47.2 + - + +
600A E4D 4.9 7.6 - - + -
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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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354A LEU* 4.5 16.4 - - + -
358A ILE* 3.7 24.2 - - + -
376A VAL* 3.7 17.7 - - + +
379A LEU* 4.3 11.0 - - + +
380A GLU* 3.6 36.8 - - + +
383A TRP* 5.5 1.1 - - + -
536A LEU* 2.9 51.4 + - + +
537A TYR 3.3 4.0 - - - +
539A LEU* 1.3 72.5 - - - +
541A LEU* 1.3 56.4 + - - +
543A MET* 3.1 11.0 + - + +
544A LEU* 2.8 38.6 + - + +
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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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372A LEU* 5.2 11.2 - - + +
373A HIS* 5.4 2.0 - - - +
376A VAL* 3.9 23.9 - - + +
537A TYR* 2.7 32.6 + - + +
538A ASP* 3.4 15.7 - - + +
540A LEU* 1.3 72.2 - - - +
542A GLU* 1.3 61.1 + - - +
544A LEU* 3.1 0.6 + - - -
545A ASP* 2.7 49.9 + - + +
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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 ASP 3.0 13.7 + - - +
539A LEU* 3.8 12.8 - - + +
541A LEU* 1.3 79.8 - - - +
543A MET* 1.3 69.7 + - + +
545A ASP* 3.9 15.1 - - - +
546A ALA* 5.0 1.9 - - - +
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Residues in contact with MET 543 (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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354A LEU* 3.7 18.8 - - + -
355A VAL* 4.3 28.7 - - + -
358A ILE* 3.9 34.4 - - + +
362A LYS* 5.0 1.6 - - - -
539A LEU* 3.2 55.8 + - + +
540A LEU* 3.1 15.5 + - + +
542A GLU* 1.3 85.5 - - + +
544A LEU* 1.3 61.3 + - - +
546A ALA* 4.3 10.0 - - - +
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Residues in contact with LEU 544 (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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358A ILE* 3.7 24.9 - - + +
362A LYS* 3.2 57.0 + - + +
367A PHE* 4.4 2.7 - - + -
372A LEU* 4.8 9.0 - - + +
375A GLN* 3.9 14.8 - - + +
376A VAL* 4.0 33.2 - - + +
379A LEU* 3.5 28.7 - - + -
540A LEU* 2.8 20.4 + - + +
541A LEU 4.1 1.1 - - - +
543A MET* 1.3 72.9 - - - +
545A ASP* 1.3 51.4 + - - +
546A ALA* 2.6 21.4 + - - +
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Residues in contact with ASP 545 (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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372A LEU* 3.4 31.2 - - + +
541A LEU* 2.7 35.2 + - + +
542A GLU* 3.9 10.8 - - - +
544A LEU* 1.3 67.7 - - - +
546A ALA* 1.3 62.9 + - - +
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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