Contacts of the helix formed by residues 492 - 501 (chain A) in PDB entry 3SJG
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 SER 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A THR 3.9 3.6 - - - -
479A LYS* 3.6 25.7 - - - +
481A LEU 3.3 8.7 - - - -
482A LYS* 4.7 0.2 - - - +
483A SER* 3.5 5.7 - - - -
490A GLY 4.4 0.2 + - - -
491A LYS* 1.3 78.4 - - - +
493A LEU* 1.3 63.5 + - - +
494A TYR* 3.3 7.8 + - - +
495A GLU* 2.9 34.8 + - - +
496A SER 3.3 9.4 + - - -
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Residues in contact with LEU 493 (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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461A THR* 6.0 0.2 - - - +
462A LEU* 4.2 15.9 - - + +
478A THR* 3.6 22.7 - - + +
481A LEU* 2.8 25.5 + - + +
482A LYS 4.1 6.7 - - - +
483A SER* 3.5 5.3 - - - +
484A PRO* 4.0 6.3 - - + -
492A SER* 1.3 68.4 - - - +
494A TYR* 1.3 67.2 + - - +
496A SER* 3.3 10.0 + - - +
497A TRP* 2.9 28.5 + - + +
537A TYR* 3.7 27.4 - - + +
575A THR* 3.6 30.1 - - + -
579A VAL* 3.6 24.7 - - + -
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Residues in contact with TYR 494 (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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475A HIS* 3.9 25.2 - + - -
478A THR* 2.9 33.7 + - - +
479A LYS* 3.6 43.1 + - + -
492A SER* 3.2 5.8 - - - +
493A LEU* 1.3 77.3 - - - +
495A GLU* 1.3 60.5 + - + +
497A TRP* 4.5 3.6 - + - -
498A THR* 2.9 51.3 + - + -
508A GLY 2.8 25.0 + - - -
509A MET* 3.6 12.8 - - - -
510A PRO* 3.6 28.0 - - + +
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Residues in contact with GLU 495 (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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488A PHE* 4.6 11.7 - - + -
491A LYS* 3.5 43.1 + - + +
492A SER* 2.9 27.3 + - - +
494A TYR* 1.3 82.1 - - + +
496A SER* 1.3 61.7 + - - +
498A THR* 4.0 2.3 - - - -
499A LYS* 3.0 24.6 + - + +
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Residues in contact with SER 496 (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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461A THR* 4.3 2.6 + - - -
483A SER* 2.7 31.4 + - - -
485A ASP* 3.4 18.0 + - - -
488A PHE* 3.6 28.6 - - - -
492A SER 3.3 2.8 + - - -
493A LEU* 3.3 13.9 + - - +
495A GLU* 1.3 76.4 - - - +
497A TRP* 1.3 67.7 + - - +
499A LYS* 3.4 1.4 + - - +
500A LYS* 3.0 29.9 + - - +
537A TYR* 4.5 0.3 + - - -
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Residues in contact with TRP 497 (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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461A THR* 3.4 13.2 - - - +
462A LEU* 3.2 52.0 + - + -
463A ARG* 4.8 0.8 - - - +
464A VAL* 3.7 18.6 - - + -
474A VAL* 3.6 33.0 - - + -
475A HIS* 4.7 3.6 - + - -
478A THR* 3.8 24.7 - - + -
493A LEU* 2.9 20.3 + - + +
494A TYR* 4.0 4.7 - + - +
496A SER* 1.3 78.9 + - - +
498A THR* 1.3 56.0 + - - +
501A SER* 2.8 38.2 + - - +
510A PRO* 3.5 31.9 - - + +
511A ARG 3.4 26.5 + - - -
512A ILE* 3.9 11.4 - - + -
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Residues in contact with THR 498 (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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494A TYR* 2.9 30.8 + - + -
495A GLU* 4.0 3.1 - - - -
497A TRP* 1.3 76.0 - - - +
499A LYS* 1.3 63.4 + - - +
502A PRO* 3.5 22.7 - - + +
508A GLY* 3.4 37.2 - - - +
509A MET 3.6 11.4 - - - +
510A PRO* 3.3 28.1 - - - +
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Residues in contact with LYS 499 (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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488A PHE* 3.5 30.3 - - + -
495A GLU* 3.0 19.3 + - + +
496A SER 3.8 3.6 - - - +
498A THR* 1.3 80.0 - - - +
500A LYS* 1.3 61.4 + - + +
501A SER 3.6 0.2 + - - -
502A PRO* 3.7 9.4 - - - +
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Residues in contact with LYS 500 (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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459A ASN 5.2 1.4 + - - -
460A TYR* 2.9 76.6 + - + +
461A THR* 3.6 15.7 - - - +
485A ASP* 2.8 37.2 + - - +
486A GLU 5.1 2.4 + - - -
488A PHE* 4.0 19.4 - - + -
496A SER 3.0 16.1 + - - +
499A LYS* 1.3 80.9 - - + +
501A SER* 1.3 59.9 + - - +
502A PRO* 3.5 5.4 - - - +
540A ASN* 5.6 0.3 - - - +
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Residues in contact with SER 501 (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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461A THR* 4.1 12.6 - - - -
462A LEU 4.7 2.0 + - - -
497A TRP* 2.8 30.6 + - - +
498A THR 3.8 0.4 - - - -
500A LYS* 1.3 81.2 - - - +
502A PRO* 1.3 61.7 - - - +
510A PRO* 3.5 6.1 - - - +
511A ARG* 2.8 50.3 + - - +
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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