Contacts of the strand formed by residues 473 - 478 (chain A) in PDB entry 3S3J
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 MET 473 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A TRP* 3.5 12.7 - - - -
472A GLY* 1.3 74.1 - - - -
474A ALA* 1.3 60.8 + - - +
495A ILE* 4.4 8.3 - - + -
496A THR 3.0 17.7 - - - +
497A ASN* 4.0 17.5 - - - +
499A THR* 4.5 0.2 - - - +
503A TYR* 3.7 48.7 + - + -
505A CYS* 4.2 8.1 - - - -
534A LEU* 4.3 17.0 - - - -
567A LEU* 3.9 18.8 - - + -
569A GLU* 5.3 4.7 - - + -
576A LEU* 3.5 27.0 - - + +
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Residues in contact with ALA 474 (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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404A TRP* 3.3 34.5 - - + -
472A GLY 4.4 0.2 + - - -
473A MET* 1.3 73.9 - - - +
475A MET* 1.3 63.6 + - - +
494A HIS 4.4 0.4 - - - -
495A ILE* 3.4 7.3 - - - +
496A THR* 2.9 42.6 + - + +
576A LEU* 4.0 4.3 - - - -
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Residues in contact with MET 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A TRP* 3.5 25.5 - - + +
474A ALA* 1.3 79.3 - - - +
476A ARG* 1.3 64.7 + - - +
493A ALA* 4.4 3.8 - - + -
494A HIS 3.4 9.2 - - - +
495A ILE* 3.8 22.7 - - + -
507A LEU* 3.9 23.8 - - - -
565A ALA* 3.5 34.3 - - + +
566A LEU 3.7 0.2 - - - +
567A LEU* 3.6 13.7 - - + +
576A LEU* 3.1 43.1 - - + +
578A ALA* 3.2 23.3 - - + +
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Residues in contact with ARG 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A TRP* 5.5 4.3 - - + -
406A GLN* 5.8 15.5 - - + -
475A MET* 1.3 77.6 - - - +
477A ILE* 1.3 72.0 + - - +
478A ARG* 3.2 40.6 - - - +
494A HIS* 2.9 50.4 + - + +
578A ALA* 4.0 4.5 - - - -
580A ARG* 4.8 1.2 - - - +
705A SO4 3.2 25.3 + - - -
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Residues in contact with ILE 477 (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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476A ARG* 1.3 77.3 + - - +
478A ARG* 1.3 71.5 + - - +
479A VAL* 4.8 3.4 - - + -
491A VAL* 4.7 4.9 - - + -
492A PHE 3.3 9.0 - - - +
493A ALA* 4.8 2.0 - - - -
509A LEU* 4.3 4.9 - - + -
563A VAL* 3.5 42.6 - - + +
565A ALA* 3.9 19.3 - - + -
578A ALA* 3.9 26.7 - - + +
579A GLU 4.0 6.7 + - - +
580A ARG* 2.9 54.2 + - + +
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Residues in contact with ARG 478 (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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476A ARG* 3.2 41.8 + - - +
477A ILE* 1.3 73.2 - - - +
479A VAL* 1.3 71.1 + - - +
480A GLY* 6.2 1.0 - - - -
491A VAL* 3.8 0.9 - - - -
492A PHE* 2.9 44.9 + - + +
494A HIS* 3.4 48.6 + - + -
541A SER* 4.5 7.7 + - - -
705A SO4 3.6 17.4 + - - +
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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