Contacts of the strand formed by residues 472 - 477 (chain A) in PDB entry 2RD0
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 CYS 472 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A CYS 3.3 12.1 - - - +
341A ALA* 3.4 11.9 - - - +
342A THR* 3.5 25.1 + - - +
442A ALA* 4.1 22.7 - - - -
443A LEU 3.7 4.5 - - - -
444A ASN* 3.6 26.2 - - - +
470A THR 3.3 8.4 + - - +
471A PRO* 1.3 74.8 - - - +
473A LEU* 1.3 62.7 + - - +
474A GLU* 3.7 7.6 + - - +
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Residues in contact with LEU 473 (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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338A ILE* 4.3 14.8 - - + -
340A CYS* 3.6 5.6 - - - +
341A ALA* 3.6 27.6 - - + +
356A VAL* 3.9 23.8 - - + -
383A TRP* 4.9 0.7 - - + -
404A LEU* 4.8 9.4 - - + -
406A ILE* 3.7 20.0 - - + -
441A MET 3.7 1.0 - - - +
442A ALA* 3.4 1.4 - - - -
443A LEU* 2.7 46.9 + - + +
445A LEU* 3.4 33.9 - - + -
471A PRO* 6.0 0.2 - - + -
472A CYS* 1.3 70.2 - - - +
474A GLU* 1.3 64.4 + - - +
475A LEU* 4.4 14.4 - - + +
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Residues in contact with GLU 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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339A LEU* 3.1 45.8 + - + +
340A CYS* 3.1 32.7 + - - +
342A THR* 5.2 7.8 - - - +
382A ARG* 5.6 0.2 + - - -
440A LYS* 6.3 2.2 - - + -
441A MET 3.5 2.2 - - - +
442A ALA* 4.3 17.6 - - + +
472A CYS* 4.9 8.0 - - - +
473A LEU* 1.3 75.9 - - - +
475A LEU* 1.3 64.7 + - - +
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Residues in contact with LEU 475 (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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336A ILE* 5.0 2.9 - - + -
337A LYS 3.6 4.5 - - - +
338A ILE* 3.8 29.6 - - + -
339A LEU* 4.0 6.3 - - - +
402A LEU* 4.2 9.9 - - + -
404A LEU* 4.4 14.4 - - + -
427A ILE* 3.6 31.2 - - + -
439A GLY 3.9 2.0 - - - -
440A LYS* 3.4 8.2 - - - +
441A MET* 2.6 40.2 + - + +
443A LEU* 4.8 5.6 - - + -
473A LEU* 4.4 15.7 - - + +
474A GLU* 1.3 83.5 - - - +
476A GLU* 1.3 65.3 + - - +
477A PHE* 3.9 16.6 - - + -
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Residues in contact with GLU 476 (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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336A ILE* 3.7 2.8 - - - +
337A LYS* 2.7 61.2 + - + +
339A LEU* 4.1 7.2 - - + -
386A TRP* 3.2 34.6 - - - -
439A GLY* 3.0 14.0 - - - +
440A LYS* 5.0 1.6 - - - +
475A LEU* 1.3 78.4 - - - +
477A PHE* 1.3 79.5 + - - +
478A ASP* 5.0 0.3 - - - -
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Residues in contact with PHE 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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334A LEU* 5.3 7.0 - - + -
335A ARG 4.9 1.6 - - - -
336A ILE* 4.1 24.9 - - + -
402A LEU* 4.0 20.9 - - + -
427A ILE* 4.3 13.2 - - + -
429A LEU* 4.0 23.3 - - + -
436A LEU* 6.0 0.9 - - + -
437A VAL* 3.4 37.2 - - + +
439A GLY* 2.7 42.4 + - - +
441A MET* 4.4 15.9 - - + -
475A LEU* 3.9 25.1 - - + -
476A GLU* 1.3 89.3 - - - +
478A ASP* 1.3 68.4 + - - +
479A TRP* 3.6 2.8 + - - +
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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