Contacts of the strand formed by residues 433 - 439 (chain A) in PDB entry 1R5M
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 433 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A PHE* 4.0 5.5 - - - -
427A TRP* 3.7 7.3 - - - +
428A SER* 2.9 31.9 + - - -
431A GLN* 3.7 26.7 - - + +
432A ASN* 1.3 79.0 - - - +
434A LEU* 1.3 79.1 + - - +
435A LEU* 3.3 3.8 + - + -
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Residues in contact with LEU 434 (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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425A ARG* 3.6 37.5 - - + +
426A LEU 3.6 7.4 - - - +
427A TRP* 3.9 26.6 - - + -
433A THR* 1.3 84.9 + - - +
435A LEU* 1.3 60.9 + - - +
436A ALA 3.5 24.0 - - - +
437A LEU* 4.0 31.6 - - + -
491A PRO* 4.3 20.1 - - + +
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Residues in contact with LEU 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LYS* 3.6 33.7 - - + -
426A LEU* 2.8 39.6 + - + +
428A SER* 4.5 17.9 - - - +
433A THR* 3.3 6.0 + - + -
434A LEU* 1.3 74.7 - - - +
436A ALA* 1.3 60.4 + - - +
474A LEU* 4.4 16.6 - - + +
491A PRO 4.1 3.0 - - - -
492A LEU* 3.5 35.2 + - + +
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Residues in contact with ALA 436 (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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426A LEU* 2.9 30.7 + - + -
434A LEU* 3.5 6.2 - - - +
435A LEU* 1.3 81.6 - - - +
437A LEU* 1.3 65.6 + - - +
474A LEU* 4.1 20.2 - - + -
491A PRO 4.8 0.2 - - - -
492A LEU* 2.9 28.0 - - + +
493A PRO 4.1 0.9 - - - +
494A ILE* 3.7 18.6 - - + -
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Residues in contact with LEU 437 (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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423A SER* 5.5 3.8 - - - -
424A VAL 3.2 13.7 - - - +
425A ARG* 3.9 37.7 - - + +
434A LEU* 4.0 17.5 - - + -
436A ALA* 1.3 79.3 - - - +
438A SER* 1.3 69.2 + - - +
439A ILE* 5.7 7.2 - - + -
491A PRO* 4.1 20.0 - - + +
492A LEU 2.8 13.9 + - - +
493A PRO* 3.4 16.8 - - - +
494A ILE* 3.7 3.8 - - - +
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Residues in contact with SER 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A GLY 4.1 0.2 - - - +
423A SER* 3.3 3.4 - - - -
424A VAL* 2.8 34.7 + - - +
437A LEU* 1.3 71.0 + - - +
439A ILE* 1.3 61.9 + - - +
469A TYR* 3.6 30.0 - - - -
493A PRO* 4.5 1.9 - - - +
494A ILE* 2.8 44.7 + - - +
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Residues in contact with ILE 439 (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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421A ASP* 3.9 15.9 - - - +
422A GLY 3.4 17.5 - - - +
423A SER* 3.9 11.9 - - - -
425A ARG* 5.8 2.9 - - - +
437A LEU* 5.7 7.6 - - + -
438A SER* 1.3 78.0 - - - +
440A VAL* 1.3 71.0 + - - +
441A ASP* 3.6 24.6 + - + +
461A PHE* 6.0 0.2 - - - -
469A TYR* 5.2 0.6 + - - -
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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