Contacts of the strand formed by residues 524 - 529 (chain A) in PDB entry 4RPP
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 524 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A THR* 4.0 4.0 - - - +
511A VAL 3.7 0.7 - - - +
512A LEU* 3.3 7.8 - - - +
513A THR* 2.8 50.2 + - - +
514A GLY 4.3 6.2 + - - -
523A ASN* 1.3 91.2 + - - +
525A MET* 1.3 65.6 + - - +
526A ARG* 4.3 14.1 - - - +
524C THR* 3.7 21.5 - - + -
525C MET 3.4 10.8 - - - +
526C ARG* 3.4 17.7 - - - +
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Residues in contact with MET 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A THR* 4.1 4.0 - - + +
415A GLY 3.7 5.2 - - - +
416A ALA* 3.6 32.3 - - - -
419A ALA* 4.4 5.8 - - + -
510A ILE* 3.7 19.7 - - + -
511A VAL 3.7 2.7 - - - -
512A LEU* 3.7 9.2 - - + -
523A ASN 4.1 0.6 + - - -
524A THR* 1.3 75.4 - - - +
526A ARG* 1.3 67.8 + - - +
527A VAL* 4.7 7.2 - - + -
411C ALA 4.5 2.7 - - - +
412C THR* 4.2 25.1 - - + +
415C GLY* 4.2 8.7 - - - -
523C ASN 3.9 0.6 - - - +
524C THR* 3.5 4.5 - - - +
525C MET* 2.8 76.2 + - + +
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Residues in contact with ARG 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A VAL* 4.7 6.9 - - - +
487A ASP* 4.7 12.5 + - - -
490A VAL* 5.0 4.0 - - - +
510A ILE* 3.4 4.4 - - - -
511A VAL* 2.8 52.6 + - + +
513A THR* 3.9 31.5 + - - +
524A THR* 4.3 9.7 - - - +
525A MET* 1.3 74.0 - - - +
527A VAL* 1.3 63.6 + - - +
528A VAL* 3.7 15.8 + - + +
523C ASN* 3.6 18.8 - - - +
524C THR* 3.4 36.4 - - - +
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Residues in contact with VAL 527 (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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419A ALA* 5.2 1.3 - - + -
423A CYS* 5.1 3.6 - - - -
508A VAL* 4.2 19.1 - - + -
509A VAL 3.7 7.9 - - - +
510A ILE* 4.6 15.7 - - + -
525A MET* 4.7 10.3 - - + -
526A ARG* 1.3 73.8 - - - +
528A VAL* 1.3 60.7 + - - +
529A PRO* 4.6 1.0 - - - +
408C PRO* 3.7 33.0 - - + +
411C ALA* 4.3 14.4 - - + -
412C THR* 3.4 33.2 - - - +
523C ASN* 3.2 27.1 + - - +
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Residues in contact with VAL 528 (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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490A VAL* 5.8 0.7 - - + -
494A MET* 4.0 23.6 - - + -
508A VAL* 3.9 5.5 - - - -
509A VAL* 3.1 37.4 + - + +
511A VAL* 4.3 11.7 - - + -
526A ARG* 4.0 24.7 - - + +
527A VAL* 1.3 78.2 - - - +
529A PRO* 1.3 78.2 - - + +
531A PRO* 5.5 0.2 - - + -
408C PRO* 5.9 0.2 - - - -
523C ASN* 3.9 14.8 - - - +
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Residues in contact with PRO 529 (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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506A GLY* 4.6 11.0 - - - +
507A ASP 3.5 9.2 - - - +
508A VAL* 4.8 4.5 - - + -
527A VAL 4.6 1.3 - - - +
528A VAL* 1.3 95.4 - - + +
530A VAL* 1.3 66.2 + - - +
531A PRO* 3.2 10.4 - - - +
408C PRO* 5.3 11.4 - - + -
523C ASN* 5.8 1.1 - - - +
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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