Contacts of the strand formed by residues 472 - 476 (chain A) in PDB entry 5JPM
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 PHE 472 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A LEU 5.5 0.4 - - - -
379A VAL* 3.9 13.7 - - + -
380A PRO* 3.6 38.8 - - + -
465A PRO* 3.8 32.3 - - + -
466A PRO 4.0 16.2 - - - -
467A SER* 5.5 3.1 - - - -
469A GLY* 4.8 13.0 - - - -
470A PRO* 6.0 0.4 - - + -
471A GLY* 1.3 87.0 - - - -
473A LEU* 1.3 61.0 + - - +
495A ALA* 3.7 0.5 - - - -
496A VAL* 2.9 45.5 + - + +
497A GLY* 5.5 3.4 - - - -
547A TYR* 3.2 9.3 + - - -
554A VAL* 3.6 8.5 - - - -
640A GLY 5.4 6.5 - - - -
641A ASP 5.5 1.8 - - - -
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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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379A VAL* 4.2 8.3 - - - +
472A PHE* 1.3 76.1 - - - +
474A SER* 1.3 67.2 + - - +
475A ILE* 4.4 10.8 - - + -
493A LEU* 4.5 5.4 - - + -
494A ARG 3.8 24.7 - - - +
495A ALA 4.1 1.1 - - - +
505A TYR* 4.0 22.4 - - + -
545A ALA* 3.3 46.9 - - + +
546A PHE* 3.8 10.3 - - - +
547A TYR* 4.0 12.1 - - + -
554A VAL* 3.8 8.7 - - + +
555A ALA 4.4 4.1 + - - -
556A ASN* 3.0 34.5 + - + +
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Residues in contact with SER 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A VAL* 4.3 6.4 - - - +
382A ALA* 3.5 30.9 - - - +
383A PRO* 5.0 2.8 + - - +
473A LEU* 1.3 73.1 - - - +
475A ILE* 1.3 63.0 + - - +
476A GLU* 3.7 18.2 + - - +
492A ASN 3.4 2.4 - - - +
493A LEU* 3.7 1.6 - - - -
494A ARG* 2.8 57.0 + - - +
496A VAL* 4.9 2.2 - - - +
556A ASN* 4.4 2.5 - - - +
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Residues in contact with ILE 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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385A LEU* 5.4 6.1 - - - +
473A LEU* 4.2 8.5 + - + -
474A SER* 1.3 74.6 + - - +
476A GLU* 1.3 61.6 + - - +
477A ARG 4.1 0.7 + - - -
491A LEU* 4.4 16.6 - - + -
492A ASN 3.2 8.1 - - - +
493A LEU* 3.9 18.8 - - + -
543A PHE* 4.0 31.6 - - + +
545A ALA* 4.0 9.6 - - + -
556A ASN* 3.3 42.5 - - + +
557A SER* 4.1 9.9 - - - +
558A LEU* 4.4 23.5 - - + +
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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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383A PRO* 3.8 15.9 - - + +
385A LEU* 5.9 6.5 - - + -
474A SER* 3.7 17.3 + - - +
475A ILE* 1.3 73.5 - - - +
477A ARG* 1.3 60.7 + - - +
478A PRO* 4.1 1.6 - - - +
491A LEU* 3.6 6.6 - - - +
492A ASN* 2.7 61.5 + - + +
494A ARG* 3.0 43.5 + - + -
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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