Contacts of the strand formed by residues 475 - 482 (chain A) in PDB entry 5E8M
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 VAL 475 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466A LEU* 3.9 26.2 - - + -
473A LYS 3.5 12.9 + - - +
474A GLN* 1.3 82.8 + - - +
476A ASP* 1.3 65.4 + - - +
516A LEU* 2.8 54.8 + - + +
517A ARG 6.1 0.2 - - - -
518A PRO* 5.7 0.2 - - - +
520A SER 5.9 0.7 - - - +
522A LEU* 4.5 9.2 - - + -
532A PHE* 3.9 28.3 - - + -
533A VAL 3.2 11.0 - - - +
534A ILE* 4.5 8.7 - - + -
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Residues in contact with ASP 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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444A ARG* 2.8 30.6 + - - -
445A TYR* 2.6 35.2 + - - +
474A GLN* 4.4 2.6 + - - +
475A VAL* 1.3 74.0 - - - +
477A LYS* 1.3 60.1 + - - +
478A TYR* 3.6 10.9 - - + -
513A GLU* 3.7 15.2 - - + +
514A LYS 3.8 3.1 - - - -
515A PRO* 3.6 18.4 - - - +
532A PHE* 3.3 5.0 - - - -
533A VAL* 2.9 38.9 + - + +
535A ARG* 3.8 11.2 - - - +
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Residues in contact with LYS 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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475A VAL 4.0 1.0 + - - -
476A ASP* 1.3 72.5 - - - +
478A TYR* 1.3 68.7 + - - +
479A LEU* 3.5 33.5 - - + +
496A ASN* 2.9 26.7 + - - +
514A LYS* 2.9 38.6 + - + +
516A LEU* 4.0 23.9 - - + +
523A GLY* 2.9 35.0 + - - +
525A PRO* 4.8 1.6 - - - +
530A SER* 3.7 5.8 - - - +
531A PHE 3.7 3.6 - - - -
532A PHE* 3.7 24.7 - - + -
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Residues in contact with TYR 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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409A LEU* 3.8 30.1 - - + +
413A LEU* 3.6 30.3 - - + +
442A ASN* 5.2 1.2 + - - -
444A ARG* 4.5 2.8 - - - -
445A TYR* 2.6 35.5 + - - -
476A ASP* 3.6 18.2 - - + -
477A LYS* 1.3 77.2 - - - +
479A LEU* 1.3 60.5 + - - +
480A LEU* 3.8 1.4 + - - +
495A LEU* 3.7 19.3 - - + -
496A ASN* 3.8 0.7 - - - +
511A LEU* 3.8 18.8 + - + -
512A MET 4.4 1.3 - - - -
513A GLU* 3.5 30.4 + - + +
529A TYR 4.3 0.2 - - - +
530A SER* 3.2 5.8 + - - -
531A PHE* 2.8 41.6 + - + +
533A VAL* 4.1 4.7 - - + -
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Residues in contact with LEU 479 (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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477A LYS* 3.5 33.2 - - - +
478A TYR* 1.3 74.5 - - - +
480A LEU* 1.3 68.8 + - - +
481A ARG* 4.0 15.3 + - + +
494A GLN 3.4 3.5 - - - +
495A LEU* 3.4 2.1 - - - +
496A ASN* 2.9 49.2 + - - +
524A LEU* 4.2 1.1 - - + -
525A PRO* 3.9 23.1 - - + -
528A SER* 3.8 21.8 - - - +
529A TYR 3.6 11.7 - - - +
530A SER* 3.4 13.5 - - - +
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Residues in contact with LEU 480 (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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359A PHE* 3.4 12.7 - - - -
402A PRO 5.7 0.4 - - - +
405A TRP* 5.4 2.0 - - + +
406A LEU* 3.9 27.6 - - + +
409A LEU* 3.9 24.9 - - + -
478A TYR 4.5 1.1 - - - +
479A LEU* 1.3 73.3 - - - +
481A ARG* 1.3 69.3 + - - +
493A VAL* 4.0 18.4 - - + -
494A GLN 3.3 11.9 - - - +
495A LEU* 4.0 21.8 - - + -
500A LEU* 4.2 12.8 - - + -
528A SER* 4.0 0.3 - - - -
529A TYR* 3.1 51.7 + - + +
531A PHE* 4.7 2.5 - - + -
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Residues in contact with ARG 481 (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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359A PHE* 3.7 6.1 - - - -
479A LEU* 4.0 21.1 + - + +
480A LEU* 1.3 81.0 - - - +
482A PRO* 1.3 76.3 - - + +
493A VAL* 3.4 1.1 - - - +
494A GLN* 2.8 38.3 + - + +
525A PRO* 3.5 41.1 - - - +
526A ALA* 3.9 1.6 + - - +
527A PHE 5.3 0.4 + - - -
528A SER* 4.4 8.3 - - - -
617A EDO 5.2 5.5 + - - -
618A EDO 3.0 33.3 + - - -
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Residues in contact with PRO 482 (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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359A PHE* 3.7 34.1 - - + -
481A ARG* 1.3 94.3 - - + +
483A LEU* 1.3 61.9 + - - +
484A GLY 3.8 1.2 + - - -
487A GLY* 3.0 41.7 - - - +
490A SER* 3.8 8.7 - - - -
492A SER 3.6 7.4 - - - +
494A GLN* 4.3 7.9 - - - +
527A PHE 5.2 1.1 - - - +
618A EDO 4.1 18.6 - - - +
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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