Contacts of the strand formed by residues 528 - 534 (chain A) in PDB entry 5E97
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 SER 528 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359A PHE* 4.3 2.9 - - - -
363A PHE* 3.8 4.5 - - - -
455A ILE* 3.6 0.9 - - - -
456A ASN 2.9 28.4 + - - +
479A LEU* 3.7 2.1 - - - +
480A LEU 3.8 7.0 - - - -
481A ARG* 3.8 27.8 - - - -
524A LEU* 3.4 16.2 - - - +
525A PRO* 2.8 27.3 + - - +
526A ALA 3.3 2.2 - - - -
527A PHE* 1.3 79.2 - - - +
529A TYR* 1.3 67.0 + - - +
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Residues in contact with TYR 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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359A PHE* 2.7 63.1 + + - -
362A GLY* 3.5 28.8 - - - -
363A PHE* 3.6 26.0 - + - -
366A LEU* 3.7 16.6 - - + -
402A PRO* 5.1 3.8 + - - +
403A ASP* 4.9 0.5 + - - -
406A LEU* 4.1 22.7 - - + +
454A ALA 3.1 13.9 - - - +
455A ILE* 4.1 5.2 - - + -
479A LEU* 3.6 0.9 - - - +
480A LEU* 3.1 56.6 + - + +
493A VAL* 5.8 0.2 - - + -
524A LEU* 4.1 2.5 - - - -
528A SER* 1.3 73.2 - - - +
530A SER* 1.3 63.2 + - - +
531A PHE* 5.9 0.7 - + - -
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Residues in contact with SER 530 (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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366A LEU* 5.0 0.8 - - - +
453A TYR* 3.2 3.6 - - - +
454A ALA 2.9 31.4 + - - -
477A LYS* 3.9 0.5 - - - +
478A TYR 3.1 19.2 + - - -
479A LEU* 3.3 13.7 + - - +
524A LEU* 3.6 13.9 - - - -
529A TYR* 1.3 77.6 - - - +
531A PHE* 1.3 80.0 + - - +
532A PHE* 3.5 27.0 - - - -
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Residues in contact with PHE 531 (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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366A LEU* 4.1 8.3 - - + -
406A LEU* 3.9 28.3 - - + -
409A LEU* 3.9 19.1 - - + -
410A PHE* 3.8 29.6 - + + -
413A LEU* 3.7 28.7 - - + -
414A VAL* 3.7 30.5 - - + -
451A THR* 4.2 7.9 - - + -
452A LEU 3.2 6.3 - - - +
453A TYR* 3.6 18.6 - + + -
476A ASP 4.4 0.2 - - - -
478A TYR* 2.8 45.5 + - + -
480A LEU* 4.6 6.1 - - + -
529A TYR* 5.9 0.2 - + - -
530A SER* 1.3 83.0 + - - +
532A PHE* 1.3 61.1 + - - +
533A VAL 4.3 0.2 - - - -
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Residues in contact with PHE 532 (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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450A LEU 3.7 0.3 - - - +
451A THR* 3.5 2.2 - - - -
452A LEU* 2.8 56.8 + - + +
454A ALA* 4.6 13.0 - - + -
464A LEU* 4.8 4.3 - - + -
475A VAL* 3.8 18.8 - - + -
476A ASP 3.3 6.1 - - - -
477A LYS* 3.7 31.9 - - + -
516A LEU* 4.5 0.9 - - + -
522A LEU* 3.6 45.8 - - + -
523A GLY 4.0 13.2 - - - -
524A LEU* 4.7 5.4 - - + -
530A SER* 3.5 33.0 - - - -
531A PHE* 1.3 77.3 - - - +
533A VAL* 1.3 61.8 + - - +
534A ILE* 3.9 3.8 + - + +
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Residues in contact with VAL 533 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413A LEU* 4.0 17.3 - - + -
438A THR* 3.7 11.0 - - + +
445A TYR* 3.5 56.3 - - + +
449A ASP* 4.5 2.5 - - + -
450A LEU 3.3 9.0 - - - +
451A THR* 3.7 18.6 - - + +
475A VAL* 3.2 4.7 - - - -
476A ASP* 2.9 33.0 + - + +
478A TYR* 4.0 7.9 - - + -
532A PHE* 1.3 72.2 - - - +
534A ILE* 1.3 69.4 + - - +
535A ARG* 3.5 2.9 + - - +
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Residues in contact with ILE 534 (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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435A LEU* 5.0 0.2 - - + -
449A ASP* 3.5 8.7 - - - +
450A LEU* 2.8 49.4 + - + +
452A LEU* 4.9 8.5 - - + -
466A LEU* 4.0 23.1 - - + -
470A PHE* 4.2 11.0 - - + +
473A LYS* 3.7 33.2 - - + -
474A GLN 3.9 2.7 - - - -
475A VAL* 4.5 7.9 - - + -
532A PHE* 4.5 6.7 - - + +
533A VAL* 1.3 71.9 - - - +
535A ARG* 1.3 61.4 + - - +
537A ALA* 3.6 12.6 - - + +
43B PHE* 3.7 31.4 - - + -
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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