Contacts of the strand formed by residues 522 - 527 (chain A) in PDB entry 3AS2
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 522 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510A PHE 4.5 3.4 - - - -
511A MET* 3.5 53.4 - - + +
517A THR 4.4 0.3 - - - +
518A GLY* 3.2 25.5 - - - +
519A ILE* 3.0 13.2 + - - +
520A ASN* 3.6 13.5 - - + -
521A GLY* 1.3 80.8 - - - +
523A GLU* 1.3 59.4 + - - +
535A VAL* 3.9 13.9 - - + -
536A TRP 3.4 12.3 - - - -
537A ASN* 3.6 28.3 - - + -
542A GLU* 3.5 49.1 - - + -
544A ILE* 4.5 5.2 - - + -
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Residues in contact with GLU 523 (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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517A THR 4.4 5.2 - - - +
518A GLY* 4.8 0.7 - - - -
521A GLY 4.1 0.2 + - - -
522A PHE* 1.3 74.5 - - - +
524A TYR* 1.3 64.8 + - - +
525A GLY 4.0 0.2 + - - -
534A TRP* 4.0 19.3 - - + -
535A VAL* 3.2 6.7 - - - -
536A TRP* 2.8 51.9 + - + +
538A ARG* 2.7 49.3 + - - +
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Residues in contact with TYR 524 (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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512A LEU* 3.5 28.7 - - + -
516A ASN* 3.9 26.0 - - + +
517A THR* 4.1 12.0 + - - -
518A GLY* 4.6 1.0 - - - +
523A GLU* 1.3 78.7 - - - +
525A GLY* 1.3 77.2 + - - +
526A TYR* 3.3 22.4 - - + +
533A PRO* 3.7 9.4 - - + -
534A TRP* 3.4 18.3 - - - -
535A VAL* 4.2 3.1 - - + -
546A PHE* 4.5 1.8 - + - -
548A ASP* 2.6 31.2 + - + -
550A ARG* 4.8 6.6 + - - +
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Residues in contact with GLY 525 (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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524A TYR* 1.3 84.7 - - - +
526A TYR* 1.3 61.9 - - - +
533A PRO* 3.4 3.1 - - - +
534A TRP* 2.9 60.8 + - - +
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Residues in contact with TYR 526 (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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524A TYR* 3.3 27.3 - - + +
525A GLY* 1.3 73.3 - - - -
527A ASP* 1.3 74.2 + - - +
528A ALA* 3.4 10.7 + - + +
531A GLU* 2.6 34.7 + - - -
532A ALA 3.5 14.6 - - - -
533A PRO* 3.7 14.4 - - + -
534A TRP* 4.4 4.7 - - - +
548A ASP* 3.6 19.1 - - - -
550A ARG* 3.2 53.8 - - + +
551A SER* 3.3 19.2 + - - -
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Residues in contact with ASP 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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403A HIS* 2.9 36.7 + - + +
410A GLY* 3.3 0.7 - - - -
411A SER* 2.9 34.7 + - - -
412A PHE* 4.7 0.9 + - - -
478A ASP* 4.9 5.0 - - - +
526A TYR* 1.3 71.3 - - - +
528A ALA* 1.3 57.2 + - - +
529A GLN* 3.0 21.0 + - - +
530A ALA* 3.1 11.1 + - + -
531A GLU* 2.8 26.0 + - - -
532A ALA 2.8 15.8 + - - +
534A TRP* 4.6 6.5 - - - +
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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