Contacts of the strand formed by residues 520 - 526 (chain A) in PDB entry 2YA6
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 TYR 520 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419A ASP* 3.5 7.1 - - - +
420A MET* 2.8 60.7 + - + +
422A PRO* 3.9 2.5 - - + -
437A ALA* 3.7 12.7 - - + +
438A TYR* 3.2 33.7 - + - -
447A GLN* 3.7 16.4 + - - -
515A ILE* 3.8 16.6 - - + +
516A ALA* 2.6 45.5 + - - +
518A ASP* 3.4 28.9 - - + -
519A SER* 1.3 77.2 + - - +
521A LEU* 1.3 61.7 + - - +
522A TRP* 4.1 6.7 - - - +
538A ASP* 4.4 2.5 - - - -
540A THR* 3.4 11.2 - - + +
544A LYS* 6.1 0.2 - - - -
551A LEU 4.2 7.4 - - - +
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Residues in contact with LEU 521 (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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417A ILE* 4.0 9.4 - - + -
418A TYR 3.7 6.7 - - - +
419A ASP* 3.6 23.6 - - - +
520A TYR* 1.3 74.5 - - - +
522A TRP* 1.3 65.3 + - - +
539A ILE* 3.0 41.1 + - + -
540A THR* 2.8 22.5 + - + +
543A VAL* 4.0 23.1 - - + -
551A LEU* 4.3 15.0 - - + +
552A GLY* 4.1 11.9 - - - -
553A VAL* 3.8 20.0 - - + +
574A VAL* 4.5 9.2 - - + -
592A ILE* 4.0 14.4 - - + -
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Residues in contact with TRP 522 (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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382A THR* 4.4 0.7 - - + -
384A LEU* 3.8 30.5 - - + -
400A ASN* 3.7 15.0 - - - -
417A ILE* 3.4 7.4 - - - +
418A TYR* 2.8 53.6 + + + +
420A MET* 3.5 38.0 - - + +
490A LYS* 3.6 26.5 - - + -
504A TYR* 3.5 23.3 - + - -
520A TYR* 4.1 6.1 - - - +
521A LEU* 1.3 85.3 - - - +
523A MET* 1.3 61.0 + - - +
536A PRO* 3.5 28.9 - - + -
537A GLN 3.3 6.3 - - - +
538A ASP* 3.7 28.3 + - + -
539A ILE* 4.5 2.5 - - - -
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Residues in contact with MET 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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415A PHE* 3.8 23.8 - - + -
416A SER 3.3 11.9 - - - +
417A ILE* 3.7 22.4 - - + -
418A TYR* 4.4 1.1 - - - -
522A TRP* 1.3 77.1 - - - +
524A SER* 1.3 83.0 + - - +
525A TYR* 3.9 14.4 - - + -
537A GLN* 2.6 63.0 + - + +
539A ILE* 4.2 13.7 - - + -
598A GLY 3.7 23.1 - - - +
599A LYS 5.9 0.2 - - - +
601A TRP* 4.1 9.0 - - - +
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Residues in contact with SER 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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381A ILE* 3.6 24.2 - - - -
382A THR* 3.6 5.4 + - - -
415A PHE* 3.5 2.8 - - - -
416A SER* 2.8 32.0 + - - +
418A TYR* 2.7 28.1 + - - -
523A MET* 1.3 78.8 + - - +
525A TYR* 1.3 62.0 + - - +
533A TRP* 3.7 5.4 - - - -
534A SER* 3.5 18.4 + - - -
536A PRO* 3.6 11.1 - - - +
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Residues in contact with TYR 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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413A ARG* 3.5 57.7 + - + -
414A ILE 3.0 11.7 - - - +
415A PHE* 4.0 9.2 - + + -
523A MET* 3.9 18.4 - - + -
524A SER* 1.3 75.4 - - - +
526A SER* 1.3 60.1 + - - +
527A ASP* 3.6 10.5 - - - -
533A TRP* 3.2 8.5 - - - -
534A SER* 2.7 66.3 + - - -
537A GLN* 4.6 15.8 + - + -
1778A FMT 3.7 9.2 - - - +
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Residues in contact with SER 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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412A LYS 4.2 1.4 - - - +
413A ARG* 3.6 1.4 - - - -
414A ILE* 2.8 38.1 + - - +
525A TYR* 1.3 75.1 - - - +
527A ASP* 1.3 64.1 + - - +
528A ASP* 2.8 15.8 + - - -
530A GLY* 3.0 20.0 + - - -
532A THR 2.8 20.3 + - - -
533A TRP* 3.7 22.9 - - - -
1778A FMT 3.3 5.2 - - - -
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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