Contacts of the helix formed by residues 517 - 526 (chain A) in PDB entry 1Y8B
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 ASP 517 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A ASP* 5.2 0.4 + - - -
514A LEU* 4.3 21.9 - - + +
515A MET 3.4 0.4 - - - -
516A ALA* 1.3 78.2 - - - +
518A MET* 1.3 64.7 + - + +
519A TYR* 2.9 11.7 + - - -
520A SER* 3.0 21.5 + - - -
521A GLN* 4.1 12.1 + - - +
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Residues in contact with MET 518 (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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508A MET* 4.9 11.7 - - + -
509A TRP* 3.5 26.5 - - + +
510A ALA* 3.9 21.1 - - + -
512A PRO* 4.6 13.9 - - + -
514A LEU 3.6 12.8 - - - +
515A MET* 3.0 32.1 - - - +
516A ALA 2.6 4.9 + - - -
517A ASP* 1.3 79.1 + - + +
519A TYR* 1.3 51.9 + - - -
520A SER 2.6 2.3 + - - -
521A GLN* 2.6 35.0 + - + +
522A LYS* 2.7 43.9 + - + +
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Residues in contact with TYR 519 (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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147A ILE* 5.7 4.5 - - + -
515A MET 4.2 0.6 + - - -
516A ALA* 2.5 31.0 + - + +
517A ASP* 3.7 11.2 - - - -
518A MET* 1.3 71.7 - - - +
520A SER* 1.3 82.6 + - - +
522A LYS* 4.7 5.8 - - - +
523A GLY* 3.0 26.0 + - - +
547A HIS* 3.6 37.2 - + + +
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Residues in contact with SER 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ASP* 3.0 12.2 + - - -
518A MET 2.6 5.1 + - - -
519A TYR* 1.3 110.2 + - - +
521A GLN* 1.3 72.8 + - - +
524A ASP* 2.5 33.8 + - - +
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Residues in contact with GLN 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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478A SER* 5.8 4.2 - - - -
508A MET* 4.8 21.5 - - + +
517A ASP* 4.7 10.9 + - - +
518A MET* 2.6 24.5 + - + +
520A SER* 1.3 83.7 - - - +
522A LYS* 1.3 65.0 + - + +
524A ASP* 3.6 4.3 + - - +
525A GLN* 3.3 24.7 + - - +
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Residues in contact with LYS 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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508A MET* 5.7 1.8 - - + -
515A MET 5.0 2.0 - - - -
518A MET* 2.7 52.3 + - + +
519A TYR* 4.7 6.4 - - - +
521A GLN* 1.3 72.8 - - + +
523A GLY* 1.3 67.4 + - - +
525A GLN* 3.1 33.8 + - - +
526A LEU* 3.0 18.4 - - - +
533A ALA* 5.6 4.5 - - + -
534A TRP 5.9 0.4 - - - +
535A VAL* 5.0 11.7 - - + -
540A ALA* 3.9 17.8 + - - +
543A LEU* 5.4 2.0 - - - +
544A HIS* 3.3 44.5 + - + +
547A HIS* 5.1 3.8 - - - -
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Residues in contact with GLY 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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519A TYR* 3.0 24.9 + - - +
520A SER 4.5 0.4 - - - -
521A GLN 3.3 0.4 - - - -
522A LYS* 1.3 78.5 - - - +
524A ASP* 1.3 59.0 + - - +
526A LEU* 2.9 31.8 - - - +
527A ARG* 4.5 1.4 - - - +
544A HIS* 4.8 0.6 + - - -
547A HIS* 4.5 18.1 - - - -
551A THR* 4.3 6.3 - - - +
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Residues in contact with ASP 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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520A SER* 2.5 23.6 - - - +
521A GLN* 3.6 5.0 + - - +
522A LYS 3.2 0.4 - - - -
523A GLY* 1.3 74.9 - - - +
525A GLN* 1.3 58.3 + - - +
526A LEU 2.9 4.0 - - - -
527A ARG* 2.6 57.4 + - + +
528A ALA* 3.4 3.3 + - - +
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Residues in contact with GLN 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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482A ILE* 5.9 4.7 - - + -
486A GLU* 4.1 1.9 - - - +
506A LYS* 3.2 35.2 + - - +
507A GLY* 3.7 7.6 - - - -
508A MET* 3.3 39.0 - - + +
521A GLN 3.3 11.0 + - - +
522A LYS* 3.1 41.2 + - - +
524A ASP* 1.3 76.3 - - - +
526A LEU* 1.3 63.1 + - + +
528A ALA* 3.4 16.1 + - - +
529A GLY 3.6 2.4 + - - -
530A ALA* 3.2 21.1 - - + +
533A ALA* 4.1 9.7 - - - +
544A HIS* 4.8 2.1 - - + -
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Residues in contact with LEU 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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522A LYS 3.0 22.9 - - - +
523A GLY* 2.9 21.1 - - - +
524A ASP 2.7 1.8 + - - -
525A GLN* 1.3 68.5 - - - +
527A ARG* 1.3 56.2 + - + +
528A ALA 2.9 1.8 - - - -
529A GLY* 2.5 28.1 + - - -
530A ALA* 3.3 26.7 + - + +
544A HIS* 3.6 22.9 - - + +
547A HIS* 4.2 0.9 - - + +
548A TYR* 3.9 24.2 - - + +
551A THR* 3.2 35.2 - - + +
553A VAL* 3.7 25.5 - - + +
556A VAL* 5.6 2.1 - - - +
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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