Contacts of the helix formed by residues 516 - 526 (chain A) in PDB entry 2MYS
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 GLY 516 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489A GLN* 3.2 34.6 + - - -
492A ASN* 3.7 12.4 + - - +
493A HIS* 4.9 0.4 - - - -
514A ASP* 2.5 22.4 + - - -
515A PHE* 1.3 69.3 - - - +
517A MET* 1.3 49.6 + - - +
518A ASP 2.5 18.2 + - - -
519A LEU* 2.5 24.6 + - - +
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Residues in contact with MET 517 (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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489A GLN* 4.1 5.1 - - - +
513A ILE* 5.0 21.1 - - + -
514A ASP* 3.8 24.9 + - + +
516A GLY* 1.3 73.0 - - - +
518A ASP* 1.3 65.9 + - - +
519A LEU 3.0 1.3 + - - -
520A ALA* 3.2 18.5 + - + +
521A ALA 4.5 1.4 + - - -
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Residues in contact with ASP 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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492A ASN* 5.6 0.4 - - - +
513A ILE* 5.8 3.1 - - - +
514A ASP 5.3 1.2 - - - +
515A PHE* 3.6 15.0 + - - +
516A GLY 2.5 5.9 + - - -
517A MET* 1.3 79.3 - - - +
519A LEU* 1.3 70.4 + - + +
520A ALA 3.8 0.2 + - - -
521A ALA* 4.4 9.7 + - - +
702A GLU* 5.9 1.1 - - - +
709A LYS* 5.6 3.8 + - - -
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Residues in contact with LEU 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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485A GLU* 3.7 29.4 - - + +
488A GLN* 4.1 6.5 - - + -
489A GLN* 3.9 20.9 - - + +
492A ASN* 3.8 22.7 - - - +
516A GLY* 2.5 25.5 + - - +
518A ASP* 1.3 83.9 - - + +
520A ALA* 1.3 62.8 + - - +
521A ALA 2.9 5.8 + - - -
522A CYS* 2.9 15.8 + - - +
523A ILE* 3.2 17.1 + - + +
584A TYR* 3.9 33.9 - - + -
702A GLU* 4.8 4.7 - - - +
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Residues in contact with ALA 520 (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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489A GLN* 3.4 19.4 - - - +
517A MET* 3.2 17.3 + - + +
519A LEU* 1.3 76.7 - - - +
521A ALA* 1.3 62.7 + - - +
523A ILE* 4.5 5.4 - - - -
524A GLU* 2.9 43.2 + - - +
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Residues in contact with ALA 521 (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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517A MET 4.5 1.4 + - - -
518A ASP 4.4 9.5 + - - +
519A LEU 3.0 0.4 - - - -
520A ALA* 1.3 80.8 - - - +
522A CYS* 1.3 66.3 + - - +
524A GLU* 3.4 10.6 + - - +
525A LEU* 3.4 12.3 + - - +
564A ASN* 3.2 23.9 - - - +
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Residues in contact with CYS 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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485A GLU* 4.1 25.6 - - - +
519A LEU* 2.9 9.5 + - - +
521A ALA* 1.3 79.5 - - - +
523A ILE* 1.3 65.2 + - - +
525A LEU* 3.2 20.7 + - - +
526A ILE* 3.4 14.3 + - - +
564A ASN* 4.0 9.8 + - - +
581A LEU* 4.2 26.7 - - - -
582A VAL 3.9 25.6 - - - +
583A HIS* 4.3 4.3 - - - -
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Residues in contact with ILE 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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482A PHE* 4.2 15.0 - - + -
485A GLU* 4.0 29.2 - - + +
486A MLY 4.4 23.8 - - + -
489A GLN* 3.7 30.5 - - - +
519A LEU* 3.2 18.7 + - + +
520A ALA* 3.9 5.6 - - - +
522A CYS* 1.3 76.9 - - - +
524A GLU* 1.3 69.5 + - - +
526A ILE* 2.9 14.6 + - - +
527A GLU* 3.0 39.1 + - + +
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Residues in contact with GLU 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 ALA* 2.9 46.1 + - - +
521A ALA* 4.2 4.5 - - - +
523A ILE* 1.3 79.7 - - - +
525A LEU* 1.3 58.4 + - - +
527A GLU* 4.7 3.5 - - - +
528A MLY 2.8 81.6 + - + +
531A GLY* 4.7 0.5 - - - -
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Residues in contact with LEU 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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521A ALA 3.4 10.2 + - - +
522A CYS* 3.2 11.4 + - - +
523A ILE 3.1 0.2 - - - -
524A GLU* 1.3 77.3 - - - +
526A ILE* 1.3 57.9 + - + +
531A GLY* 3.1 23.9 - - - -
532A ILE* 3.1 14.3 + - + +
558A HIS* 3.6 31.4 - - + +
562A SER* 3.8 22.9 - - - +
564A ASN* 3.9 34.3 - - + -
565A PHE* 4.2 10.1 - - + +
581A LEU* 4.3 22.9 - - + -
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Residues in contact with ILE 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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478A LEU* 4.2 15.7 - - + -
482A PHE* 3.7 32.8 - - + -
485A GLU* 6.3 0.7 - - + -
522A CYS* 3.5 21.1 - - - +
523A ILE* 2.9 8.0 + - + +
525A LEU* 1.3 83.0 - - + +
527A GLU* 1.3 60.0 + - - +
528A MLY 3.6 0.9 + - - +
531A GLY 3.9 2.3 - - - -
532A ILE* 3.8 12.5 + - + -
533A PHE* 3.4 56.5 + - + +
581A LEU* 4.0 28.7 - - + -
583A HIS* 4.6 7.2 - - + -
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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