Contacts of the helix formed by residues 460 - 474 (chain A) in PDB entry 3MDY
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 460 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414A CYS* 6.0 0.5 - - - -
416A SER* 4.2 22.5 - - - +
456A ARG 4.6 1.8 - - - +
457A TRP 3.2 7.2 + - - +
458A SER 3.4 1.6 + - - -
459A SER* 1.3 80.4 - - - +
461A GLU* 1.3 68.6 + - - +
462A CYS* 3.4 12.9 + - - +
463A LEU* 3.0 40.4 + - + +
464A ARG* 3.0 23.6 + - - +
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Residues in contact with GLU 461 (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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459A SER 4.4 0.2 - - - -
460A ASP* 1.3 73.4 - - - +
462A CYS* 1.3 58.9 + - - +
464A ARG* 3.3 27.0 + - - +
465A GLN* 2.8 58.6 + - - +
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Residues in contact with CYS 462 (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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298A ALA* 4.4 7.9 - - + -
301A MET* 3.6 27.6 - - + -
302A LEU* 4.4 5.2 - - - -
460A ASP* 3.2 11.0 + - - +
461A GLU* 1.3 79.2 - - - +
463A LEU* 1.3 57.2 + - + +
465A GLN* 3.1 11.3 + - - +
466A MET* 2.9 29.3 + - - +
494A MET* 3.7 19.1 - - - -
498A GLN* 3.4 37.3 + - - +
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Residues in contact with LEU 463 (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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301A MET* 3.9 32.5 - - + -
411A ALA* 4.1 22.4 - - + +
414A CYS* 4.1 10.8 - - + +
416A SER* 3.6 19.3 - - - +
456A ARG* 3.3 29.2 - - - +
457A TRP* 3.9 41.3 - - + +
460A ASP* 3.0 15.2 + - + +
462A CYS* 1.3 76.0 - - + +
464A ARG* 1.3 56.8 + - - +
466A MET* 3.3 4.4 + - + +
467A GLY* 2.8 27.0 + - - -
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Residues in contact with ARG 464 (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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457A TRP* 3.4 14.3 + - - +
458A SER* 3.2 38.5 + - - -
459A SER 5.2 0.2 - - - -
460A ASP 3.0 19.8 + - - +
461A GLU* 3.4 29.9 + - - +
462A CYS 3.3 0.2 - - - -
463A LEU* 1.3 77.5 - - - +
465A GLN* 1.3 60.7 + - - +
467A GLY* 3.2 3.9 + - - -
468A LYS* 3.1 21.7 + - - +
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Residues in contact with GLN 465 (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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461A GLU* 2.8 49.2 + - - +
462A CYS* 3.1 9.7 + - - +
464A ARG* 1.3 73.2 - - + +
466A MET* 1.3 65.5 + - - +
468A LYS* 3.3 14.5 + - + +
469A LEU* 3.0 23.8 + - - +
490A THR* 5.9 1.3 - - + +
494A MET* 3.3 38.9 - - + +
497A SER* 5.6 3.0 + - - -
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Residues in contact with MET 466 (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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301A MET* 3.9 37.5 - - + -
302A LEU* 4.1 7.9 - - - -
305A ALA* 4.5 4.0 - - + -
407A LEU* 4.1 37.5 - - + +
410A VAL* 5.7 1.1 - - + -
411A ALA* 4.5 11.0 - - + +
457A TRP* 5.7 0.2 - - + -
462A CYS 2.9 18.9 + - - +
463A LEU* 3.5 10.1 - - + +
465A GLN* 1.3 74.6 - - - +
467A GLY* 1.3 63.7 + - - +
469A LEU* 3.2 7.3 + - - +
470A MET* 3.0 37.0 + - + +
491A LEU* 3.8 19.5 - - + -
494A MET* 3.7 19.0 - - + +
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Residues in contact with GLY 467 (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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453A PHE* 3.4 28.3 - - - -
457A TRP* 4.4 5.2 - - - -
463A LEU 2.8 14.6 + - - -
464A ARG* 3.2 5.1 + - - -
466A MET* 1.3 77.4 - - - +
468A LYS* 1.3 58.4 + - - +
470A MET* 3.4 8.6 + - - +
471A THR* 3.1 28.6 + - - -
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Residues in contact with LYS 468 (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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464A ARG 3.1 12.6 + - - +
465A GLN* 3.6 16.2 - - + +
466A MET 3.3 0.2 - - - -
467A GLY* 1.3 76.0 - - - +
469A LEU* 1.3 63.6 + - - +
471A THR* 3.4 6.8 + - - -
472A GLU* 2.8 67.1 + - - +
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Residues in contact with LEU 469 (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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407A LEU* 4.0 20.6 - - + -
465A GLN 3.0 13.2 + - - +
466A MET* 3.4 15.3 - - - +
468A LYS* 1.3 74.4 - - - +
470A MET* 1.3 65.2 + - - +
472A GLU* 3.2 7.9 + - - +
473A CYS* 3.0 27.4 + - - -
482A LEU* 3.7 24.2 - - + +
487A VAL* 4.2 14.6 - - + -
490A THR* 3.8 32.8 - - + +
491A LEU* 3.6 37.2 - - + -
494A MET* 4.6 3.1 - - - -
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Residues in contact with MET 470 (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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404A GLY* 3.7 19.3 - - - +
407A LEU* 3.6 21.7 - - + +
408A TRP* 3.6 19.3 - - - -
411A ALA* 3.5 31.9 - - + -
453A PHE* 3.8 20.4 - - - -
457A TRP* 3.7 14.6 - - + -
466A MET* 3.0 29.2 + - + +
467A GLY* 3.5 4.9 - - - +
469A LEU* 1.3 73.2 - - - +
471A THR* 1.3 65.1 + - - +
473A CYS* 3.0 17.7 + - - +
474A TRP* 3.0 33.0 + - + -
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Residues in contact with THR 471 (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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453A PHE* 3.4 19.2 - - - -
467A GLY 3.1 16.1 + - - -
468A LYS* 3.7 8.9 - - - -
469A LEU 3.3 0.2 - - - -
470A MET* 1.3 81.3 - - - +
472A GLU* 1.3 65.3 + - + +
473A CYS 3.4 0.2 + - - -
474A TRP* 3.4 26.2 + - + +
475A ALA* 3.4 14.2 + - - +
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Residues in contact with GLU 472 (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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468A LYS* 2.8 55.9 + - + +
469A LEU* 3.8 1.4 - - - +
470A MET 3.1 0.4 - - - -
471A THR* 1.3 82.8 - - + +
473A CYS* 1.3 58.0 + - - +
475A ALA* 4.4 5.8 + - - +
480A SER 3.9 5.1 - - - +
481A ARG* 3.3 9.7 - - - -
482A LEU* 3.0 55.2 + - + +
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Residues in contact with CYS 473 (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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400A MET* 3.6 25.5 - - - +
401A TYR* 3.4 9.5 + - - -
403A PHE* 5.0 1.1 - - - -
404A GLY* 3.7 17.3 - - - -
407A LEU* 4.6 9.0 - - - -
469A LEU* 3.0 19.7 + - - +
470A MET 3.0 8.9 + - - +
472A GLU* 1.3 79.8 - - - +
474A TRP* 1.3 57.9 + - - +
475A ALA 3.5 0.4 - - - -
481A ARG* 3.2 25.9 - - - +
482A LEU* 4.4 8.1 - - - +
487A VAL* 3.6 30.3 - - - -
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Residues in contact with TRP 474 (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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401A TYR* 3.6 30.9 - - + +
404A GLY 3.6 33.7 - - - -
405A LEU* 3.8 11.4 - - + -
408A TRP* 4.0 13.5 - + + -
450A ARG* 2.8 62.4 + - + +
451A PRO* 3.8 32.1 - - + -
453A PHE* 3.7 37.2 - + - -
470A MET* 3.0 22.3 + - + -
471A THR* 3.4 24.4 + - + +
473A CYS* 1.3 76.0 - - + +
475A ALA* 1.3 67.4 + - - +
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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