Contacts of the helix formed by residues 483 - 497 (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 THR 483 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A GLN* 6.2 0.2 - - - +
396A ILE* 6.5 1.6 - - + -
400A MET* 3.9 4.5 - - - -
481A ARG 4.9 3.8 - - - +
482A LEU* 1.3 76.7 - - - +
484A ALA* 1.3 59.7 + - - +
485A LEU* 3.6 8.7 + - - +
486A ARG* 2.9 25.8 + - - +
487A VAL* 3.0 27.5 + - - +
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Residues in contact with ALA 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A VAL* 3.6 14.8 - - + +
312A LEU* 4.5 1.1 - - + -
313A CYS* 3.8 30.7 - - + +
316A HIS* 3.8 16.0 + - + +
396A ILE* 6.3 0.2 - - - +
400A MET* 3.7 30.5 - - - +
483A THR* 1.3 74.2 - - - +
485A LEU* 1.3 58.6 + - - +
487A VAL 3.4 0.5 + - - -
488A LYS* 2.9 29.6 + - - +
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Residues in contact with LEU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A CYS* 3.8 23.8 - - - -
483A THR* 3.2 7.7 + - - +
484A ALA* 1.3 76.8 - - - +
486A ARG* 1.3 67.5 + - - +
488A LYS* 3.2 14.1 + - + +
489A LYS* 2.9 57.1 + - + +
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Residues in contact with ARG 486 (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 LEU* 4.0 24.5 - - + -
483A THR* 2.9 29.3 + - - +
485A LEU* 1.3 77.2 - - - +
487A VAL* 1.3 58.6 + - - +
489A LYS* 3.3 39.6 + - - +
490A THR* 2.8 42.0 + - - +
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Residues in contact with VAL 487 (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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309A VAL* 3.9 15.9 - - + -
400A MET* 3.7 9.6 - - + -
403A PHE* 4.2 10.5 - - + -
407A LEU* 4.6 2.5 - - + -
469A LEU* 4.2 18.6 - - + -
473A CYS* 3.6 26.7 - - - -
482A LEU* 3.8 14.6 - - + -
483A THR 3.0 19.0 + - - +
484A ALA 3.7 5.6 - - - +
486A ARG* 1.3 70.8 - - - +
488A LYS* 1.3 67.5 + - - +
490A THR* 3.2 5.5 + - - -
491A LEU* 2.8 43.1 + - + +
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Residues in contact with LYS 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A HIS* 6.1 1.0 + - - -
306A TYR* 3.5 35.7 - - + -
309A VAL* 3.6 17.9 - - + +
310A SER* 3.6 28.8 + - - +
313A CYS* 4.4 19.2 - - - +
484A ALA 2.9 18.1 + - - +
485A LEU* 3.4 15.1 - - + +
487A VAL* 1.3 78.1 - - - +
489A LYS* 1.3 58.4 + - + +
491A LEU 3.7 0.3 - - - -
492A ALA* 2.9 29.2 + - - +
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Residues in contact with LYS 489 (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 LEU* 2.9 56.7 + - + +
486A ARG* 3.3 39.0 - - - +
488A LYS* 1.3 75.5 - - + +
490A THR* 1.3 62.2 + - - +
492A ALA* 3.2 7.6 + - - +
493A LYS* 3.0 23.7 + - - +
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Residues in contact with THR 490 (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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465A GLN* 5.9 1.3 - - + +
469A LEU* 3.8 26.3 - - + +
482A LEU* 5.3 0.9 - - - +
486A ARG* 2.8 36.5 + - - +
487A VAL 3.2 4.9 + - - -
489A LYS* 1.3 69.4 - - - +
491A LEU* 1.3 63.8 + - - +
493A LYS* 3.2 10.8 + - + +
494A MET* 3.0 35.6 + - + +
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Residues in contact with LEU 491 (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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302A LEU* 3.7 26.3 - - + +
305A ALA* 3.8 40.8 - - + +
306A TYR* 3.9 16.4 - - + +
309A VAL* 4.0 4.0 - - + -
407A LEU* 4.9 2.7 - - + -
466A MET* 3.8 12.1 - - + -
469A LEU* 3.6 24.2 - - + -
487A VAL* 2.8 38.4 + - + +
488A LYS 3.8 3.1 - - - +
490A THR* 1.3 71.8 - - - +
492A ALA* 1.3 62.1 + - - +
494A MET* 3.3 7.7 + - - +
495A SER* 3.0 28.3 + - - +
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Residues in contact with ALA 492 (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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306A TYR* 3.9 21.7 - - + +
488A LYS 2.9 18.1 + - - +
489A LYS* 3.2 8.7 + - - +
491A LEU* 1.3 75.4 - - - +
493A LYS* 1.3 63.5 + - - +
495A SER* 3.2 8.5 + - - -
496A GLU* 3.0 26.6 + - - +
502A LEU 5.8 0.2 - - - -
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Residues in contact with LYS 493 (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 LYS 3.0 12.2 + - - +
490A THR* 3.4 12.1 - - + +
492A ALA* 1.3 78.4 - - - +
494A MET* 1.3 59.4 + - + +
496A GLU* 3.8 10.2 - - + +
497A SER* 2.9 30.2 + - - -
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Residues in contact with MET 494 (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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302A LEU* 3.9 12.8 - - + -
462A CYS* 3.7 42.0 - - - +
465A GLN* 3.3 36.6 - - + +
466A MET* 3.7 19.5 - - + +
469A LEU* 4.6 4.3 - - - -
490A THR* 3.0 33.2 + - + +
491A LEU* 3.3 21.7 + - - +
493A LYS* 1.3 74.2 - - + +
495A SER* 1.3 63.3 + - - +
497A SER* 3.2 19.2 + - - -
498A GLN* 3.6 15.7 + - - +
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Residues in contact with SER 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 3.8 24.7 + - - +
306A TYR* 5.1 1.4 - - - +
491A LEU 3.0 14.2 + - - -
492A ALA* 3.4 11.6 - - - -
494A MET* 1.3 77.1 - - - +
496A GLU* 1.3 59.7 + - - +
497A SER 3.2 0.9 + - - -
498A GLN 3.3 2.3 + - - -
500A ILE* 2.9 45.1 + - - +
502A LEU* 3.0 29.1 + - - -
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Residues in contact with GLU 496 (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 ALA 3.0 14.2 + - - +
493A LYS* 3.8 16.4 - - + +
495A SER* 1.3 76.5 - - - +
497A SER* 1.3 59.4 + - - +
498A GLN 3.1 4.6 + - - -
499A ASP* 3.4 15.0 + - - +
500A ILE 4.0 8.3 + - - +
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Residues in contact with SER 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A GLN* 5.6 2.8 + - - -
493A LYS* 2.9 24.3 + - - -
494A MET* 3.4 10.7 + - - -
495A SER 3.1 1.0 - - - -
496A GLU* 1.3 78.6 - - - +
498A GLN* 1.3 64.6 + - - +
499A ASP* 3.6 0.9 - - - -
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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