Contacts of the helix formed by residues 485 - 498 (chain D) in PDB entry 3MSS
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 SER 485 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355D GLU* 3.6 19.5 - - - -
419D LYS* 3.4 13.6 - - - +
422D VAL* 4.8 0.9 - - - -
484D PRO* 1.3 76.1 - - - +
486D PHE* 1.3 59.6 + - - +
487D ALA* 3.6 6.6 + - - +
488D GLU* 3.0 34.4 + - - +
489D ILE* 2.9 27.0 + - - +
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Residues in contact with PHE 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D SER* 4.4 5.7 - - - +
351D MET* 3.4 35.4 - - + -
352D GLU* 3.6 22.6 - - - +
355D GLU* 2.9 24.6 + - - +
364D LEU* 4.5 0.2 - - + -
418D ILE* 3.7 26.2 - - + -
421D ASP* 3.5 20.4 - - + -
422D VAL* 3.4 36.3 - - + -
425D PHE* 3.6 29.2 - + + -
485D SER* 1.3 69.0 - - - +
487D ALA* 1.3 61.0 + - - +
489D ILE* 3.7 18.0 - - + +
490D HIS* 2.8 34.1 + - - +
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Residues in contact with ALA 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D GLU* 3.7 28.1 - - + +
355D GLU* 3.1 14.4 + - - +
485D SER* 3.7 8.3 - - - +
486D PHE* 1.3 76.2 - - - +
488D GLU* 1.3 58.7 + - + +
490D HIS* 4.0 1.4 - - - +
491D GLN* 3.0 29.0 + - - +
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Residues in contact with GLU 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D LEU* 5.8 0.4 - - - -
483D ARG 4.9 0.2 - - - +
484D PRO* 3.3 17.4 - - + +
485D SER* 3.0 35.4 + - - +
487D ALA* 1.3 76.2 - - + +
489D ILE* 1.3 67.0 + - - +
491D GLN* 3.5 7.3 + - - +
492D ALA* 3.0 23.9 + - - +
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Residues in contact with ILE 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D SER* 3.8 9.0 - - - -
422D VAL* 3.9 14.8 - - + -
425D PHE* 3.6 26.5 - - + -
471D LEU* 4.3 13.4 - - + +
475D CYS* 3.9 24.2 - - - -
484D PRO* 3.8 18.6 - - + -
485D SER 2.9 21.4 + - - +
486D PHE* 3.7 26.0 - - + +
488D GLU* 1.3 76.3 - - - +
490D HIS* 1.3 58.9 + - - +
492D ALA* 3.2 7.8 + - - +
493D PHE* 3.0 40.9 + - + -
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Residues in contact with HIS 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345D THR* 3.5 26.5 + - + +
348D SER* 3.3 29.0 + - - +
349D SER* 3.5 26.5 + - - -
352D GLU* 3.3 24.2 - - - +
486D PHE 2.8 18.1 + - - +
487D ALA 4.0 0.9 - - - +
489D ILE* 1.3 76.0 - - - +
491D GLN* 1.3 56.7 + - - +
493D PHE* 3.2 1.8 + - - +
494D GLU* 2.7 62.6 + - + +
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Residues in contact with GLN 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487D ALA 3.0 19.5 + - - +
488D GLU* 3.6 9.0 - - - +
489D ILE 3.3 0.2 - - - -
490D HIS* 1.3 77.2 - - - +
492D ALA* 1.3 58.5 + - - +
494D GLU* 3.0 30.9 - - - +
495D THR* 2.9 41.0 + - - +
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Residues in contact with ALA 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D LEU* 3.9 23.8 - - + -
488D GLU 3.0 15.3 + - - +
489D ILE 3.2 8.0 + - - +
491D GLN* 1.3 76.1 - - - +
493D PHE* 1.3 61.5 + - - +
495D THR* 3.4 8.5 + - - +
496D MET* 3.1 31.4 + - + +
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Residues in contact with PHE 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D LEU* 3.7 23.6 - - + +
344D ALA* 3.9 15.0 - - + -
345D THR* 3.4 21.5 - - - +
348D SER* 3.8 11.0 - - - +
425D PHE* 3.5 28.9 - + - -
429D LEU* 3.3 31.6 - - + -
468D VAL* 4.6 5.8 - - + -
471D LEU* 3.7 21.3 - - + -
489D ILE* 3.0 30.8 + - + -
490D HIS 3.8 4.5 - - - +
492D ALA* 1.3 70.8 - - - +
494D GLU* 1.3 56.0 + - - +
495D THR 3.1 2.0 - - - -
496D MET* 3.2 13.9 + - + +
497D PHE* 2.5 38.3 + - - +
516D MS7 4.6 4.9 - + - -
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Residues in contact with GLU 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345D THR* 4.4 7.1 - - + +
490D HIS* 2.7 42.7 + - + +
491D GLN* 3.0 31.1 - - - +
493D PHE* 1.3 71.5 - - - +
495D THR* 1.3 66.4 + - - +
497D PHE* 3.9 6.4 - - - +
498D GLN* 3.0 36.3 + - + +
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Residues in contact with THR 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491D GLN* 2.9 25.4 + - - +
492D ALA* 3.4 12.6 - - - +
493D PHE 3.1 0.2 - - - -
494D GLU* 1.3 79.5 - - - +
496D MET* 1.3 68.3 + - + +
497D PHE 3.2 0.2 + - - -
498D GLN* 3.2 19.1 + - - +
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Residues in contact with MET 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D LEU* 4.0 15.3 - - + +
467D LYS* 3.9 45.5 - - + +
468D VAL* 3.9 22.4 - - + +
471D LEU* 3.9 23.6 - - + -
492D ALA* 3.1 17.0 + - + +
493D PHE* 3.5 16.4 - - + +
495D THR* 1.3 83.7 - - + +
497D PHE* 1.3 61.6 + - - +
498D GLN 3.4 5.5 + - - +
516D MS7 4.0 28.8 - - + +
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Residues in contact with PHE 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D VAL* 4.3 17.9 - - + +
341D LEU* 3.7 24.0 - - + +
342D TYR* 3.8 43.5 - + + -
345D THR* 3.9 22.0 - - + +
493D PHE 2.5 27.4 + - - +
494D GLU* 3.9 5.2 - - - +
496D MET* 1.3 73.4 - - - +
498D GLN* 1.3 74.1 + - + +
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Residues in contact with GLN 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494D GLU* 3.0 28.1 + - + +
495D THR* 3.2 15.1 + - - +
496D MET 3.5 5.2 - - - +
497D PHE* 1.3 93.6 - - + +
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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