Contacts of the helix formed by residues 465 - 476 (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 PRO 465 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337D ALA* 6.0 1.6 - - + -
463D GLY 3.5 6.9 - - - +
464D CYS* 1.3 92.9 - - - +
466D GLU* 1.3 65.3 + - - +
467D LYS* 4.5 2.9 - - + +
468D VAL* 3.2 16.5 + - + +
469D TYR* 3.0 18.7 + - - +
496D MET* 6.1 0.2 - - - -
516D MS7 3.5 55.9 - - + +
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Residues in contact with GLU 466 (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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460D ARG* 4.3 28.0 + - - +
464D CYS 3.6 0.6 + - - -
465D PRO* 1.3 72.3 - - - +
467D LYS* 1.3 52.5 + - + +
469D TYR* 3.3 3.3 + - - +
470D GLU* 2.8 48.2 + - + +
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Residues in contact with LYS 467 (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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465D PRO* 3.3 3.4 - - + +
466D GLU* 1.3 79.8 - - + +
468D VAL* 1.3 58.0 + - + +
470D GLU* 3.5 22.8 + - - +
471D LEU* 3.1 25.6 + - - +
496D MET* 3.9 29.3 - - + +
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Residues in contact with VAL 468 (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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429D LEU* 3.9 19.2 - - + +
464D CYS* 3.8 17.0 - - - -
465D PRO* 3.2 19.6 + - + +
467D LYS* 1.3 74.2 - - - +
469D TYR* 1.3 60.5 + - - +
471D LEU* 3.2 6.8 + - - +
472D MET* 2.9 26.7 + - + +
493D PHE* 4.6 4.0 - - + -
496D MET* 3.9 25.4 - - + -
516D MS7 3.7 51.6 - - + +
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Residues in contact with TYR 469 (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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457D ARG 4.7 0.5 + - - -
458D MET 2.5 29.7 + - - -
459D GLU* 3.4 9.4 - - - -
460D ARG* 3.4 57.4 - - + -
461D PRO* 4.3 0.9 - - + -
464D CYS* 3.9 5.3 - - - -
465D PRO 3.0 6.4 + - - +
466D GLU* 3.6 7.4 - - - +
468D VAL* 1.3 78.8 - - - +
470D GLU* 1.3 58.5 + - + +
472D MET* 3.1 26.9 + - - +
473D ARG* 2.9 74.4 + - + +
476D TRP* 4.5 1.3 - + - -
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Residues in contact with GLU 470 (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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466D GLU* 2.8 41.8 + - + +
467D LYS* 3.7 22.6 + - - +
469D TYR* 1.3 75.2 - - + +
471D LEU* 1.3 61.3 + - - +
473D ARG* 3.4 8.1 + - - +
474D ALA* 3.1 22.3 + - - +
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Residues in contact with LEU 471 (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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429D LEU* 4.4 5.6 - - + -
467D LYS 3.1 10.4 + - - +
468D VAL 3.2 9.4 + - - +
470D GLU* 1.3 73.2 - - - +
472D MET* 1.3 66.7 + - - +
474D ALA* 3.2 7.3 + - + +
475D CYS* 3.1 28.9 + - - -
484D PRO* 4.8 8.7 - - + -
488D GLU 5.5 0.2 - - - +
489D ILE* 4.3 24.7 - - + +
492D ALA* 3.9 23.6 - - + -
493D PHE* 3.7 35.7 - - + -
496D MET* 3.9 21.5 - - + -
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Residues in contact with MET 472 (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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426D GLY* 3.8 10.1 - - - +
429D LEU* 3.7 35.1 - - + +
430D TRP* 3.7 34.1 - - + -
433D ALA* 4.2 4.9 - - + -
461D PRO* 4.2 4.7 - - + -
464D CYS* 3.9 27.8 - - - -
468D VAL* 2.9 11.8 + - + +
469D TYR* 3.1 24.0 + - + +
471D LEU* 1.3 76.2 - - - +
473D ARG* 1.3 61.9 + - - +
475D CYS* 3.1 18.2 + - - +
476D TRP* 3.2 44.2 + - + -
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Residues in contact with ARG 473 (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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455D ASP 5.3 3.6 + - - -
457D ARG* 3.8 28.0 + - - +
469D TYR* 2.9 65.1 + - + +
470D GLU* 3.7 7.9 - - - +
471D LEU 3.3 0.2 - - - -
472D MET* 1.3 73.7 - - - +
474D ALA* 1.4 64.0 + - - +
476D TRP* 3.2 32.7 + - - +
477D GLN* 3.5 18.9 + - - +
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Residues in contact with ALA 474 (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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470D GLU 3.1 13.6 + - - +
471D LEU* 3.2 13.4 + - + +
473D ARG* 1.4 74.2 - - - +
475D CYS* 1.3 64.9 + - - +
477D GLN* 3.3 29.3 + - + +
482D ASP 5.6 0.7 - - - +
483D ARG* 3.6 4.0 - - - -
484D PRO* 3.4 29.7 - - + +
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Residues in contact with CYS 475 (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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422D VAL* 3.3 39.5 - - - +
423D TRP* 3.4 11.3 - - - -
425D PHE* 4.1 14.4 - - - -
426D GLY* 3.7 15.3 - - - -
429D LEU* 5.3 0.2 - - - -
471D LEU* 3.1 21.0 + - - -
472D MET* 3.2 9.9 - - - +
474D ALA* 1.3 79.3 - - - +
476D TRP* 1.3 57.4 + - + +
477D GLN 3.3 0.2 - - - -
483D ARG* 3.1 23.6 + - - -
484D PRO* 4.4 2.0 - - - -
489D ILE* 3.9 21.1 - - - -
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Residues in contact with TRP 476 (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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423D TRP* 3.2 52.3 + + + -
426D GLY* 3.3 25.3 - - - -
427D VAL* 3.3 14.9 - - + +
430D TRP* 4.3 2.0 - + + -
440D TYR* 5.2 4.7 - - - -
457D ARG* 2.9 46.7 + - - +
458D MET* 3.9 58.6 - - + -
469D TYR* 4.5 0.2 - + - -
472D MET* 3.2 38.3 + - + -
473D ARG* 3.2 29.7 + - - +
474D ALA 3.1 1.2 - - - -
475D CYS* 1.3 80.8 - - + +
477D GLN* 1.3 65.8 + - - +
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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