Contacts of the helix formed by residues 402 - 406 (chain C) 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 402 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C ARG 5.4 5.8 - - - +
363C ASP* 3.5 15.5 - - - +
367C ARG* 3.3 31.6 - - - +
392C THR 3.2 18.6 - - - +
393C TYR* 3.7 15.5 - - + -
400C LYS 4.6 0.2 - - - +
401C PHE* 1.3 87.4 - - + +
403C ILE* 1.3 60.6 + - - +
404C LYS 3.1 2.5 - - - -
405C TRP* 2.9 25.6 + - + -
406C THR* 2.7 27.6 + - - +
416C PHE* 6.4 0.2 - - + -
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Residues in contact with ILE 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C THR 4.1 4.0 + - - -
394C THR* 3.5 26.4 + - - +
395C ALA 5.8 1.8 - - - +
396C HIS* 6.2 2.2 - - + -
401C PHE* 3.2 18.0 + - + +
402C PRO* 1.3 71.0 - - - +
404C LYS* 1.3 56.9 - - - +
406C THR* 3.1 27.0 + - - +
411C LEU* 3.7 30.3 - - + +
445C LEU* 4.0 31.6 - - + +
448C VAL* 4.0 30.7 - - + +
449C TYR 5.7 0.2 - - - +
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Residues in contact with LYS 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C THR 5.4 0.2 + - - -
402C PRO 3.0 1.8 + - - -
403C ILE* 1.3 76.3 - - - +
405C TRP* 1.3 70.0 + - + +
406C THR 3.5 0.7 - - - -
423C TRP* 5.1 1.1 + - - -
427C VAL* 3.7 13.7 - - - +
438C SER* 6.1 1.1 - - - -
439C PRO* 3.4 33.8 + - + +
440C TYR* 2.6 67.6 + - + +
441C PRO* 4.9 0.4 - - - +
442C GLY 4.7 2.0 - - - +
443C ILE* 2.9 23.1 + - - +
445C LEU* 3.3 31.8 - - + +
448C VAL* 4.5 9.8 - - + +
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Residues in contact with TRP 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C LEU* 6.3 0.9 - - + -
363C ASP* 5.6 0.2 - - - +
364C LEU 3.5 25.4 - - - +
365C ALA* 3.4 4.6 - - + +
367C ARG* 3.4 31.0 - - - +
392C THR* 4.1 18.2 - - + -
402C PRO* 2.9 27.3 + - + +
404C LYS* 1.3 91.9 - - + +
406C THR* 1.3 60.9 + - - +
407C ALA 3.8 2.1 + - - -
420C SER 4.9 0.3 - - - +
423C TRP* 3.8 6.5 - - - -
424C ALA* 3.5 29.1 + - + +
427C VAL* 3.4 30.7 - - + +
431C GLU* 2.9 40.5 + - - -
438C SER* 5.9 0.2 - - - -
439C PRO* 3.5 30.7 - - + -
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Residues in contact with THR 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C PHE* 4.4 8.0 - - + +
402C PRO* 2.7 38.4 + - - +
403C ILE* 3.1 12.5 + - - +
404C LYS 3.5 0.8 - - - -
405C TRP* 1.3 77.5 - - - +
407C ALA* 1.3 62.2 + - - +
408C PRO* 3.8 0.9 - - - +
410C SER* 3.4 29.8 - - - -
411C LEU* 3.6 37.9 - - + +
416C PHE* 4.7 11.5 - - + -
423C TRP* 3.8 8.7 + - - +
452C LEU* 4.8 3.8 - - - +
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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
------------------------------------------------------------
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