Contacts of the helix formed by residues 371 - 378 (chain C) in PDB entry 5MG3
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 371 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368C ILE 4.0 9.2 - - - +
369C MET 4.0 0.4 - - - -
370C TYR* 1.4 104.3 - - + +
372C LEU* 1.3 67.0 + - + +
373C THR 3.5 0.4 - - - -
374C LYS* 3.0 12.5 + - + +
375C ALA* 2.7 36.6 + - + +
279F ILE* 4.6 18.4 - - + -
282F SER* 5.5 5.4 - - - +
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Residues in contact with LEU 372 (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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368C ILE* 3.8 22.2 - - + +
369C MET* 3.4 33.7 + - + -
371C PRO* 1.3 88.5 - - + +
373C THR* 1.3 56.4 + - - +
375C ALA* 3.3 10.0 + - - +
376C GLN* 2.9 29.1 + - - +
424C PHE* 5.8 9.0 - - + +
425C PRO* 5.5 2.1 - - - +
428C ILE* 4.0 29.8 - - + -
429C GLN* 3.7 11.8 - - + +
279F ILE* 6.0 1.8 - - + -
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Residues in contact with THR 373 (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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366C ARG* 3.4 32.1 - - - +
369C MET* 2.8 26.3 + - - +
370C TYR* 5.3 0.7 - - - -
372C LEU* 1.3 69.6 - - - +
374C LYS* 1.3 65.4 + - + +
376C GLN* 3.3 4.9 + - - +
377C TYR* 3.2 20.5 + - - +
429C GLN* 2.7 25.7 + - - +
524C THR* 4.1 18.6 - - - +
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Residues in contact with LYS 374 (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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370C TYR* 2.9 40.1 + - - +
371C PRO* 3.0 9.8 + - + +
373C THR* 1.3 78.4 - - + +
375C ALA* 1.3 58.4 + - - +
377C TYR* 3.4 9.3 + - + +
378C THR* 3.0 39.9 + - + +
524C THR* 5.7 8.1 - - + +
527C GLN* 2.7 38.1 + - + +
30F SER* 5.2 5.2 - - - -
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Residues in contact with ALA 375 (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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371C PRO* 2.7 19.9 + - + +
372C LEU* 3.3 13.2 + - - +
374C LYS* 1.3 72.3 - - - +
376C GLN* 1.4 52.3 + - - +
378C THR* 3.9 7.8 + - - -
379C SER* 2.8 33.6 + - - -
425C PRO* 4.0 15.1 - - + +
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Residues in contact with GLN 376 (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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372C LEU 2.9 12.8 + - - +
373C THR 3.6 8.7 - - - +
374C LYS 3.2 0.4 - - - -
375C ALA* 1.4 75.3 - - - +
377C TYR* 1.3 62.8 + - - +
379C SER* 3.5 9.3 + - - -
380C MET* 3.5 30.0 - - - +
425C PRO* 3.3 20.5 - - - +
426C LEU* 4.5 14.0 - - + +
429C GLN* 3.9 21.7 - - + +
498C MET* 4.4 11.5 - - - +
1Y MET* 2.8 38.9 + - - +
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Residues in contact with TYR 377 (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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373C THR 3.2 10.1 + - - +
374C LYS* 3.4 12.1 + - + +
376C GLN* 1.3 75.6 - - - +
378C THR* 1.3 76.7 + - + +
379C SER 3.2 4.5 - - - -
380C MET* 3.3 24.5 + - + +
381C ALA* 3.5 12.9 + - + +
478C ILE 4.1 10.1 - - - -
479C GLN* 2.7 46.6 + - - -
480C LYS 3.3 7.4 + - - -
481C MET 3.3 24.8 + - - -
482C SER* 4.4 10.3 - - - -
483C PRO 3.8 5.9 - - - -
495C MET* 3.8 25.2 - - + +
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Residues in contact with THR 378 (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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374C LYS* 3.0 29.7 + - + +
375C ALA* 3.9 8.0 + - - -
377C TYR* 1.3 94.1 - - + +
379C SER* 1.4 53.7 + - - +
380C MET 3.4 1.8 - - - -
381C ALA* 2.8 31.1 - - + +
418C ASN* 4.8 2.9 + - - -
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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