Contacts of the helix formed by residues 365 - 380 (chain C) in PDB entry 1MFQ
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 GLU 365 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364C ASN* 1.3 76.8 - - - +
366C GLN* 1.3 62.5 + - - +
367C GLU* 4.2 0.2 + - - -
368C SER* 2.7 31.2 + - - -
369C MET* 3.2 22.2 + - + +
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Residues in contact with GLN 366 (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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365C GLU* 1.3 75.1 - - - +
367C GLU* 1.3 79.6 + - - +
368C SER 2.9 10.8 + - - -
369C MET* 3.1 23.5 + - + +
370C ALA* 3.5 8.0 + - - +
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Residues in contact with GLU 367 (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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364C ASN* 3.7 36.5 + - + +
365C GLU 3.4 0.8 + - - -
366C GLN* 1.3 98.5 + - - +
368C SER* 1.3 56.2 + - - +
370C ALA* 4.6 6.4 - - - +
371C ARG* 3.1 35.5 + - - +
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Residues in contact with SER 368 (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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355C PHE 4.0 20.0 - - - -
364C ASN* 3.2 17.1 + - - -
365C GLU* 2.7 16.7 + - - -
366C GLN 2.9 0.4 - - - -
367C GLU* 1.3 78.2 - - - +
369C MET* 1.3 89.2 + - - +
370C ALA 3.1 1.8 - - - -
371C ARG* 2.7 22.8 + - - +
372C LEU* 2.8 22.7 + - - +
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Residues in contact with MET 369 (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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365C GLU* 3.5 24.5 - - + +
366C GLN* 3.1 14.3 + - + +
368C SER* 1.3 96.1 + - - +
370C ALA* 1.3 50.2 + - - +
372C LEU* 2.9 20.3 + - + +
373C LYS* 2.6 42.3 + - - +
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Residues in contact with ALA 370 (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 GLN 3.5 9.3 + - - +
367C GLU* 4.8 7.0 - - - +
368C SER 3.1 0.4 - - - -
369C MET* 1.3 76.6 - - - +
371C ARG* 1.3 56.3 + - + +
373C LYS* 2.7 10.7 + - - +
374C LYS* 2.6 37.3 + - - +
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Residues in contact with ARG 371 (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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354C GLY 6.0 2.5 - - - +
355C PHE 4.9 15.3 - - - +
367C GLU* 3.1 27.5 + - - +
368C SER* 2.7 16.7 + - - +
370C ALA* 1.3 73.5 - - + +
372C LEU* 1.3 61.6 + - + +
374C LYS* 3.9 8.4 - - - +
375C LEU* 3.1 34.0 + - + +
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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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345C PHE* 6.4 1.6 - - + -
349C LEU* 5.6 13.7 - - + -
354C GLY 5.9 1.3 - - - +
355C PHE* 5.4 10.8 - - - +
368C SER* 2.8 38.0 + - - +
369C MET* 3.3 23.1 - - + +
371C ARG* 1.3 83.3 - - + +
373C LYS* 1.3 61.9 + - - +
375C LEU* 3.7 14.2 + - + +
376C MET* 2.9 34.4 + - + +
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Residues in contact with LYS 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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194A G 6.1 2.7 - - - +
369C MET* 2.6 22.4 + - - +
370C ALA* 2.7 7.1 + - - +
372C LEU* 1.3 70.9 - - - +
374C LYS* 1.3 67.8 + - - +
376C MET* 3.1 12.2 + - + +
377C THR* 2.9 38.5 + - + +
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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 ALA 2.6 21.2 + - - +
371C ARG* 3.9 8.5 - - - +
373C LYS* 1.3 70.4 - - - +
375C LEU* 1.3 62.0 + - + +
377C THR* 2.6 40.1 + - - +
378C ILE* 3.0 15.4 + - + +
412C VAL* 3.6 26.0 - - + +
416C ASP* 3.1 31.3 + - - -
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Residues in contact with LEU 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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354C GLY 5.6 3.6 - - - +
371C ARG* 3.1 20.7 + - + +
372C LEU* 3.8 16.8 - - + +
373C LYS 3.4 0.2 - - - -
374C LYS* 1.3 81.9 - - + +
376C MET* 1.3 62.6 + - + +
378C ILE* 3.7 6.0 - - + +
379C MET* 3.3 16.5 + - + +
416C ASP 5.5 1.1 - - - +
420C LEU* 3.2 60.6 - - + +
423C GLN* 4.0 22.4 - - + +
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Residues in contact with MET 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 24.4 + - + +
373C LYS* 3.1 15.0 + - + +
374C LYS 2.7 5.5 + - - -
375C LEU* 1.3 73.6 - - + +
377C THR* 1.3 61.1 + - + +
379C MET* 2.9 15.1 + - - +
380C ASP* 2.8 35.9 + - - +
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Residues in contact with THR 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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193A G 3.1 34.0 + - - +
194A G 4.2 32.3 + - - +
373C LYS* 2.9 27.2 + - + +
374C LYS* 2.6 33.4 + - - +
376C MET* 1.3 72.1 - - + +
378C ILE* 1.3 58.3 + - - +
380C ASP* 2.7 39.4 + - - +
410C SER* 4.4 1.8 + - - -
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Residues in contact with ILE 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 24.0 + - + +
375C LEU* 3.7 4.7 - - + +
377C THR* 1.3 78.8 + - - +
379C MET* 1.3 58.7 + - - +
381C SER* 3.0 24.6 + - - -
382C MET* 3.8 5.7 + - + -
406C VAL* 3.7 25.4 - - + +
410C SER* 3.9 8.5 - - - +
412C VAL* 4.0 34.1 - - + -
416C ASP* 4.1 8.1 - - + +
417C VAL* 4.1 28.9 - - + +
420C LEU* 3.5 30.1 - - + -
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Residues in contact with MET 379 (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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375C LEU* 3.3 16.4 - - + +
376C MET* 2.9 13.9 + - - +
378C ILE* 1.3 70.7 - - - +
380C ASP* 1.3 59.7 + - - +
381C SER 2.7 11.6 + - - -
382C MET* 2.9 44.7 + - + +
387C LEU* 4.5 21.7 - - + +
420C LEU* 4.0 25.4 - - + -
424C TYR* 5.5 12.3 - - + -
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Residues in contact with ASP 380 (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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192A A 3.2 42.0 + - - +
193A G 3.9 12.5 + - - +
208A A 3.4 15.1 + - - +
376C MET* 2.8 21.9 + - - +
377C THR* 2.7 37.4 + - - +
379C MET* 1.3 77.5 - - - +
381C SER* 1.3 57.1 + - - +
382C MET 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