Contacts of the helix formed by residues 373 - 382 (chain A) in PDB entry 1MMG
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 THR 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A ASP* 2.6 33.8 + - - -
372A LYS* 1.3 74.0 - - - +
374A ALA* 1.3 63.5 + - - +
376A ASN* 3.0 17.6 + - + +
377A ALA* 3.0 14.8 + - + +
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Residues in contact with ALA 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A HIS* 3.5 25.9 - - - +
356A ASN* 3.7 26.0 - - + +
357A ILE* 3.7 12.1 - - + -
371A ASP* 5.4 1.3 + - - +
372A LYS 3.4 0.2 - - - -
373A THR* 1.3 73.9 - - - +
375A LEU* 1.3 69.5 + - - +
377A ALA* 2.9 8.5 + - - +
378A ALA* 2.8 24.8 + - - +
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A ILE* 3.9 16.3 - - + +
369A LEU* 4.0 16.8 - - + -
372A LYS* 3.4 15.5 + - + +
373A THR 3.3 0.4 - - - -
374A ALA* 1.3 79.5 - - - +
376A ASN* 1.3 73.2 + - - +
378A ALA* 3.1 2.6 + - - +
379A SER* 2.3 36.3 + - - +
386A PRO* 3.6 34.8 - - + +
389A LEU* 4.0 18.7 - - + +
390A GLU* 3.8 39.0 - - + +
393A LEU* 4.5 8.5 - - + -
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Residues in contact with ASN 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A LYS* 2.5 44.0 + - - +
373A THR* 3.3 9.2 - - + +
375A LEU* 1.3 85.4 - - - +
377A ALA* 1.3 54.5 + - - +
379A SER* 3.6 5.4 + - - -
380A THR* 2.7 39.4 + - - +
386A PRO* 4.7 8.5 - - + +
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Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A HIS* 4.5 16.8 - - + -
353A HIS* 3.5 32.1 - - + +
373A THR* 3.0 14.1 + - + +
374A ALA* 2.9 9.3 + - - +
376A ASN* 1.3 75.3 - - - +
378A ALA* 1.3 70.5 + - - +
380A THR* 3.2 6.4 + - - -
381A VAL* 3.0 24.6 + - - +
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Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A GLY 3.7 4.7 - - - +
353A HIS* 3.5 21.4 - - + +
354A LEU* 3.4 33.9 - - + +
374A ALA 2.8 16.6 + - - +
375A LEU* 3.8 3.8 - - - +
377A ALA* 1.3 77.4 - - - +
379A SER* 1.3 63.6 + - - +
381A VAL* 2.9 21.9 + - - +
382A PHE* 3.0 14.8 + - + -
389A LEU* 4.9 1.1 - - + -
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Residues in contact with SER 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A LEU* 2.3 34.9 + - - +
376A ASN* 3.6 4.7 + - - -
378A ALA* 1.3 74.0 - - - +
380A THR* 1.3 56.5 + - - +
382A PHE* 4.2 0.2 - - - -
383A GLY* 2.6 31.5 + - - -
384A VAL* 3.3 39.1 + - - +
386A PRO* 3.8 29.1 - - - +
389A LEU* 4.1 6.3 - - - +
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Residues in contact with THR 380 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A ALA 5.8 0.4 - - - +
297A HIS* 4.3 21.5 - - + -
346A LYS* 5.4 0.7 - - - +
376A ASN* 2.7 26.9 + - - +
377A ALA* 3.5 7.2 - - - +
378A ALA 3.1 0.2 - - - -
379A SER* 1.3 84.0 - - - +
381A VAL* 1.3 65.9 + - + +
383A GLY* 3.2 9.7 + - - -
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Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ALA 4.8 1.8 - - - +
296A LEU* 4.0 37.7 - - + +
297A HIS* 4.7 8.1 - - - +
346A LYS* 3.0 46.1 - - + +
347A ILE* 5.9 0.3 - - - +
349A ALA* 4.5 5.2 - - + -
350A GLY* 3.1 33.2 - - - +
353A HIS* 4.3 2.9 - - + -
377A ALA 3.0 14.8 + - - +
378A ALA* 2.9 20.6 - - - +
380A THR* 1.3 75.2 - - + +
382A PHE* 1.3 61.2 + - - +
383A GLY* 4.8 0.2 - - - -
605A ASP* 4.8 4.7 - - - +
608A VAL* 5.7 0.2 - - - +
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Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A ILE* 4.0 25.8 - - + -
350A GLY* 3.3 41.3 - - - -
351A ILE 3.4 2.9 - - - -
354A LEU* 3.7 22.4 - - + -
378A ALA* 3.0 26.8 + - + +
379A SER* 4.2 2.2 - - - -
381A VAL* 1.3 77.9 - - - +
383A GLY* 1.3 56.7 + - - +
384A VAL* 3.8 11.0 - - + -
389A LEU* 5.0 0.4 - - + -
425A LEU* 3.9 24.2 - - + -
600A PHE* 3.5 32.5 - + + -
603A SER* 2.4 27.8 + - - +
605A ASP* 3.3 13.1 - - - +
608A VAL* 4.0 16.2 - - + +
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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