Contacts of the helix formed by residues 372 - 376 (chain A) in PDB entry 3MY0
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 372 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A ASP* 2.5 31.0 + - - -
332A LYS* 3.1 34.4 + - + +
370A VAL 3.7 1.0 + - - -
371A GLY* 1.3 69.4 - - - -
373A LYS* 1.3 69.9 + - - +
374A ARG* 4.1 11.4 - - + +
375A TYR* 3.1 29.6 + - + +
376A MET* 3.3 9.5 + - - +
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Residues in contact with LYS 373 (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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370A VAL* 5.0 11.6 - - + +
371A GLY 3.2 4.0 + - - +
372A THR* 1.3 75.7 - - - +
374A ARG* 1.3 63.3 + - - +
375A TYR 2.9 1.8 + - - -
376A MET* 3.0 37.5 + - + +
432A ASP 5.7 1.1 - - - -
433A PRO* 3.3 29.2 - - + +
434A SER* 4.5 4.0 - - - +
435A PHE* 4.1 23.3 - - + +
438A MET* 3.6 21.5 - - + +
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Residues in contact with ARG 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A THR* 3.3 6.2 - - + +
373A LYS* 1.3 77.8 - - - +
375A TYR* 1.3 79.6 + - + +
376A MET 5.0 0.3 - - - +
399A TRP* 5.4 0.3 + - - -
403A LEU* 3.9 12.5 - - - +
423A PRO* 3.7 33.8 - - - +
424A PRO* 3.0 37.0 + - + +
425A PHE* 4.0 8.7 - - + -
426A TYR* 4.4 1.8 - - - +
429A VAL* 3.8 16.8 + - - +
430A PRO 3.7 8.7 + - - -
431A ASN* 2.8 31.9 + - - +
433A PRO* 3.8 16.0 - - + +
438A MET* 3.5 25.2 - - - +
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Residues in contact with TYR 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A TYR* 5.9 0.2 - - - -
330A ASP* 5.6 1.3 - - - +
331A PHE 3.6 22.7 - - - +
332A LYS* 3.5 33.4 - - + +
333A SER* 3.2 12.5 + - - -
334A ARG 5.3 0.2 + - - -
372A THR* 3.1 21.4 + - + +
373A LYS 3.0 1.4 - - - -
374A ARG* 1.3 102.0 - - + +
376A MET* 1.3 63.0 + - - +
377A ALA 3.5 0.9 + - - -
396A THR 4.9 1.7 - - - +
399A TRP* 3.4 17.4 - - - -
400A ALA* 4.1 17.2 - - + +
403A LEU* 4.2 21.3 - - + -
404A VAL* 4.2 6.7 - - + -
407A GLU* 2.5 32.2 + - - -
421A TYR* 5.0 0.7 + - - -
423A PRO* 5.8 0.3 - - - +
424A PRO* 4.0 9.3 - - + +
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Residues in contact with MET 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A VAL* 3.8 24.9 - - + -
371A GLY* 3.2 27.6 - - - +
372A THR 3.3 14.4 - - - +
373A LYS* 3.0 24.2 + - + +
374A ARG 3.5 1.2 - - - +
375A TYR* 1.3 78.5 - - - +
377A ALA* 1.3 64.5 + - - +
378A PRO* 4.6 0.2 - - - +
380A VAL* 3.8 25.6 - - + -
381A LEU* 3.4 24.3 - - + +
399A TRP* 3.6 7.5 + - - -
435A PHE* 3.6 35.4 - - + -
438A MET* 5.1 1.2 - - - +
442A VAL* 4.7 4.0 - - - +
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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