Contacts of the helix formed by residues 374 - 378 (chain A) in PDB entry 3MDY
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 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A ARG* 2.7 20.4 + - - +
332A ASP* 2.7 14.4 + - - +
333A LEU 5.6 0.4 - - - -
334A LYS* 3.2 33.7 + - + +
373A GLY* 1.3 70.9 - - - -
375A LYS* 1.3 69.4 + - - +
376A ARG* 4.3 8.3 - - + +
377A TYR* 3.0 32.4 + - + +
378A MET* 3.4 11.7 + - - +
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Residues in contact with LYS 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLY 3.8 3.3 + - - +
374A THR* 1.3 73.7 - - - +
376A ARG* 1.3 62.7 + - - +
378A MET* 3.1 31.8 + - + +
383A LEU* 4.0 2.5 - - + +
434A ASP* 4.4 11.5 + - - -
435A PRO* 3.5 27.7 + - + +
436A SER* 4.1 2.9 - - - +
437A TYR* 3.8 57.2 - - + +
440A MET* 3.6 21.8 - - + +
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Residues in contact with ARG 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A THR* 3.2 7.0 + - + +
375A LYS* 1.3 77.7 - - - +
377A TYR* 1.3 73.2 + - + +
378A MET 3.8 0.9 + - - +
401A TYR* 4.9 0.2 + - - -
405A LEU* 3.9 5.0 - - - +
425A LEU* 4.0 33.0 - - - +
426A PRO* 2.7 53.0 + - + +
427A TYR* 3.9 17.9 - - + -
428A HIS* 3.8 16.4 - - - +
431A VAL* 4.0 7.3 + - - +
432A PRO 3.8 2.8 + - - -
433A SER* 3.8 18.6 - - - +
434A ASP 4.1 1.6 - - - +
435A PRO* 3.6 35.5 - - + +
440A MET* 3.5 24.8 - - + +
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Residues in contact with TYR 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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333A LEU 3.6 20.9 - - - +
334A LYS* 3.4 34.3 - - + +
335A SER* 3.1 15.9 + - - -
374A THR* 3.0 20.9 + - + +
376A ARG* 1.3 97.6 - - + +
378A MET* 1.3 62.3 + - - +
401A TYR* 3.4 9.4 - - - -
402A SER* 2.6 38.0 + - - +
405A LEU* 3.7 20.0 - - + -
406A ILE* 3.9 8.5 - - + -
409A GLU* 2.5 33.6 + - - -
425A LEU* 3.6 11.0 - - + +
426A PRO* 3.9 12.1 - - + -
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Residues in contact with MET 378 (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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371A ARG* 4.2 1.1 - - + -
372A VAL 3.4 37.9 - - - +
373A GLY 3.7 15.5 - - - +
374A THR 3.5 10.3 - - - +
375A LYS* 3.1 24.0 + - + +
376A ARG 3.5 1.4 - - - +
377A TYR* 1.3 76.8 - - - +
379A PRO* 1.3 70.4 - - + +
382A VAL* 3.8 21.1 - - + -
383A LEU* 3.5 30.8 - - + +
401A TYR* 3.4 11.0 + - - -
437A TYR* 3.7 39.3 - - + +
440A MET* 5.3 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