Contacts of the helix formed by residues 343 - 350 (chain A) in PDB entry 3MDR
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 ASP 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A MET* 4.0 5.3 - - - +
339A LYS* 2.7 28.8 + - - -
341A TYR* 4.1 17.7 - - - -
342A LEU* 1.3 76.0 - - - +
344A PHE* 1.3 67.5 + - - +
345A GLU* 4.2 15.6 - - + +
346A ASP* 2.7 30.7 + - - +
347A LEU* 3.7 2.6 + - - +
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Residues in contact with PHE 344 (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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147A ARG* 3.6 46.2 - - - -
150A LEU* 5.6 0.4 - - + -
151A VAL* 3.9 30.3 - - + -
154A MET* 4.1 22.2 - - + +
343A ASP* 1.3 72.4 - - - +
345A GLU* 1.3 65.2 - - + +
347A LEU* 3.2 25.8 + - + +
348A GLY 4.1 1.9 + - - -
445A MET* 3.5 44.0 - - + -
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Residues in contact with GLU 345 (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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343A ASP* 3.2 14.9 - - + +
344A PHE* 1.3 84.3 - - + +
346A ASP* 1.3 69.3 + - - +
347A LEU 3.4 0.5 + - - -
348A GLY* 3.6 9.7 + - - -
349A ARG* 2.8 49.4 + - - +
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Residues in contact with ASP 346 (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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335A VAL* 3.6 22.9 - - - +
336A ILE* 3.9 21.0 - - + +
339A LYS* 2.8 25.0 + - - -
342A LEU* 3.7 8.7 - - + -
343A ASP* 2.7 38.1 + - - +
345A GLU* 1.3 83.1 - - - +
347A LEU* 1.3 61.6 + - - +
349A ARG* 3.2 23.5 + - - +
350A LEU* 3.6 15.2 + - - +
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Residues in contact with LEU 347 (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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154A MET* 3.8 23.1 - - + -
342A LEU* 4.1 17.7 - - + -
343A ASP 4.2 5.2 - - - +
344A PHE* 3.2 16.9 + - + +
346A ASP* 1.3 76.5 - - - +
348A GLY* 1.3 61.5 + - - +
350A LEU* 3.1 15.5 + - + +
445A MET* 3.8 40.6 - - + +
448A LYS* 2.8 48.0 + - + +
449A VAL* 3.8 21.3 - - + -
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Residues in contact with GLY 348 (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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344A PHE 4.1 2.6 + - - -
345A GLU 3.6 6.5 + - - -
346A ASP 3.4 0.6 - - - -
347A LEU* 1.3 79.3 - - - +
349A ARG* 1.3 61.6 + - - +
350A LEU 3.4 1.2 + - - -
351A GLN* 4.4 12.3 + - - +
448A LYS* 4.4 6.5 + - - -
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Residues in contact with ARG 349 (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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331A GLU* 4.0 3.1 - - - +
335A VAL* 3.9 34.5 + - + +
345A GLU* 2.8 49.0 + - - +
346A ASP* 3.2 14.3 + - - +
347A LEU 3.2 1.0 - - - -
348A GLY* 1.3 74.1 - - - +
350A LEU* 1.3 60.9 + - - +
351A GLN* 2.9 14.0 + - - +
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Residues in contact with LEU 350 (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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331A GLU* 3.3 28.9 - - + +
332A VAL* 4.3 18.6 - - + -
335A VAL* 3.3 25.1 - - + -
336A ILE* 4.9 2.7 - - + -
342A LEU* 4.2 13.7 - - + -
346A ASP 3.7 14.8 - - - +
347A LEU* 3.1 20.3 + - + +
348A GLY 4.4 1.3 - - - -
349A ARG* 1.3 75.5 - - - +
351A GLN* 1.3 56.1 + - - +
353A LEU* 4.1 15.3 - - + -
354A SER* 3.1 20.4 + - - -
448A LYS* 3.4 16.0 - - - +
452A ALA* 4.1 24.2 - - + -
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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