Contacts of the helix formed by residues 395 - 400 (chain B) 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 THR 395 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361B LEU 5.3 1.4 + - - +
362B ARG 4.2 5.4 + - - +
365B PRO* 3.7 24.9 - - + -
367B ALA 4.0 6.7 - - - +
368B TRP 2.8 16.6 + - - +
369B GLY 4.8 0.2 - - - +
394B SER* 1.3 71.4 - - - +
396B TYR* 1.3 67.1 + - - +
398B MET* 4.1 2.5 - - - +
399B GLY* 3.1 20.8 + - - -
426B THR 4.8 0.3 - - - +
427B TYR* 3.6 11.1 - - - -
428B PHE* 2.8 65.5 + - + +
429B PRO* 4.0 4.1 - - + +
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Residues in contact with TYR 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B VAL* 4.4 2.9 - - + +
61B GLN* 3.6 33.0 - - + +
62B ASP* 2.3 37.6 + - - -
65B LEU* 5.0 3.6 - - + -
362B ARG 4.8 2.2 - - - +
363B LEU 3.8 2.7 - - - -
365B PRO* 3.8 26.9 - - + -
368B TRP* 3.5 12.7 + - + -
394B SER* 3.2 8.4 + - - +
395B THR* 1.3 85.0 - - - +
397B VAL* 1.3 66.9 + - - +
399B GLY* 3.4 1.2 + - - -
400B ARG* 3.2 58.1 + - - +
470B LEU* 3.7 25.8 - - + +
476B LEU* 3.6 18.2 - - + -
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Residues in contact with VAL 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLN* 3.7 29.4 - - - +
64B PHE* 3.9 9.6 - - + -
65B LEU* 3.6 23.0 - - - +
68B ALA* 3.8 19.7 - - + -
86B ILE* 4.0 3.8 - - + -
88B THR* 3.7 23.8 - - + -
394B SER* 3.0 30.8 + - - +
395B THR 3.4 0.2 - - - -
396B TYR* 1.3 77.9 - - + +
398B MET* 1.3 63.1 + - - +
400B ARG 3.1 11.3 + - - -
401B MET* 3.4 16.7 + - - +
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Residues in contact with MET 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B VAL 5.1 1.1 - - - +
88B THR* 3.3 42.0 - - + +
90B PRO* 3.7 17.5 - - + -
93B VAL* 3.7 13.5 - - + -
394B SER 3.3 13.0 + - - +
395B THR* 4.4 2.0 - - - +
397B VAL* 1.3 75.2 - - - +
399B GLY* 1.3 61.0 + - - +
401B MET* 3.1 17.6 + - - +
404B TYR* 3.7 24.8 - - + -
405B PHE* 3.5 14.4 - - - -
425B PHE 3.4 20.0 - - - +
426B THR* 3.5 18.4 - - - +
428B PHE* 3.6 28.0 - - - -
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Residues in contact with GLY 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ARG* 2.8 45.4 + - - -
395B THR 3.1 18.6 + - - -
396B TYR 3.9 1.3 - - - -
397B VAL 3.3 0.4 - - - -
398B MET* 1.3 76.1 - - - +
400B ARG* 1.3 62.3 + - - +
401B MET 3.4 0.2 - - - -
405B PHE* 3.5 21.0 - - - -
408B PRO* 4.0 1.7 - - - +
426B THR 4.2 1.7 + - - -
427B TYR* 6.2 0.7 - - - -
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Residues in contact with ARG 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ASP* 4.6 2.8 + - - -
65B LEU* 3.8 29.3 - - + +
69B LYS* 5.1 4.3 + - - +
362B ARG 5.2 0.2 + - - -
363B LEU* 2.7 52.1 + - + +
364B TYR* 3.8 18.8 + - - -
396B TYR* 3.2 55.0 + - - +
397B VAL 3.1 6.7 + - - +
399B GLY* 1.3 82.5 - - - +
401B MET* 1.3 59.9 + - - +
402B ASP 3.7 1.4 + - - -
408B PRO* 3.6 17.3 - - + +
409B LEU* 3.5 30.2 - - + +
470B LEU* 4.6 5.5 - - - +
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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