Contacts of the strand formed by residues 389 - 394 (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 389 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ARG* 3.0 21.3 + - - +
83B THR* 6.0 1.3 - - + +
84B SER* 4.7 1.1 - - - -
85B VAL* 3.6 32.5 - - + +
373B LEU* 4.3 1.8 - - - -
374B LEU* 2.9 37.2 + - - +
385B VAL* 3.8 9.9 - - + -
386B PRO* 2.7 25.7 + - - +
387B GLY 3.8 1.4 + - - -
388B ASN* 1.3 79.1 + - - +
390B PRO* 1.3 77.2 - - + +
391B LEU* 3.4 2.3 + - + -
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Residues in contact with PRO 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B THR* 3.4 26.9 - - + +
84B SER* 2.8 25.5 + - - +
85B VAL 3.0 13.3 + - - -
105B ASP* 3.1 29.1 - - + +
107B LYS* 3.4 26.2 - - - +
108B MET* 3.9 21.3 - - + -
371B PHE* 4.5 2.7 - - + -
372B ARG 3.7 4.3 - - - +
388B ASN 3.9 0.4 - - - +
389B THR* 1.3 84.9 - - + +
391B LEU* 1.3 60.7 + - - +
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 3.4 16.4 - - + +
87B VAL* 3.9 20.6 - - + -
96B PHE* 3.8 49.4 - - + -
102B TYR* 5.9 0.4 - - + -
371B PHE* 3.0 9.9 - - - -
372B ARG* 2.7 46.6 + - + +
374B LEU* 4.0 28.0 - - + -
380B ILE* 4.0 11.7 - - + -
385B VAL* 4.5 3.4 - - + -
389B THR* 4.4 1.6 - - + +
390B PRO* 1.3 72.3 - - - +
392B LEU* 1.3 60.3 + - - +
393B PHE* 3.5 17.3 - - + -
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 3.8 23.8 - - + -
77B VAL* 4.4 6.7 - - + -
79B VAL* 3.8 27.4 - - + -
84B SER* 3.5 14.2 + - - +
85B VAL 2.9 11.7 + - - +
86B ILE* 3.4 31.4 - - + +
87B VAL* 2.9 29.5 + - - +
368B TRP* 3.7 30.7 - - + -
370B THR 3.6 3.6 - - - -
371B PHE* 3.8 10.5 - - + -
391B LEU* 1.3 72.5 - - - +
393B PHE* 1.3 71.2 + - - +
394B SER* 4.0 2.7 - - - -
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Residues in contact with PHE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B VAL* 4.2 22.9 - - + -
92B SER 4.0 13.9 - - - -
93B VAL* 4.2 18.6 - - + -
96B PHE* 3.4 40.2 - + + -
97B LEU* 3.9 17.3 - - + -
368B TRP* 3.8 0.7 - - - -
369B GLY* 3.2 4.3 - - - -
370B THR* 3.0 42.9 + - + +
372B ARG* 3.7 19.7 - - + -
391B LEU* 3.5 35.9 - - + -
392B LEU* 1.3 78.2 - - - +
394B SER* 1.3 60.5 + - - +
428B PHE* 4.0 18.2 - - + -
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Residues in contact with SER 394 (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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61B GLN* 2.6 27.4 + - - -
86B ILE* 4.1 3.7 - - - +
87B VAL 4.9 3.4 + - - -
88B THR* 5.5 1.0 - - - +
368B TRP* 3.3 8.2 + - - -
392B LEU* 4.0 13.4 + - - +
393B PHE* 1.3 75.4 - - - +
395B THR* 1.3 61.7 + - - +
396B TYR* 3.3 4.9 + - - +
397B VAL* 3.0 29.2 + - - +
398B MET* 3.3 26.3 + - - +
428B PHE* 3.6 5.7 - - - -
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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