Contacts of the helix formed by residues 59 - 72 (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 VAL 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ARG* 1.3 75.0 - - - +
60A LEU* 1.3 66.6 + - - +
61A GLN* 4.1 12.1 - - + +
62A ASP* 3.0 41.6 + - - +
63A VAL* 3.6 8.7 + - - +
396A TYR* 4.2 8.3 - - + +
470A LEU* 3.9 20.2 - - + +
471A GLN* 3.7 14.8 - - - +
472A GLU* 3.6 36.6 - - + +
476A LEU* 4.7 8.3 - - + -
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Residues in contact with LEU 60 (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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59A VAL* 1.3 74.2 - - - +
61A GLN* 1.3 62.7 + - - +
63A VAL* 3.0 31.4 + - + +
64A PHE* 3.1 44.9 + - + -
67A TRP* 6.2 0.4 - - + -
78A ASN 4.5 9.6 - - - +
79A VAL* 4.6 13.9 - - + -
80A PHE* 5.1 6.5 - - + +
227A ASN* 5.0 14.8 - - - +
472A GLU* 4.3 14.4 + - - +
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Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 3.2 8.1 - - + +
60A LEU* 1.3 78.7 - - - +
62A ASP* 1.3 56.4 + - - +
64A PHE* 3.1 30.6 + - - +
65A LEU* 2.9 28.4 + - - +
368A TRP* 3.1 61.9 - - + +
392A LEU* 4.8 0.2 - - - +
394A SER* 2.5 32.7 + - - -
396A TYR* 3.5 22.4 - - + +
397A VAL* 3.7 6.6 - - - +
472A GLU* 4.5 7.0 + - - +
476A LEU* 4.6 5.4 - - + -
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Residues in contact with ASP 62 (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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58A ARG* 2.7 44.5 + - - +
59A VAL* 3.0 35.4 + - - +
61A GLN* 1.3 76.9 - - - +
63A VAL* 1.3 60.6 + - - +
65A LEU* 3.4 15.9 + - + +
66A ASP* 3.2 20.8 + - - +
396A TYR* 2.4 28.6 + - - -
400A ARG* 4.5 5.4 + - - -
470A LEU* 6.0 0.2 - - - +
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Residues in contact with VAL 63 (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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58A ARG* 4.6 13.0 - - + +
59A VAL 3.6 10.3 + - - +
60A LEU* 3.0 24.5 + - + +
62A ASP* 1.3 73.8 - - - +
64A PHE* 1.3 68.7 + - + +
66A ASP* 3.3 10.0 + - - +
67A TRP* 3.1 61.6 + - + +
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Residues in contact with PHE 64 (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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60A LEU* 3.1 38.3 + - + -
61A GLN* 3.4 35.7 - - - +
63A VAL* 1.3 81.8 - - + +
65A LEU* 1.3 56.0 + - - +
67A TRP* 3.3 17.1 + + - +
68A ALA* 2.9 28.2 + - - +
77A VAL* 3.6 37.7 - - + -
78A ASN 3.7 21.5 - - - -
79A VAL* 3.9 11.2 - - + -
86A ILE* 4.3 17.2 - - + +
392A LEU* 3.9 21.1 - - + -
397A VAL* 4.0 13.1 - - + +
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Residues in contact with LEU 65 (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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58A ARG* 5.9 0.7 - - - +
61A GLN 2.9 12.4 + - - +
62A ASP* 3.4 20.6 - - + +
64A PHE* 1.3 73.8 - - - +
66A ASP* 1.3 70.5 + - - +
68A ALA* 3.2 1.2 + - - +
69A LYS* 2.9 40.4 + - + +
396A TYR* 5.1 1.1 - - + -
397A VAL* 3.5 39.2 - - + +
400A ARG* 3.8 34.1 - - + +
401A MET* 3.7 17.7 - - + -
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Residues in contact with ASP 66 (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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58A ARG* 2.8 33.4 + - - -
62A ASP 3.2 10.6 + - - +
63A VAL* 3.6 10.0 - - + +
65A LEU* 1.3 83.9 - - - +
67A TRP* 1.3 65.9 + - + +
69A LYS* 3.3 11.2 + - - +
70A LYS* 2.8 32.0 + - - +
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Residues in contact with TRP 67 (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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60A LEU* 6.2 0.9 - - + -
63A VAL* 3.1 38.6 + - + +
64A PHE* 3.9 16.8 - + - +
66A ASP* 1.3 81.2 - - + +
68A ALA* 1.3 59.6 + - - +
70A LYS* 5.6 2.7 - - + -
71A TYR* 2.8 65.9 + + + +
72A GLY 3.7 0.5 + - - -
75A VAL* 3.8 13.4 - - + +
76A ARG 5.0 2.0 - - - -
77A VAL* 3.8 37.7 - - + -
78A ASN 5.3 1.8 - - - -
86A ILE* 6.1 0.7 - - + -
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Residues in contact with ALA 68 (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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64A PHE 2.9 17.8 + - - +
65A LEU 3.6 5.2 - - - +
67A TRP* 1.3 73.9 - - - +
69A LYS* 1.3 64.2 + - - +
72A GLY* 3.1 32.2 + - - +
75A VAL* 4.6 4.0 - - - +
86A ILE* 5.5 4.4 - - + +
88A THR* 3.9 20.0 - - + +
397A VAL* 3.7 23.6 - - + -
401A MET* 4.1 13.0 - - - +
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Residues in contact with LYS 69 (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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65A LEU* 2.9 46.0 + - + +
66A ASP* 3.6 10.5 - - - +
68A ALA* 1.3 80.1 - - - +
70A LYS* 1.3 60.1 + - - +
72A GLY* 4.5 1.7 + - - -
400A ARG 4.9 4.6 + - - +
401A MET* 4.3 16.6 - - + -
402A ASP* 4.2 26.8 + - - +
403A THR* 6.1 0.7 - - - +
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Residues in contact with LYS 70 (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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66A ASP 2.8 20.2 + - - +
67A TRP* 5.6 2.2 - - + -
69A LYS* 1.3 76.0 - - - +
71A TYR* 1.3 104.7 + - + +
72A GLY 3.7 0.2 - - - -
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Residues in contact with TYR 71 (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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67A TRP* 2.8 57.3 + + + +
70A LYS* 1.3 115.5 - - + +
72A GLY* 1.3 60.7 + - - +
73A PRO* 4.7 0.5 - - - +
74A VAL 4.2 5.2 - - - +
75A VAL* 3.8 20.2 - - + +
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Residues in contact with GLY 72 (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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68A ALA* 3.1 26.9 + - - +
69A LYS 4.5 1.5 + - - -
70A LYS 3.7 1.4 - - - -
71A TYR* 1.3 78.9 - - - +
73A PRO* 1.3 72.8 - - - +
74A VAL 3.3 4.6 + - - -
75A VAL* 3.5 11.8 - - - +
86A ILE 5.3 0.2 - - - +
88A THR* 3.9 2.2 + - - -
401A MET* 6.3 0.7 - - - -
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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