Contacts of the helix formed by residues 75 - 84 (chain A) in PDB entry 1MBE
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 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TRP* 3.7 33.4 - - + +
64A LYS* 3.1 36.6 - - + +
67A ALA* 3.5 11.7 - - + +
74A THR* 1.3 77.7 - - - +
76A VAL* 1.3 73.2 + - - +
78A CYS* 3.8 2.9 - - - +
79A GLN* 2.8 35.0 + - - +
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Residues in contact with VAL 76 (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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74A THR* 3.1 8.7 - - - +
75A ASP* 1.3 93.3 - - - +
77A GLN* 1.3 59.5 + - + +
79A GLN* 3.8 7.7 - - - +
80A HIS* 2.9 63.8 + - + +
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Residues in contact with GLN 77 (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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41A THR* 3.5 25.9 - - - +
43A TRP* 3.9 14.2 + - + +
72A ASN 2.8 26.2 + - - +
73A ARG* 2.9 37.7 + - - +
74A THR* 3.0 30.1 + - - +
76A VAL* 1.3 79.8 - - + +
78A CYS* 1.3 55.8 + - - +
80A HIS* 3.9 3.8 - - - +
81A ARG* 2.8 34.1 + - - +
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Residues in contact with CYS 78 (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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43A TRP* 4.4 5.4 - - - -
51A LEU* 3.8 27.3 - - + +
63A TRP* 3.7 19.9 - - + +
66A ILE* 4.2 7.9 - - + -
67A ALA* 4.3 6.1 - - - -
70A LEU* 4.1 11.2 - - - -
73A ARG* 3.4 28.5 - - - -
74A THR 2.9 19.5 + - - +
75A ASP* 3.8 5.2 - - - +
77A GLN* 1.3 77.0 - - - +
79A GLN* 1.3 61.7 + - - +
82A TRP* 3.0 25.6 + - - +
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Residues in contact with GLN 79 (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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63A TRP* 3.4 32.5 - - + +
75A ASP* 2.8 25.0 + - - +
76A VAL* 3.8 7.2 - - - +
78A CYS* 1.3 72.6 - - - +
80A HIS* 1.3 66.2 + - + +
82A TRP 3.1 1.2 + - - -
83A GLN* 2.8 66.3 + - + +
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Residues in contact with HIS 80 (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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76A VAL* 2.9 45.7 + - + +
77A GLN* 3.9 3.8 - - - +
79A GLN* 1.3 83.4 + - + +
81A ARG* 1.3 65.2 + - - +
83A GLN* 5.4 0.4 - - - -
84A LYS* 2.8 57.6 + - + +
85A VAL* 3.7 1.5 + - - +
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Residues in contact with ARG 81 (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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43A TRP* 3.5 58.0 + - + +
44A THR 5.1 0.2 - - - -
48A ASP* 2.7 42.5 + - - +
51A LEU* 3.8 11.9 - - + -
77A GLN 2.8 23.3 + - - +
78A CYS 3.8 3.6 - - - +
80A HIS* 1.3 72.9 - - - +
82A TRP* 1.3 56.6 + - - +
85A VAL* 3.2 44.3 - - - +
86A LEU* 3.2 16.6 - - + +
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Residues in contact with TRP 82 (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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48A ASP 5.0 1.6 - - - -
51A LEU* 4.2 16.6 - - + -
52A LYS* 3.6 49.6 - - + -
55A VAL* 3.9 23.2 - - + +
56A GLU* 5.4 3.8 - - + -
60A THR* 4.0 12.8 - - + +
63A TRP* 3.6 25.1 - + + -
78A CYS 3.0 17.8 + - - +
80A HIS 3.0 0.8 + - - -
81A ARG* 1.3 73.2 - - - +
83A GLN* 1.3 66.8 + - + +
84A LYS 3.1 1.3 - - - -
85A VAL 2.8 6.8 + - - -
86A LEU* 2.7 77.7 + - + +
87A ASN* 4.5 9.8 + - - +
88A PRO* 4.0 21.7 - - + +
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Residues in contact with GLN 83 (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 THR* 4.9 10.0 - - + +
63A TRP* 3.0 27.5 + - + -
79A GLN* 2.8 48.8 + - + +
80A HIS* 5.4 0.2 - - - -
82A TRP* 1.3 83.4 - - + +
84A LYS* 1.3 58.1 + - - +
85A VAL 3.7 0.2 + - - -
87A ASN* 4.2 22.3 - - - +
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Residues in contact with LYS 84 (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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80A HIS* 2.8 46.4 + - + +
83A GLN* 1.3 78.0 - - - +
85A VAL* 1.3 65.8 + - + +
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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