Contacts of the helix formed by residues 45 - 58 (chain A) in PDB entry 1MBF
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 ARG 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A THR* 1.3 74.2 + - - +
46A GLU* 1.3 56.7 + - - +
48A ASP* 2.7 43.3 + - - +
49A GLU* 2.9 32.9 + - - +
81A ARG* 4.3 5.3 - - - +
86A LEU* 5.0 11.9 - - - +
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Residues in contact with GLU 46 (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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44A THR* 3.1 14.2 + - + +
45A ARG* 1.3 79.4 - - - +
47A GLU* 1.3 57.5 + - - +
49A GLU* 3.5 4.7 + - - +
50A LYS* 3.0 31.3 + - + +
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Residues in contact with GLU 47 (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* 3.3 29.8 - - + -
44A THR* 3.0 21.9 + - + +
46A GLU* 1.3 77.0 - - - +
48A ASP* 1.3 61.1 + - - +
50A LYS* 3.5 19.4 + - - +
51A LEU* 2.8 33.1 + - - +
70A LEU* 3.6 18.6 - - + +
71A PRO* 5.1 3.0 - - - +
73A ARG* 2.7 39.4 + - - +
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Residues in contact with ASP 48 (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* 3.3 12.0 - - - +
44A THR 2.9 15.8 + - - +
45A ARG* 2.7 49.5 + - - +
47A GLU* 1.3 76.0 - - - +
49A GLU* 1.3 57.8 + - - +
51A LEU* 3.3 5.7 + - - +
52A LYS* 2.9 31.1 + - - +
81A ARG* 2.7 44.9 + - - +
86A LEU* 5.6 11.7 - - + +
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Residues in contact with GLU 49 (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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45A ARG 2.9 17.0 + - - +
46A GLU* 3.8 5.8 - - - +
48A ASP* 1.3 75.8 - - - +
50A LYS* 1.3 63.9 + - - +
52A LYS* 2.6 32.6 + - - +
53A LYS* 2.9 26.3 + - + +
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Residues in contact with LYS 50 (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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46A GLU* 3.0 22.1 + - + +
47A GLU* 3.5 24.5 + - - +
49A GLU* 1.3 76.5 - - - +
51A LEU* 1.3 62.4 + - - +
53A LYS* 3.4 7.0 + - - +
54A LEU* 3.1 41.8 + - + +
69A TYR* 2.8 28.4 + - - -
70A LEU* 3.8 18.2 - - + +
71A PRO* 4.1 6.7 - - - +
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Residues in contact with LEU 51 (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* 3.9 10.3 - - + -
47A GLU 2.8 20.6 + - - +
48A ASP* 3.3 4.7 + - - +
50A LYS* 1.3 70.4 - - - +
52A LYS* 1.3 67.0 + - - +
54A LEU* 3.1 3.0 + - - +
55A VAL* 2.8 37.8 + - + +
63A TRP* 4.3 0.9 - - + -
66A ILE* 3.9 14.8 - - + -
70A LEU* 3.5 31.6 - - + +
78A CYS* 3.8 21.3 - - + +
81A ARG* 3.1 47.8 - - + +
82A TRP* 4.7 5.6 - - + -
86A LEU* 5.5 0.7 - - + -
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Residues in contact with LYS 52 (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 2.9 15.2 + - - +
49A GLU* 2.6 41.8 + - - +
51A LEU* 1.3 75.4 - - - +
53A LYS* 1.3 67.1 + - + +
55A VAL* 3.3 0.5 + - - +
56A GLU* 2.9 63.4 + - - +
82A TRP* 3.7 27.3 - - + -
86A LEU* 5.5 5.6 - - + -
88A PRO* 5.5 1.3 - - + -
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLU* 2.9 18.6 + - + +
50A LYS* 3.6 7.9 - - - +
51A LEU 3.2 0.2 - - - -
52A LYS* 1.3 83.4 - - + +
54A LEU* 1.3 63.0 + - + +
56A GLU* 3.8 3.1 - - - +
57A GLN* 2.8 61.9 + - + +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A LYS* 3.1 37.1 + - + +
51A LEU* 3.7 3.6 - - - +
53A LYS* 1.3 79.8 - - + +
55A VAL* 1.3 58.4 + - - +
57A GLN* 4.2 10.5 - - - +
58A ASN* 2.9 52.7 + - - +
66A ILE* 4.8 9.8 - - + +
69A TYR* 3.8 28.5 - - + -
70A LEU* 3.6 29.4 - - + -
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Residues in contact with VAL 55 (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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51A LEU* 2.8 37.2 + - + +
52A LYS 3.7 4.0 - - - +
54A LEU* 1.3 72.4 - - - +
56A GLU* 1.3 57.6 + - + +
59A GLY* 2.7 40.1 + - - -
60A THR* 3.3 29.2 + - + +
63A TRP* 3.5 30.7 - - + -
66A ILE* 4.3 6.7 - - + -
82A TRP* 3.6 31.2 - - + +
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Residues in contact with GLU 56 (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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52A LYS* 2.9 49.2 + - - +
53A LYS* 3.9 3.2 - - - +
55A VAL* 1.3 74.2 - - - +
57A GLN* 1.3 66.0 + - - +
58A ASN 4.6 0.2 - - - -
59A GLY* 4.2 3.3 + - - -
82A TRP* 3.7 11.8 - - + -
88A PRO* 3.4 26.5 - - + +
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Residues in contact with GLN 57 (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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53A LYS* 2.8 54.5 + - + +
54A LEU* 3.7 10.0 - - - +
56A GLU* 1.3 80.6 - - - +
58A ASN* 1.3 77.9 + - - +
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Residues in contact with ASN 58 (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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54A LEU* 2.9 45.1 + - - +
56A GLU 4.6 0.2 - - - -
57A GLN* 1.3 97.2 + - - +
59A GLY* 1.3 63.6 + - - +
61A ASP* 5.7 2.0 - - - +
65A VAL* 5.9 2.8 - - + +
66A ILE* 5.5 5.8 - - + +
69A TYR* 4.2 22.8 + - + -
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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