Contacts of the helix formed by residues 50 - 60 (chain A) in PDB entry 1MHO
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 GLN 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LYS* 4.0 16.2 - - - +
48A LYS 3.9 2.0 + - - -
49A GLU* 1.3 72.5 + - - +
51A GLU* 1.3 59.3 + - - +
52A VAL 3.2 0.2 + - - -
53A VAL* 3.2 15.4 + - - +
54A ASP* 2.7 57.5 + - - +
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Residues in contact with GLU 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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49A GLU* 3.1 9.1 - - + +
50A GLN* 1.3 82.3 - - - +
52A VAL* 1.3 67.5 + - + +
54A ASP* 3.7 11.7 - - - +
55A LYS* 3.1 27.4 + - - +
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Residues in contact with VAL 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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47A ILE* 3.9 28.9 - - + -
48A LYS 5.9 0.4 - - - +
49A GLU* 2.9 25.9 + - + +
51A GLU* 1.3 81.4 - - + +
53A VAL* 1.3 68.9 + - - +
55A LYS* 3.2 6.1 + - + +
56A VAL* 2.9 31.6 + - + +
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Residues in contact with VAL 53 (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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29A LYS* 3.6 38.8 - - + +
32A LEU* 5.0 6.0 - - + +
33A LYS* 4.1 28.7 - - + +
47A ILE* 3.5 27.1 - - + -
48A LYS 5.8 0.2 - - - -
49A GLU 3.6 8.7 - - - +
50A GLN* 3.2 20.6 + - - +
52A VAL* 1.3 79.7 - - - +
54A ASP* 1.3 61.6 + - - +
56A VAL* 3.4 4.9 + - - +
57A MET* 3.1 22.9 + - - +
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Residues in contact with ASP 54 (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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29A LYS* 2.7 38.6 + - - +
50A GLN* 2.7 49.4 + - - +
51A GLU* 3.7 9.2 - - - +
52A VAL 3.2 0.2 - - - -
53A VAL* 1.3 75.0 - - - +
55A LYS* 1.3 64.6 + - - +
57A MET* 3.4 3.1 + - - +
58A GLU* 3.0 23.4 + - - +
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Residues in contact with LYS 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 GLU 3.1 15.6 + - - +
52A VAL* 3.2 7.2 + - + +
54A ASP* 1.3 78.0 - - - +
56A VAL* 1.3 69.0 + - + +
58A GLU* 3.2 27.8 + - - +
59A THR* 3.0 44.3 + - - +
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Residues in contact with VAL 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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32A LEU* 3.7 22.0 - - + -
36A ILE* 4.2 15.7 - - + -
47A ILE* 4.7 9.6 - - + -
52A VAL* 2.9 32.0 + - + +
53A VAL* 3.9 4.9 - - - +
55A LYS* 1.3 77.0 - - + +
57A MET* 1.4 63.5 + - - +
59A THR* 3.2 7.5 + - - -
60A LEU* 3.0 36.5 + - + +
76A PHE* 5.2 4.7 - - + -
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Residues in contact with MET 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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27A LEU 3.5 17.3 - - - +
28A LYS 3.6 2.9 - - - +
29A LYS* 3.4 50.0 - - + +
32A LEU* 4.1 17.7 - - + +
53A VAL 3.1 17.8 + - - +
54A ASP 3.9 3.1 - - - +
56A VAL* 1.4 75.9 - - - +
58A GLU* 1.3 57.5 + - - +
60A LEU* 3.2 2.2 + - - -
61A ASP* 2.9 34.7 + - + +
66A GLY* 3.7 27.1 - - - +
67A GLU 3.8 17.5 - - - +
68A CYS* 3.8 10.3 - - - +
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Residues in contact with GLU 58 (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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54A ASP 3.0 14.4 + - - +
55A LYS* 3.2 35.2 + - - +
57A MET* 1.3 77.3 - - - +
59A THR* 1.3 65.4 + - - +
61A ASP* 3.7 15.6 + - - +
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Residues in contact with THR 59 (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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55A LYS* 3.0 32.0 + - - +
56A VAL* 3.4 11.9 - - - -
58A GLU* 1.3 82.7 - - - +
60A LEU* 1.3 73.3 + - + +
61A ASP 4.8 1.2 - - - -
62A SER* 5.1 2.1 + - - -
79A MET* 4.3 19.6 - - + +
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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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32A LEU* 4.3 16.8 - - + -
56A VAL* 3.0 32.7 + - + +
57A MET* 3.2 4.2 + - - +
59A THR* 1.3 85.3 - - + +
61A ASP* 1.4 60.5 + - - +
62A SER* 3.0 13.0 + - - -
68A CYS* 4.4 20.2 - - + -
72A GLU* 3.4 23.6 - - - +
75A ALA* 5.7 1.1 - - + +
76A PHE* 3.8 52.9 - - + +
79A MET* 4.2 18.4 - - + -
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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