Contacts of the helix formed by residues 42 - 52 (chain O) in PDB entry 1MVW
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 42 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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788M THR* 2.5 42.6 - - + +
789M ALA* 3.9 4.9 - - - -
792M ALA* 2.3 43.2 - - + +
41O PRO* 1.3 76.4 - - - +
43O ASN* 1.3 61.0 + - - +
44O ALA 3.9 0.5 + - - -
45O GLU* 3.0 41.4 + - - +
46O ILE* 3.1 10.7 + - - +
81O GLN* 4.5 4.0 - - - +
116O GLU* 3.7 9.4 - - - -
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Residues in contact with ASN 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795M ARG* 1.2 99.7 + - - +
31O GLY* 5.5 2.8 - - - -
32O ASP* 5.5 2.6 + - - -
35O ARG* 3.6 17.2 + - - +
42O THR* 1.3 73.4 - - - +
44O ALA* 1.3 55.2 + - - +
46O ILE* 3.3 16.9 + - - +
47O ASN* 2.9 29.4 + - - +
116O GLU* 3.2 1.2 + - - -
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Residues in contact with ALA 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788M THR* 5.0 9.2 - - + -
795M ARG* 4.5 0.6 - - - +
42O THR* 3.2 3.3 - - - +
43O ASN* 1.3 77.2 - - - +
45O GLU* 1.3 58.0 + - - +
47O ASN* 3.5 8.2 - - - +
48O LYS* 2.8 36.9 + - + +
116O GLU* 3.0 16.2 + - + +
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Residues in contact with GLU 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O ASN 5.0 0.2 - - - +
41O PRO* 3.5 22.6 - - + +
42O THR* 3.0 36.4 + - - +
44O ALA* 1.3 78.4 - - - +
46O ILE* 1.3 59.9 + - - +
47O ASN 3.2 0.4 - - - -
48O LYS* 3.9 4.6 - - - +
49O ILE* 2.8 50.1 + - + +
75O ALA* 5.0 0.3 - - - -
78O ASN* 2.9 36.0 + - - +
81O GLN* 5.2 6.1 + - - +
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Residues in contact with ILE 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O VAL* 5.0 5.8 - - + -
31O GLY* 3.7 39.9 - - - +
34O ALA* 5.7 0.4 - - + -
35O ARG* 4.7 1.3 - - - +
41O PRO* 3.4 43.1 - - + +
42O THR 3.1 10.1 + - - +
43O ASN* 3.6 22.0 - - - +
45O GLU* 1.3 76.9 - - - +
47O ASN* 1.3 52.9 + - - +
49O ILE* 4.2 6.5 - - + +
50O LEU* 2.5 56.3 + - + +
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Residues in contact with ASN 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O ASN 2.9 17.6 + - - +
44O ALA* 3.5 9.8 - - - +
46O ILE* 1.3 76.8 - - - +
48O LYS* 1.3 77.8 + - - +
50O LEU* 3.4 8.6 - - - +
51O GLY* 3.1 19.2 + - - -
57O GLU* 3.6 18.8 - - - +
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Residues in contact with LYS 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44O ALA* 2.8 21.5 + - + +
45O GLU* 3.9 7.0 - - - +
46O ILE 3.5 0.2 - - - -
47O ASN* 1.3 86.4 - - - +
49O ILE* 1.3 54.4 + - + +
51O GLY* 3.1 2.7 + - - -
52O ASN* 1.9 63.0 + - - +
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Residues in contact with ILE 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41O PRO* 6.1 0.9 - - + -
45O GLU* 2.8 41.5 + - + +
46O ILE* 4.2 7.0 - - + +
48O LYS* 1.3 77.2 - - + +
50O LEU* 1.3 55.2 - - + +
52O ASN* 2.3 14.5 - - - +
53O PRO* 1.6 48.9 - - + +
71O MET* 5.5 14.6 - - + +
74O ALA* 5.6 13.0 - - + -
75O ALA* 5.6 9.0 - - + -
78O ASN* 5.4 5.2 - - - +
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Residues in contact with LEU 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27O ALA* 4.9 14.8 - - + +
30O VAL* 5.5 7.0 - - + -
46O ILE* 2.5 42.8 - - + +
47O ASN* 3.4 5.6 - - - +
48O LYS 3.1 0.4 - - - -
49O ILE* 1.3 79.6 - - + +
51O GLY* 1.3 55.9 + - - +
53O PRO* 2.6 23.9 - - - +
55O LYS* 2.9 37.5 + - + +
57O GLU* 0.9 52.0 - - + +
71O MET* 4.6 21.1 - - + -
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Residues in contact with GLY 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O ASN 3.1 6.7 + - - -
48O LYS* 3.1 5.5 + - - -
50O LEU* 1.3 76.7 - - - +
52O ASN* 1.3 59.4 + - - +
54O SER* 2.7 24.7 + - - -
55O LYS 3.6 10.9 + - - -
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Residues in contact with ASN 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48O LYS* 1.9 68.0 + - - +
49O ILE* 2.3 14.9 - - + +
51O GLY* 1.3 73.3 - - - +
53O PRO* 1.3 64.9 - - + +
54O SER* 3.3 2.6 + - - -
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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