Contacts of the helix formed by residues 42 - 52 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788G THR* 2.3 47.1 - - + +
789G ALA* 3.5 8.5 - - - -
792G ALA* 2.0 52.6 - - + +
41I PRO* 1.3 72.8 - - - +
43I ASN* 1.3 58.8 + - - +
44I ALA 3.9 0.2 + - - -
45I GLU* 3.0 41.6 + - - +
46I ILE* 3.1 11.4 + - - +
81I GLN* 4.5 2.9 - - - +
116I GLU* 3.7 6.7 - - - -
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Residues in contact with ASN 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795G ARG* 1.4 91.2 - - - +
31I GLY* 5.5 3.0 - - - -
32I ASP* 5.5 2.8 + - - -
35I ARG* 3.6 20.1 + - - +
42I THR* 1.3 72.7 - - - +
44I ALA* 1.3 56.4 + - - +
46I ILE* 3.3 17.4 + - - +
47I ASN* 2.9 29.0 + - - +
116I GLU* 3.2 2.2 + - - -
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Residues in contact with ALA 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788G THR* 4.6 12.6 - - + +
795G ARG* 3.4 2.9 - - - +
42I THR* 3.2 3.3 - - - +
43I ASN* 1.3 77.9 - - - +
45I GLU* 1.3 58.6 + - - +
46I ILE 3.3 0.2 - - - -
47I ASN* 3.4 7.8 + - - +
48I LYS* 2.8 36.7 + - + +
116I GLU* 3.0 16.6 + - + +
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Residues in contact with GLU 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788G THR* 5.5 1.5 - - + +
41I PRO* 3.5 22.2 - - + +
42I THR* 3.0 36.6 + - - +
44I ALA* 1.3 78.8 - - - +
46I ILE* 1.3 59.4 + - - +
47I ASN 3.2 0.4 - - - -
48I LYS* 3.9 4.4 - - - +
49I ILE* 2.8 51.1 + - + +
75I ALA* 5.0 0.3 - - - -
78I ASN* 2.9 37.2 + - - +
81I GLN* 5.2 6.4 + - - +
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Residues in contact with ILE 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I ALA 5.9 0.7 - - - +
30I VAL* 5.0 6.1 - - + -
31I GLY* 3.7 40.4 - - - +
35I ARG* 4.7 1.3 - - - +
41I PRO* 3.4 43.3 - - + +
42I THR 3.1 10.5 + - - +
43I ASN* 3.3 22.0 + - - +
45I GLU* 1.3 76.5 - - - +
47I ASN* 1.3 53.7 + - - +
49I ILE* 4.2 6.5 - - + +
50I LEU* 2.5 53.4 + - + +
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Residues in contact with ASN 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I ASN 2.9 16.9 + - - +
44I ALA* 3.5 10.5 - - - +
46I ILE* 1.3 77.2 - - - +
48I LYS* 1.3 77.8 + - - +
50I LEU* 3.4 8.9 - - - +
51I GLY* 3.1 19.2 + - - -
57I GLU* 3.6 18.7 - - - +
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Residues in contact with LYS 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I ALA* 2.8 21.2 + - + +
45I GLU* 3.9 7.0 - - - +
47I ASN* 1.3 88.1 - - - +
49I ILE* 1.3 54.7 - - + +
51I GLY* 3.1 2.5 + - - +
52I ASN* 1.9 62.6 + - - +
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Residues in contact with ILE 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I PRO* 6.1 1.1 - - + -
45I GLU* 2.8 41.5 + - + +
46I ILE* 4.2 7.6 - - + +
48I LYS* 1.3 78.2 - - + +
50I LEU* 1.3 55.7 - - + +
52I ASN* 2.3 14.8 - - - +
53I PRO* 1.6 48.6 - - + +
71I MET* 5.5 16.2 - - + +
74I ALA* 5.6 13.2 - - + -
75I ALA* 5.6 9.0 - - + -
78I ASN* 5.4 4.9 - - - +
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Residues in contact with LEU 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I ALA* 4.9 14.8 - - + +
30I VAL* 5.5 6.3 - - + -
46I ILE* 2.5 42.4 - - + +
47I ASN* 3.4 5.4 - - - +
49I ILE* 1.3 79.3 - - + +
51I GLY* 1.3 56.1 + - - +
53I PRO* 2.6 23.3 - - + +
55I LYS* 2.9 38.1 + - + +
57I GLU* 0.9 52.5 - - + +
63I ILE* 6.4 0.9 - - + -
71I MET* 4.6 21.8 - - + -
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Residues in contact with GLY 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I ASN 3.1 7.7 + - - -
48I LYS* 3.1 5.7 + - - -
50I LEU* 1.3 77.6 - - - +
52I ASN* 1.3 57.8 - - - +
54I SER* 2.7 24.5 + - - -
55I LYS 3.6 11.2 + - - -
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Residues in contact with ASN 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I LYS* 1.9 68.1 + - - +
49I ILE* 2.3 14.4 - - - +
51I GLY* 1.3 71.9 - - - +
53I PRO* 1.3 64.5 - - + +
54I SER* 3.3 3.1 + - - -
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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