Contacts of the helix formed by residues 46 - 55 (chain I) in PDB entry 3MQT
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 PRO 46 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45I GLY* 1.3 80.1 - - - +
47I PRO* 1.3 75.5 - - + +
48I GLU 3.5 2.0 - - - +
49I CYS* 3.2 8.2 + - + +
50I MET* 2.9 28.7 + - - +
97I LEU* 4.7 6.5 - - + -
53L PHE* 5.7 1.1 - - + -
56L ILE* 3.8 46.0 - - + -
57L GLU 5.8 0.2 - - - +
59L GLU* 3.9 11.3 - - - +
63L LEU* 4.5 5.1 - - + -
92L ILE* 3.8 24.7 - - + -
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Residues in contact with PRO 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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14I PRO* 3.7 28.3 - - + +
15I VAL 4.5 0.9 - - - +
16I ASN* 3.8 15.3 - - - +
25I ASN* 3.6 43.7 - - + +
26I THR 3.9 12.1 - - - +
27I VAL* 3.5 15.2 - - + +
45I GLY 3.3 7.2 - - - +
46I PRO* 1.3 83.3 - - + -
48I GLU* 1.3 63.5 + - + +
50I MET* 3.1 4.9 + - - +
51I LYS* 3.0 21.5 + - - +
59L GLU* 4.3 1.1 - - - +
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Residues in contact with GLU 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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14I PRO* 3.7 21.9 - - + +
16I ASN* 5.9 3.1 - - - +
46I PRO 3.5 0.8 - - - -
47I PRO* 1.3 79.9 - - + +
49I CYS* 1.3 56.5 + - - +
51I LYS* 3.3 24.8 + - - +
52I ALA* 3.0 26.3 + - - +
52L ALA* 4.8 4.8 - - + +
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Residues in contact with CYS 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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46I PRO* 3.2 12.6 + - + +
47I PRO 3.2 0.4 - - - -
48I GLU* 1.3 76.7 - - - +
50I MET* 1.3 60.0 + - - +
52I ALA* 3.2 2.6 + - - +
53I PHE* 2.9 27.0 + - - +
97I LEU* 4.4 15.3 - - - -
49L CYS* 4.2 13.4 - - - -
52L ALA* 4.1 14.8 - - + +
53L PHE* 3.8 40.6 - - - -
56L ILE* 4.2 21.2 - - + +
97L LEU* 5.6 0.2 - - - -
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Residues in contact with MET 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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12I PHE* 3.7 9.7 - - + -
27I VAL* 3.6 21.5 - - + -
43I ALA* 4.9 2.7 - - + -
44I ASP 3.3 26.2 - - - +
45I GLY* 3.8 12.6 - - - -
46I PRO* 2.9 18.3 + - - +
47I PRO 3.5 6.3 - - - +
49I CYS* 1.3 76.8 - - - +
51I LYS* 1.3 61.9 + - - +
53I PHE* 3.3 7.3 + - + +
54I SER* 3.1 22.0 + - - -
97I LEU* 3.7 52.0 - - + +
100I PHE* 3.9 0.9 - - + -
101I ALA* 3.8 28.7 - - + +
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Residues in contact with LYS 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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12I PHE* 3.7 21.6 + - + +
14I PRO* 3.4 32.8 - - + -
27I VAL* 5.3 0.4 - - - +
47I PRO 3.0 12.3 + - - +
48I GLU* 3.4 22.4 - - - +
49I CYS 3.2 0.2 - - - -
50I MET* 1.3 76.1 - - - +
52I ALA* 1.3 61.9 + - - +
54I SER* 2.5 26.2 + - - +
55I GLU* 3.2 41.8 + - - +
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Residues in contact with ALA 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 GLU 3.0 13.9 + - - +
49I CYS 3.2 6.5 + - - +
51I LYS* 1.3 75.7 - - - +
53I PHE* 1.3 64.4 - - - +
55I GLU* 2.9 20.8 + - - +
56I ILE* 3.4 12.6 + - - +
48L GLU* 4.8 4.0 - - + +
49L CYS* 4.1 16.7 - - - +
52L ALA* 4.1 19.5 - - + -
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Residues in contact with PHE 53 (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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49I CYS 2.9 14.0 + - - +
50I MET* 3.4 13.5 - - + +
52I ALA* 1.3 75.9 - - - +
54I SER* 1.3 63.6 + - - +
55I GLU 3.2 1.7 + - - -
56I ILE* 3.3 24.6 - - + +
66I ILE* 4.5 19.9 - - + +
89I THR* 5.1 7.9 - - + -
92I ILE* 3.9 35.4 - - + -
97I LEU* 3.9 20.2 - - + -
98I GLY* 3.6 27.1 - - - -
101I ALA* 3.7 30.5 - - + -
46L PRO* 5.6 0.4 - - + -
49L CYS* 3.7 14.0 - - - -
97L LEU* 3.9 20.6 - - + -
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Residues in contact with SER 54 (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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12I PHE* 3.6 45.1 - - - +
50I MET 3.1 6.2 + - - -
51I LYS* 2.5 25.5 + - - -
53I PHE* 1.3 77.3 - - - +
55I GLU* 1.3 65.6 + - - +
56I ILE 3.6 0.9 - - - -
65I ASN* 3.0 18.3 + - - -
66I ILE* 4.3 11.7 - - - -
67I LYS* 3.1 23.9 + - - +
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Residues in contact with GLU 55 (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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11I GLU* 6.1 0.9 - - - +
12I PHE 5.1 2.6 + - - +
51I LYS* 3.2 49.7 + - - +
52I ALA* 2.9 12.5 + - - +
54I SER* 1.3 90.4 + - - +
56I ILE* 1.3 63.8 + - - +
57I GLU* 4.9 4.0 - - - +
65I ASN* 3.7 3.6 - - - +
67I LYS* 4.4 15.1 + - - +
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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