Contacts of the helix formed by residues 46 - 54 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45M GLY* 1.4 79.8 - - - +
47M PRO* 1.3 74.5 - - + +
48M GLU 3.5 2.0 - - - -
49M CYS* 3.1 9.1 + - + +
50M MET* 3.0 30.3 + - - +
97M LEU* 4.3 7.4 - - + -
53V PHE* 5.4 0.4 - - + -
56V ILE* 3.5 39.7 - - + -
57V GLU 5.8 0.2 - - - +
59V GLU* 4.0 11.1 - - - +
63V LEU* 4.9 2.9 - - + -
92V ILE* 3.9 32.3 - - + -
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Residues in contact with PRO 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M PRO* 3.6 24.1 - - + +
15M VAL 4.5 0.9 - - - +
16M ASN* 3.5 25.6 - - - +
25M ASN* 3.6 33.2 - - + +
26M THR 3.8 16.4 - - - +
27M VAL* 3.5 15.8 - - + +
45M GLY 3.2 4.9 - - - +
46M PRO* 1.3 83.5 - - + +
48M GLU* 1.3 64.6 + - + +
50M MET* 3.3 4.2 + - - +
51M LYS* 3.0 20.4 + - - +
59V GLU* 4.2 2.0 - - - +
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Residues in contact with GLU 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M PRO* 3.8 19.5 - - + +
16M ASN* 5.5 8.1 + - - +
46M PRO 3.5 0.2 - - - -
47M PRO* 1.3 78.3 - - + +
49M CYS* 1.3 58.1 + - - +
51M LYS* 3.1 21.5 + - - +
52M ALA* 2.9 27.7 + - - +
52V ALA* 5.0 4.4 - - + +
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Residues in contact with CYS 49 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46M PRO* 3.1 22.7 + - + +
48M GLU* 1.3 78.7 - - - +
50M MET* 1.3 57.6 + - - +
52M ALA* 3.2 4.2 + - - +
53M PHE* 2.9 25.5 + - - +
97M LEU* 4.6 15.0 - - - -
49V CYS* 4.1 12.8 - - - -
52V ALA* 4.3 14.7 - - - +
53V PHE* 3.8 42.0 - - - -
56V ILE* 4.1 10.0 - - + +
97V LEU* 5.5 0.4 - - - -
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Residues in contact with MET 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M PHE* 3.5 18.7 - - + -
27M VAL* 3.9 14.1 - - + -
43M ALA* 4.8 2.9 - - + -
44M ASP 3.4 27.4 - - - +
45M GLY* 3.8 12.3 - - - +
46M PRO* 3.0 17.4 + - - +
47M PRO 3.7 6.1 - - - +
49M CYS* 1.3 73.6 - - - +
51M LYS* 1.3 66.3 + - - +
53M PHE* 3.3 7.0 + - + +
54M SER 3.2 16.8 + - - -
97M LEU* 3.6 56.1 - - + +
100M PHE* 3.7 7.9 - - + -
101M ALA* 3.8 20.9 - - + +
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Residues in contact with LYS 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M GLU* 5.5 6.1 + - - +
12M PHE* 3.7 22.5 + - + +
14M PRO* 3.7 29.0 - - + +
27M VAL* 5.3 0.2 - - - +
47M PRO 3.0 13.5 + - - +
48M GLU* 3.1 19.3 + - - +
50M MET* 1.3 76.4 - - - +
52M ALA* 1.3 60.6 + - - +
54M SER* 2.5 25.1 + - - +
55M GLU* 2.8 45.6 + - - +
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Residues in contact with ALA 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48M GLU 2.9 12.2 + - - +
49M CYS 3.2 8.3 + - - +
51M LYS* 1.3 74.6 - - - +
53M PHE* 1.3 63.9 + - - +
55M GLU* 3.0 17.7 + - - +
56M ILE* 3.3 16.1 + - - +
48V GLU* 5.0 3.4 - - + +
49V CYS* 4.1 23.2 - - - +
52V ALA* 4.2 12.8 - - + -
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Residues in contact with PHE 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M CYS 2.9 14.0 + - - +
50M MET* 3.5 13.5 - - + +
52M ALA* 1.3 75.9 - - - +
54M SER* 1.3 62.6 + - - +
56M ILE* 3.2 26.6 - - + +
66M ILE* 4.4 20.3 + - + +
89M THR* 5.2 6.5 - - + -
92M ILE* 3.7 37.0 - - + -
93M GLY* 5.3 0.2 - - - -
97M LEU* 4.1 13.0 - - + -
98M GLY* 3.6 25.1 - - - -
101M ALA* 3.6 32.1 - - + -
46V PRO* 5.4 0.4 - - + -
49V CYS* 3.8 14.7 - - - -
97V LEU* 4.0 27.4 - - + -
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Residues in contact with SER 54 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M PHE* 3.4 52.3 - - - +
50M MET 3.2 1.0 + - - -
51M LYS 2.5 20.1 + - - -
53M PHE* 1.3 79.2 - - - +
55M GLU* 1.3 62.5 + - - +
56M ILE 3.6 0.9 - - - -
65M ASN* 3.0 16.0 + - - -
66M ILE* 4.1 14.1 - - - -
67M LYS* 3.1 25.4 - - - +
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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