Contacts of the helix formed by residues 46 - 54 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45J GLY* 1.3 81.3 - - - +
47J PRO* 1.3 73.5 - - + +
48J GLU 3.4 1.6 - - - -
49J CYS* 3.1 12.0 + - + +
50J MET* 3.1 29.0 + - + +
97J LEU* 4.6 5.8 - - + -
53W PHE* 5.5 0.4 - - + -
56W ILE* 3.7 38.1 - - + -
57W GLU 5.7 1.3 - - - +
59W GLU* 4.0 13.1 - - - +
63W LEU* 5.1 1.1 - - + -
92W ILE* 4.0 29.5 - - + -
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Residues in contact with PRO 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J PRO* 3.6 26.1 - - + +
15J VAL 4.6 1.8 - - - +
16J ASN* 4.4 14.1 - - - +
25J ASN* 3.2 46.2 - - + +
26J THR 3.8 10.8 - - - +
27J VAL* 3.4 19.5 - - + +
45J GLY 3.4 3.4 - - - +
46J PRO* 1.3 82.8 - - + -
48J GLU* 1.3 59.0 + - + +
50J MET* 3.2 4.2 + - - +
51J LYS* 2.9 27.5 + - - +
59W GLU* 4.4 1.1 - - - +
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Residues in contact with GLU 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J PRO* 3.8 21.8 - - + +
16J ASN* 5.8 4.5 - - - +
46J PRO* 3.4 0.8 - - - +
47J PRO* 1.3 77.6 - - + +
49J CYS* 1.3 57.6 + - - +
51J LYS* 3.3 23.7 + - - +
52J ALA* 2.9 27.9 + - - +
52W ALA* 4.9 4.2 - - + +
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Residues in contact with CYS 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J PRO* 3.1 22.6 + - + +
48J GLU* 1.3 76.6 - - - +
50J MET* 1.3 59.7 + - - +
52J ALA* 3.2 3.8 + - - +
53J PHE* 2.9 26.9 + - - +
97J LEU* 4.5 13.5 - - - -
49W CYS* 4.1 14.7 - - - -
52W ALA* 4.1 12.7 - - + +
53W PHE* 3.7 42.8 - - - -
56W ILE* 4.1 11.6 - - + +
97W LEU* 5.5 0.2 - - - -
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Residues in contact with MET 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J PHE* 3.5 20.9 - - + -
27J VAL* 4.0 12.6 - - + -
43J ALA* 4.9 1.6 - - + -
44J ASP 3.4 25.8 - - - +
45J GLY* 3.7 13.2 - - - +
46J PRO* 3.1 15.1 + - - +
47J PRO 3.7 6.3 - - - +
49J CYS* 1.3 72.1 - - - +
51J LYS* 1.3 65.9 + - - +
53J PHE* 3.4 6.4 + - + +
54J SER 3.1 17.8 + - - -
97J LEU* 3.6 55.6 - - + +
100J PHE* 3.9 0.9 - - + -
101J ALA* 3.8 27.6 - - + +
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Residues in contact with LYS 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J PHE* 4.0 16.5 + - + +
14J PRO* 3.6 32.5 - - + -
27J VAL* 5.2 0.6 - - + +
47J PRO 2.9 13.4 + - - +
48J GLU* 3.3 22.2 - - - +
50J MET* 1.3 75.1 - - - +
52J ALA* 1.3 65.5 + - - +
54J SER* 2.6 24.1 + - - -
55J GLU* 3.0 44.4 + - - +
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Residues in contact with ALA 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J GLU 2.9 17.1 + - - +
49J CYS 3.4 8.3 - - - +
51J LYS* 1.3 71.5 - - - +
53J PHE* 1.3 58.2 + - - +
55J GLU* 2.8 25.7 + - - +
56J ILE* 3.4 15.5 + - - +
48W GLU* 4.8 3.1 - - + +
49W CYS* 4.1 14.6 - - - +
52W ALA* 4.1 20.4 - - + -
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Residues in contact with PHE 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J CYS 2.9 16.8 + - - +
50J MET* 3.5 12.3 - - + +
51J LYS 3.2 0.2 - - - -
52J ALA* 1.3 72.8 - - - +
54J SER* 1.3 64.8 + - - +
55J GLU 3.1 0.9 + - - -
56J ILE* 3.5 23.5 - - + +
65J ASN* 4.7 0.2 + - - -
66J ILE* 4.7 19.5 + - + +
89J THR* 5.2 7.6 - - + -
92J ILE* 3.8 35.4 - - + -
97J LEU* 4.0 15.7 - - + -
98J GLY* 3.6 28.0 - - - -
101J ALA* 3.7 31.9 - - + -
46W PRO* 5.4 1.6 - - + -
49W CYS* 3.7 22.6 - - + -
97W LEU* 4.0 15.5 - - + -
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Residues in contact with SER 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J PHE* 3.6 46.8 - - - +
50J MET 3.1 7.2 + - - -
51J LYS* 2.6 21.5 + - - -
53J PHE* 1.3 76.9 - - - +
55J GLU* 1.3 63.5 + - - +
65J ASN* 2.8 19.6 + - - +
66J ILE* 4.2 12.3 - - - -
67J LYS* 3.3 24.0 - - - +
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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