Contacts of the helix formed by residues 51 - 63 (chain I) in PDB entry 5AKF
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 HIS 51 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13I TYR* 2.7 37.2 + + - -
17I LEU* 5.0 1.8 - - + -
47I LEU* 2.8 41.3 + - + +
50I GLN* 1.3 76.6 - - + +
52I ILE* 1.3 79.0 + - + +
54I PRO* 3.6 8.2 - - - +
55I LEU* 3.6 24.2 - - + +
115I VAL* 5.7 2.4 - - + +
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Residues in contact with ILE 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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14I LEU* 4.3 5.6 - - + -
17I LEU* 4.0 16.8 - - + -
40I ILE* 3.7 44.2 - - + -
42I ALA* 5.0 3.1 - - + -
47I LEU* 3.1 25.6 + - + +
48I ILE* 3.8 27.6 - - + +
51I HIS* 1.3 93.4 - - + +
53I ALA* 1.3 66.8 + - - +
55I LEU* 3.1 17.8 + - - +
56I MET* 3.1 11.9 + - + +
80I LEU* 4.2 12.3 - - + -
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Residues in contact with ALA 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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48I ILE 2.9 20.0 + - - +
49I LYS* 4.0 9.0 - - - +
52I ILE* 1.3 75.1 - - - +
54I PRO* 1.3 64.9 - - + +
56I MET 3.2 0.4 + - - +
57I GLN* 2.8 31.5 + - - +
69I ILE* 3.5 16.1 - - + +
71I ILE* 4.8 7.4 - - + -
80I LEU* 3.9 18.6 - - + -
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Residues in contact with PRO 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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49I LYS 3.6 12.8 - - - +
50I GLN* 3.4 18.6 - - - +
51I HIS 3.6 13.2 - - - +
52I ILE 3.4 4.5 - - - -
53I ALA* 1.3 94.1 - - + +
55I LEU* 1.3 63.0 + - + +
57I GLN* 3.7 7.2 - - + +
58I PHE* 3.1 22.2 + - - +
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Residues in contact with LEU 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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10I ILE* 4.1 37.6 - - + +
13I TYR* 3.8 33.9 - - + -
14I LEU* 4.1 11.0 - - + -
51I HIS* 3.6 28.3 - - + +
52I ILE* 3.1 9.2 + - - +
54I PRO* 1.3 78.0 - - + +
56I MET* 1.3 64.5 + - - +
58I PHE* 3.3 8.5 + - + +
59I LEU* 3.2 19.8 + - - +
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Residues in contact with MET 56 (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 LEU* 3.9 24.1 - - + +
18I ILE* 4.6 2.5 - - + -
38I VAL* 4.1 20.6 - - + -
40I ILE* 4.1 26.7 - - + -
52I ILE* 3.1 12.2 + - + +
53I ALA* 3.2 4.2 + - - +
55I LEU* 1.3 77.1 - - - +
57I GLN* 1.3 58.2 + - - +
59I LEU* 3.1 6.9 + - - +
60I ILE* 2.9 34.6 + - + +
69I ILE* 3.8 13.2 - - + -
80I LEU* 4.2 17.0 - - + -
82I VAL* 3.9 19.7 - - + -
87I LEU* 3.8 22.2 - - - -
91I PHE* 4.2 9.4 - - + -
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Residues in contact with GLN 57 (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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53I ALA 2.8 18.1 + - - +
54I PRO* 3.7 8.3 - - + +
56I MET* 1.3 73.9 - - - +
58I PHE* 1.3 66.1 + - - +
60I ILE* 3.3 16.1 + - - +
61I ASP* 2.9 59.1 + - - +
69I ILE* 3.5 24.2 + - + +
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Residues in contact with PHE 58 (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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6I ASN* 3.8 20.0 - - + -
7I VAL* 3.6 34.8 - - + -
10I ILE* 3.5 34.5 - - + -
54I PRO 3.1 10.8 + - - +
55I LEU* 3.4 13.0 - - + +
56I MET 3.2 0.2 - - - -
57I GLN* 1.3 79.9 - - - +
59I LEU* 1.3 61.1 + - + +
61I ASP* 3.2 11.6 + - + +
62I GLU* 2.9 41.7 + - + +
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Residues in contact with LEU 59 (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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7I VAL* 4.6 17.9 - - + +
10I ILE* 5.3 3.1 - - + -
11I SER* 3.7 20.6 - - - +
14I LEU* 4.3 11.4 - - + -
55I LEU 3.2 8.6 + - - +
56I MET* 3.1 12.6 + - - +
58I PHE* 1.3 85.3 - - + +
60I ILE* 1.3 63.3 + - - +
62I GLU* 3.2 3.4 + - + +
63I LEU* 3.0 43.5 + - + +
87I LEU* 4.1 8.7 - - + -
90I TYR* 3.9 15.0 - - + +
91I PHE* 3.4 37.0 - - + -
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Residues in contact with ILE 60 (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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56I MET* 2.9 23.5 + - + +
57I GLN* 3.5 21.5 - - - +
58I PHE 3.2 0.2 - - - -
59I LEU* 1.3 76.8 - - - +
61I ASP* 1.3 63.7 + - - +
63I LEU 3.3 0.7 + - - -
64I ASN* 3.0 3.6 + - - -
65I VAL* 3.0 66.3 + - + +
67I SER 4.3 13.7 - - - +
69I ILE* 3.5 34.8 - - + +
82I VAL* 4.1 17.9 - - + -
87I LEU* 4.7 11.2 - - + -
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Residues in contact with ASP 61 (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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57I GLN* 2.9 44.0 + - - +
58I PHE* 3.5 11.5 - - + +
60I ILE* 1.3 77.6 - - - +
62I GLU* 1.3 63.6 + - - +
64I ASN* 3.2 22.3 + - - +
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Residues in contact with GLU 62 (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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5I GLU* 4.5 7.7 - - - +
7I VAL* 3.4 33.6 - - + +
58I PHE* 2.9 32.3 + - + +
59I LEU* 3.5 8.3 - - + +
60I ILE 3.2 0.2 - - - -
61I ASP* 1.3 78.9 - - - +
63I LEU* 1.3 65.9 + - + +
64I ASN* 3.7 5.7 + - - +
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Residues in contact with LEU 63 (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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59I LEU* 3.0 43.8 + - + +
62I GLU* 1.3 83.5 - - + +
64I ASN* 1.3 70.5 + - - +
65I VAL* 3.0 13.6 + - + -
86I LYS* 2.8 33.6 + - + +
87I LEU* 4.0 14.1 - - + -
90I TYR* 4.0 41.5 - - + +
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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