Contacts of the helix formed by residues 51 - 63 (chain F) in PDB entry 5AKM
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13F TYR* 2.6 35.1 + + - -
17F LEU* 5.2 0.9 - - + -
47F LEU* 2.9 35.9 + - + +
50F GLN* 1.3 80.3 - - + +
52F ILE* 1.3 82.7 + - + +
53F ALA 3.7 0.2 - - - -
54F PRO* 3.7 6.4 - - - +
55F LEU* 3.5 38.7 + - + +
115F VAL* 5.5 3.6 - - + +
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Residues in contact with ILE 52 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F LEU* 4.4 5.5 - - + +
17F LEU* 4.2 20.0 - - + -
40F ILE* 3.9 38.8 - - + -
42F GLN* 4.5 8.5 - - + +
47F LEU* 3.2 24.2 + - + +
48F ILE* 3.9 24.9 - - + +
51F HIS* 1.3 93.0 - - + +
53F ALA* 1.3 62.8 + - - +
55F LEU* 3.1 10.0 + - - +
56F MET* 3.0 24.8 + - + +
80F LEU* 3.9 16.8 - - + -
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Residues in contact with ALA 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F ILE* 2.8 25.6 + - + +
49F LYS* 4.1 8.1 - - - +
52F ILE* 1.3 73.6 - - - +
54F PRO* 1.3 61.4 - - + +
56F MET* 3.2 0.6 + - - -
57F GLN* 2.7 30.3 + - - +
69F ILE* 3.3 21.3 - - + +
71F ILE* 4.8 4.9 - - + -
80F LEU* 3.7 19.9 - - + +
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Residues in contact with PRO 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F LYS 3.3 20.9 - - - +
50F GLN 3.5 22.4 - - - +
51F HIS 3.7 4.0 - - - +
52F ILE 3.7 2.9 - - - -
53F ALA* 1.3 89.4 - - + +
55F LEU* 1.3 57.2 + - + +
57F GLN* 3.7 7.9 - - + +
58F PHE* 2.9 28.6 + - - +
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Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ILE* 3.9 38.3 - - + +
13F TYR* 3.8 24.2 - - + -
14F LEU* 3.8 15.7 - - + +
51F HIS* 3.5 39.5 - - + +
52F ILE* 3.1 8.1 + - - +
54F PRO* 1.3 75.9 - - + +
56F MET* 1.3 66.4 + - - +
58F PHE* 3.4 7.1 + - + +
59F LEU* 3.2 17.3 + - - +
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Residues in contact with MET 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LEU* 3.8 23.4 - - + +
18F ILE* 4.5 2.9 - - + -
38F VAL* 4.0 24.9 - - + -
40F ILE* 4.2 16.8 - - + -
52F ILE* 3.0 13.3 + - + +
53F ALA* 3.7 8.3 - - - +
55F LEU* 1.3 76.3 - - - +
57F GLN* 1.3 57.9 + - - +
59F LEU* 3.2 7.0 + - - +
60F ILE* 2.9 30.5 + - + +
69F ILE* 3.9 11.0 - - + -
80F LEU* 4.1 21.5 - - + -
82F VAL* 3.9 19.7 - - + -
87F LEU* 3.9 20.9 - - + -
91F PHE* 4.4 10.1 - - + -
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Residues in contact with GLN 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F ALA 2.7 21.0 + - - +
54F PRO* 3.7 9.9 - - + +
56F MET* 1.3 69.5 - - - +
58F PHE* 1.3 64.9 - - - +
60F ILE* 3.4 15.0 + - - +
61F ASP* 2.7 65.5 + - - +
67F SER 5.7 0.7 + - - +
68F LYS* 5.7 1.0 - - - -
69F ILE* 3.5 26.3 + - + +
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Residues in contact with PHE 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ASN* 3.9 36.6 - - + -
7F VAL* 4.7 9.0 - - + -
10F ILE* 3.9 29.8 - - + -
54F PRO 2.9 18.6 + - - +
55F LEU* 3.5 9.9 - - + +
57F GLN* 1.3 77.0 - - - +
59F LEU* 1.3 65.2 + - + +
61F ASP* 3.4 7.1 + - + +
62F GLU* 3.1 63.1 + - + +
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Residues in contact with LEU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F VAL* 3.5 26.5 - - + +
10F ILE* 5.0 4.5 - - + -
11F SER* 3.4 23.8 - - - +
14F LEU* 4.4 11.4 - - + -
55F LEU 3.2 10.6 + - - +
56F MET* 3.2 10.5 + - - +
58F PHE* 1.3 80.4 - - + +
60F ILE* 1.3 66.9 + - - +
62F GLU* 3.2 3.8 + - - +
63F LEU* 2.9 32.9 + - + +
87F LEU* 3.9 13.5 - - + -
90F TYR* 3.9 16.2 - - + +
91F PHE* 3.5 32.1 - - + -
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Residues in contact with ILE 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F MET* 2.9 19.4 + - + +
57F GLN* 3.6 20.6 - - - +
59F LEU* 1.3 76.5 - - - +
61F ASP* 1.3 64.0 + - - +
63F LEU* 3.4 0.6 + - - -
64F ASN* 3.1 3.8 + - - -
65F VAL* 2.9 65.9 + - + +
67F SER 4.1 18.4 - - - +
69F ILE* 3.8 31.0 - - + +
82F VAL* 4.1 20.0 - - + -
87F LEU* 4.5 14.1 - - + -
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Residues in contact with ASP 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F GLN* 2.7 48.2 + - - +
58F PHE* 3.8 6.8 - - + +
60F ILE* 1.3 78.2 - - - +
62F GLU* 1.3 65.9 + - + +
64F ASN* 3.2 21.1 + - - +
65F VAL 5.4 0.7 - - - -
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Residues in contact with GLU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F VAL* 4.5 27.0 - - + +
58F PHE* 3.1 55.8 + - + +
59F LEU 3.2 5.1 + - - +
61F ASP* 1.3 79.1 - - - +
63F LEU* 1.3 60.8 + - + +
64F ASN* 3.3 6.6 + - - +
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Residues in contact with LEU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F VAL* 4.6 8.1 - - + -
59F LEU* 2.9 28.6 + - + +
62F GLU* 1.3 79.9 - - + +
64F ASN* 1.3 64.8 + - - +
65F VAL* 3.3 13.4 + - + -
86F LYS* 2.8 35.9 + - + -
87F LEU* 3.9 18.8 - - + -
90F TYR* 3.7 57.0 - - + +
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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