Contacts of the helix formed by residues 51 - 63 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A TYR* 5.9 2.5 - - - +
46A ASN* 3.7 17.0 - - - -
47A LEU* 2.9 40.3 + - + +
50A GLN* 1.3 92.0 + - + +
52A ILE* 1.3 66.7 + - + +
54A PRO* 3.4 9.4 - - - +
55A LEU* 3.4 23.5 + - + +
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Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TYR* 5.2 4.3 - - + +
14A LEU* 4.2 9.6 - - + +
17A LEU* 4.1 25.4 - - + -
40A ILE* 3.9 41.1 - - + -
42A GLN* 4.7 3.4 - - - +
47A LEU* 2.6 51.6 + - + +
48A ILE* 3.7 15.7 - - + +
51A HIS* 1.3 68.8 - - + +
53A ALA* 1.3 66.0 + - - +
55A LEU* 3.0 20.2 + - - +
56A MET* 3.1 12.2 + - + +
80A LEU* 4.2 13.2 - - + -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ILE 2.6 22.9 + - - +
49A LYS* 3.9 10.8 - - - +
52A ILE* 1.3 72.2 - - - +
54A PRO* 1.3 61.7 - - + +
56A MET* 3.2 1.9 + - - -
57A GLN* 2.8 26.6 + - - +
69A ILE* 3.4 18.3 - - + +
71A ILE* 4.6 8.5 - - + -
80A LEU* 3.7 20.6 - - + +
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Residues in contact with PRO 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LYS 3.3 21.1 - - - +
50A GLN* 3.4 19.1 - - - +
51A HIS 3.4 15.5 - - - +
53A ALA* 1.3 90.1 - - + +
55A LEU* 1.3 59.8 + - - +
57A GLN* 3.5 7.6 + - + +
58A PHE* 3.1 23.2 + - - +
185A LEU* 4.4 19.4 - - + +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 3.8 30.2 - - + +
13A TYR* 3.6 37.2 - - + +
14A LEU* 4.2 9.6 - - + -
51A HIS* 3.4 17.5 - - + +
52A ILE* 3.0 8.1 + - - +
54A PRO* 1.3 76.8 - - - +
56A MET* 1.3 63.3 + - - +
58A PHE* 3.6 4.3 + - - +
59A LEU* 3.2 20.6 + - - +
184A PRO* 5.7 0.9 - - + -
185A LEU* 3.7 35.0 - - + +
1188A ACT 4.5 13.9 - - - +
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Residues in contact with MET 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 4.0 25.9 - - + +
18A ILE* 4.8 0.4 - - + -
38A VAL* 4.2 20.0 - - + -
40A ILE* 4.1 23.6 - - + -
52A ILE* 3.1 12.1 + - + +
53A ALA* 3.6 9.0 - - - +
55A LEU* 1.3 75.4 - - - +
57A GLN* 1.3 59.3 + - - +
59A LEU* 3.2 7.5 + - - +
60A ILE* 2.8 30.3 + - + +
69A ILE* 4.0 10.1 - - + -
80A LEU* 4.3 14.6 - - + -
82A VAL* 3.9 19.3 - - + -
87A LEU* 3.8 24.2 - - - -
91A PHE* 4.3 10.5 - - + -
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Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ALA 2.8 17.9 + - - +
54A PRO* 3.8 9.4 - - + +
56A MET* 1.3 75.7 - - - +
58A PHE* 1.3 58.3 + - - +
60A ILE* 3.3 19.0 + - - +
61A ASP* 2.9 66.4 + - - +
67A SER 5.4 2.0 + - - -
69A ILE* 3.5 27.7 + - + +
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Residues in contact with PHE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ASN* 4.2 15.9 - - - -
7A VAL* 3.4 24.9 - - + -
10A ILE* 3.7 24.7 - - + -
54A PRO 3.1 14.6 + - - +
55A LEU 3.7 4.3 - - - +
57A GLN* 1.3 80.3 - - - +
59A LEU* 1.3 58.0 + - - +
61A ASP* 3.3 8.2 + - + +
62A GLU* 2.9 56.7 + - + +
184A PRO 5.7 0.7 - - - -
185A LEU* 3.8 12.8 - - + -
186A PRO* 3.3 38.8 - - + -
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 3.9 20.6 - - + -
10A ILE* 4.9 4.5 - - + -
11A SER* 3.7 21.8 - - - +
14A LEU* 4.1 12.3 - - + -
55A LEU 3.2 10.9 + - - +
56A MET* 3.2 11.1 + - - +
58A PHE* 1.3 81.7 - - - +
60A ILE* 1.3 58.3 + - - +
62A GLU* 3.1 5.0 + - + +
63A LEU* 2.9 56.6 + - + +
87A LEU* 4.0 9.2 - - + -
90A TYR* 4.1 7.9 - - + +
91A PHE* 3.5 37.5 - - + -
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A MET* 2.8 18.4 + - + +
57A GLN* 3.4 24.9 - - - +
59A LEU* 1.3 76.8 - - - +
61A ASP* 1.3 64.1 + - - +
63A LEU 3.4 0.5 + - - -
64A ASN* 3.1 2.6 + - - -
65A VAL* 2.8 65.9 + - + +
67A SER 4.1 15.5 - - - +
69A ILE* 3.7 31.0 - - + +
82A VAL* 3.8 26.2 - - + -
87A LEU* 4.6 8.5 - - + -
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Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLN* 2.9 47.1 + - - +
58A PHE* 3.7 8.2 - - + +
60A ILE* 1.3 78.7 - - - +
62A GLU* 1.3 70.5 + - - +
64A ASN* 3.0 21.9 + - - +
65A VAL 5.1 1.3 - - - +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ASN* 3.1 23.0 + - - +
7A VAL* 3.9 19.3 - - + -
58A PHE* 2.9 56.7 + - + +
59A LEU 3.6 4.9 - - - +
61A ASP* 1.3 79.6 - - - +
63A LEU* 1.3 63.8 + - + +
64A ASN* 3.2 8.9 + - - -
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 5.2 6.5 - - + -
59A LEU* 2.9 44.0 + - + +
62A GLU* 1.3 80.9 - - + +
64A ASN* 1.3 63.5 + - - +
65A VAL* 3.9 14.6 - - + -
86A LYS* 2.4 46.6 + - + +
87A LEU* 4.1 12.8 - - + -
90A TYR* 3.9 43.3 - - + -
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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