Contacts of the helix formed by residues 54 - 66 (chain B) in PDB entry 5A72
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 GLN 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A LEU* 3.5 37.0 + - + +
140A ASP* 5.4 3.6 - - - +
50B GLN* 2.7 35.3 + - + +
51B SER* 2.7 13.1 + - - +
53B THR* 1.3 92.2 + - - +
55B HIS* 1.3 62.1 + - - +
56B PHE* 3.0 24.2 + - + -
57B ILE* 3.1 21.0 + - - +
614D C 4.3 4.3 + - - -
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Residues in contact with HIS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B SER 3.5 1.8 + - - -
52B THR* 2.8 25.5 + - + +
53B THR 3.5 0.4 - - - -
54B GLN* 1.3 76.3 - - - +
56B PHE* 1.3 61.4 + - - +
58B LEU* 3.1 21.7 + - - +
59B LEU* 3.3 30.3 + - + +
70B VAL* 3.3 27.4 - - + +
71B ARG* 4.7 2.0 - - - -
72B LYS* 3.7 35.2 - - + +
78B SER* 3.2 26.1 + - - +
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Residues in contact with PHE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASN* 5.8 2.7 - - + -
101A LEU* 4.3 17.7 - - + -
53B THR 4.9 2.9 - - - -
54B GLN* 3.0 29.0 + - + -
55B HIS* 1.3 80.5 - - - +
57B ILE* 1.3 69.8 + - + +
59B LEU* 2.9 33.0 + - + +
60B ASP* 3.1 33.8 + - - +
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Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASN* 4.1 23.3 - - + -
101A LEU* 3.8 36.8 - - + -
15B TRP* 4.2 22.0 - - + -
19B PHE* 4.8 5.6 - - + -
50B GLN* 4.0 18.4 - - + -
54B GLN 3.1 16.8 + - - +
56B PHE* 1.3 89.4 - - + +
58B LEU* 1.3 74.3 + - + +
60B ASP* 3.0 20.7 + - + +
61B ILE* 3.0 26.1 + - + +
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE* 5.2 0.2 - - + -
48B VAL* 3.7 34.5 - - + +
50B GLN* 4.1 19.7 - - + -
55B HIS 3.1 12.3 + - - +
57B ILE* 1.3 83.8 - - + +
59B LEU* 1.3 60.3 + - - +
61B ILE* 3.2 9.1 + - + +
62B GLN* 3.2 21.8 + - - +
70B VAL* 3.8 17.6 - - + +
78B SER* 3.5 24.2 - - - +
79B GLU* 3.4 39.5 - - - +
80B PHE* 4.1 10.5 - - + -
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B HIS* 3.3 33.7 - - + +
56B PHE* 2.9 18.6 + - + +
58B LEU* 1.3 76.6 - - - +
60B ASP* 1.3 60.8 + - - +
62B GLN* 3.5 18.1 + - - +
63B LYS* 3.1 25.6 + - - +
70B VAL* 3.5 31.0 - - + -
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Residues in contact with ASP 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B PHE* 3.4 36.5 - - - +
57B ILE* 3.0 20.1 + - + +
59B LEU* 1.3 79.5 - - - +
61B ILE* 1.3 64.4 + - + +
63B LYS* 3.4 7.9 + - - +
64B ILE* 3.0 32.9 + - + +
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Residues in contact with ILE 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TRP* 4.2 15.3 - - + -
16B LEU* 3.8 40.4 - - + -
19B PHE* 4.1 12.6 - - + -
46B LEU* 6.0 0.2 - - + -
48B VAL* 4.0 28.5 - - + -
57B ILE* 3.0 19.3 + - + +
58B LEU* 3.2 14.1 + - + +
60B ASP* 1.3 77.8 - - + +
62B GLN* 1.3 57.1 + - - +
64B ILE* 3.0 12.7 + - + +
65B LEU* 2.9 27.9 + - + +
80B PHE* 3.7 29.2 - - + -
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU 3.2 8.9 + - - +
59B LEU* 3.7 26.3 - - - +
61B ILE* 1.3 78.9 - - - +
63B LYS* 1.3 57.8 + - - +
65B LEU 4.5 0.4 - - - +
66B GLY* 2.9 27.1 + - - -
67B CYS 3.7 13.2 + - - +
68B GLY 2.6 26.8 + - - +
69B THR* 3.7 9.5 - - - +
70B VAL* 3.9 11.7 - - + +
80B PHE* 3.5 20.8 - - + -
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Residues in contact with LYS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU 3.1 14.5 + - - +
60B ASP* 3.6 11.4 - - - +
61B ILE 3.2 0.2 - - - -
62B GLN* 1.3 78.0 - - - +
64B ILE* 1.3 65.3 + - + +
65B LEU 3.4 0.3 + - - -
66B GLY* 3.5 8.8 + - - -
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LYS* 4.2 38.1 - - + +
13B PHE* 3.9 35.2 - - + -
15B TRP* 4.9 16.8 - - + -
16B LEU* 4.2 18.2 - - + -
60B ASP* 3.0 22.7 + - + +
61B ILE* 3.0 14.5 + - - +
63B LYS* 1.3 78.2 - - + +
65B LEU* 1.3 60.6 + - + +
94B LYS* 4.9 2.6 + - - -
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PHE* 4.3 16.4 - - + -
16B LEU* 4.0 27.8 - - + -
46B LEU* 4.9 3.8 - - + -
61B ILE* 2.9 15.1 + - + +
62B GLN 4.3 0.2 - - - +
64B ILE* 1.3 79.7 - - - +
66B GLY* 1.3 62.6 + - - +
67B CYS* 3.2 22.1 + - - +
80B PHE* 3.8 29.2 - - + -
82B VAL* 4.5 1.8 - - + -
90B THR* 6.0 0.2 - - - +
91B THR* 3.6 36.5 + - + +
94B LYS* 3.6 28.0 + - + +
95B LEU* 5.3 2.9 - - + -
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Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLN* 2.9 13.0 + - - -
63B LYS* 3.5 6.5 + - - -
64B ILE 3.5 2.0 - - - -
65B LEU* 1.3 77.0 - - - +
67B CYS* 1.3 64.2 + - - +
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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