Contacts of the helix formed by residues 78 - 87 (chain E) in PDB entry 2Q6W
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 TYR 78 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D ILE* 5.4 0.5 + - - +
9D GLN* 2.9 32.0 + - - +
24D PHE* 3.6 6.1 - + - -
13E SER* 3.4 9.2 + - - -
15E CYS* 3.3 21.2 - - - -
26E TYR* 3.5 27.6 - + - -
74E ARG* 3.0 26.4 + - - +
76E ASP 2.9 1.4 - - - -
77E ASN* 1.3 83.7 - - - +
79E CYS* 1.3 80.8 + - - +
80E ARG 3.5 0.2 - - - -
81E HIS* 3.7 1.3 - - - -
82E ASN* 2.7 43.6 + - - +
26F ARG* 3.0 31.9 - - + -
27F SER 4.0 3.1 - - - -
28F ASP* 3.3 27.1 - - + -
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Residues in contact with CYS 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E CYS* 2.2 51.8 - - + -
17E PHE* 3.1 12.9 - - - -
24E VAL* 3.3 17.0 - - + -
26E TYR* 3.6 25.8 - - - -
74E ARG 2.9 12.0 + - - +
75E VAL* 3.3 11.4 - - - +
78E TYR* 1.3 83.0 - - - +
80E ARG* 1.3 58.4 + - - +
82E ASN* 3.8 1.5 - - - +
83E TYR 2.9 25.5 + - - -
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Residues in contact with ARG 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E PHE* 4.3 0.2 - - - -
21E THR* 2.5 48.3 + - + +
22E GLU* 2.6 22.0 + - - +
24E VAL* 3.5 21.1 - - + +
75E VAL* 2.7 54.8 + - - +
76E ASP* 3.1 26.6 + - + +
79E CYS* 1.3 68.8 - - - +
81E HIS* 1.3 69.5 + - - +
83E TYR* 3.4 7.1 + - - +
84E GLY* 3.1 17.2 + - - -
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Residues in contact with HIS 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ASP 3.2 12.8 + - - +
77E ASN 3.4 20.2 - - - +
78E TYR 3.7 0.2 - - - +
79E CYS 3.1 0.8 - - - -
80E ARG* 1.3 77.5 - - - +
82E ASN* 1.3 69.0 + - - +
84E GLY* 2.9 19.6 + - - -
85E VAL* 3.0 25.8 + - + +
24F ALA 2.5 38.0 + - - -
26F ARG* 3.3 47.3 + - + +
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Residues in contact with ASN 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ILE* 5.2 8.3 - - + +
24D PHE* 3.8 3.4 - - - -
15E CYS* 6.0 1.1 - - - -
17E PHE* 6.0 0.2 - - + -
78E TYR* 2.7 35.3 + - - +
79E CYS* 4.0 2.2 - - - +
81E HIS* 1.3 79.2 + - - +
83E TYR* 1.3 63.5 + - - +
85E VAL* 3.1 5.7 + - - +
86E GLY* 2.9 20.1 + - - -
25F TRP* 3.3 39.8 - - + +
26F ARG* 2.5 52.0 + - - -
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Residues in contact with TYR 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D GLU* 4.4 1.0 + - - -
5D HIS* 4.0 10.8 - + + -
7D ILE* 5.3 5.5 - - + +
26D PHE* 5.5 1.8 - + - -
17E PHE* 3.4 50.2 - + + -
20E GLY* 3.9 22.7 + - - -
21E THR* 3.7 18.2 - - + +
79E CYS 2.9 18.8 + - - +
80E ARG 3.5 6.1 - - - +
82E ASN* 1.3 76.5 - - - +
84E GLY* 1.4 54.4 + - - +
86E GLY* 5.3 0.2 - - - -
87E GLU* 2.7 66.5 + - + +
91E VAL* 3.3 39.2 - - + +
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Residues in contact with GLY 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E ARG 3.1 9.3 + - - -
81E HIS 2.9 7.7 + - - -
83E TYR* 1.4 76.2 - - - +
85E VAL* 1.3 66.2 + - - +
86E GLY 3.4 0.2 + - - -
87E GLU* 3.7 19.8 + - - +
88E SER 4.9 0.9 + - - -
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Residues in contact with VAL 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D PHE* 4.3 6.2 - - - +
52D ALA* 3.1 35.0 - - + -
81E HIS* 3.0 26.6 + - + +
82E ASN* 3.1 8.7 + - - +
84E GLY* 1.3 81.6 - - - +
86E GLY* 1.3 57.8 + - - +
88E SER* 4.8 3.1 + - - -
89E PHE* 3.4 12.7 - - + -
24F ALA 3.5 26.7 - - - +
25F TRP* 3.3 21.3 - - + +
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Residues in contact with GLY 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E ASN 2.9 10.4 + - - -
83E TYR 3.7 0.4 - - - -
85E VAL* 1.3 76.5 - - - +
87E GLU* 1.3 60.7 + - - +
88E SER 3.0 4.0 + - - -
89E PHE* 3.2 11.3 + - - -
90E THR* 2.5 33.6 + - - +
25F TRP* 3.3 28.3 - - - -
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Residues in contact with GLU 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E TYR* 2.7 39.7 + - + +
84E GLY* 3.9 15.0 - - - +
85E VAL 3.4 1.2 - - - -
86E GLY* 1.3 78.5 - - - +
88E SER* 1.3 59.7 + - - +
90E THR* 3.5 5.8 - - - -
91E VAL* 3.2 22.1 + - + +
92E GLN* 2.8 53.0 + - - +
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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