Contacts of the helix formed by residues 66 - 76 (chain E) in PDB entry 3F6W
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 ASP 66 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ARG* 5.2 2.0 - - - +
64E GLY 4.2 1.2 + - - -
65E THR* 1.3 74.7 + - - +
67E PRO* 1.3 68.0 - - - +
68E TYR* 2.8 26.4 + - - +
69E ALA* 3.3 23.5 + - + +
70E LEU* 3.0 27.4 + - - +
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Residues in contact with PRO 67 (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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56E PHE* 4.1 2.9 - - + -
57E MSE 3.8 26.5 - - - +
60E CYS* 3.8 32.3 - - + -
61E ARG* 3.6 37.0 - - - +
65E THR 3.3 4.0 - - - +
66E ASP* 1.3 92.8 - - - +
68E TYR* 1.3 69.7 + - + +
70E LEU* 3.8 2.2 - - + +
71E LEU* 2.8 37.1 + - - +
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Residues in contact with TYR 68 (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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57E MSE 3.3 35.4 - - + +
61E ARG* 4.6 9.6 - - - -
66E ASP* 2.8 14.4 + - - +
67E PRO* 1.3 84.4 - - + +
69E ALA* 1.3 60.5 + - - +
71E LEU* 4.1 10.6 - - + +
72E SER* 2.9 31.4 + - - -
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Residues in contact with ALA 69 (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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66E ASP* 3.3 27.9 + - + +
68E TYR* 1.3 79.5 - - - +
70E LEU* 1.3 59.1 + - - +
72E SER* 3.3 5.3 + - - -
73E LYS* 2.9 32.7 + - - +
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Residues in contact with LEU 70 (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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12E LEU* 3.5 32.5 - - + +
15E LEU* 3.6 39.0 - - + +
16E LEU* 3.3 27.8 - - + -
19E ALA* 4.5 1.1 - - + -
56E PHE* 3.9 9.6 - - + -
60E CYS* 4.6 3.1 - - - -
65E THR* 4.0 16.2 - - - +
66E ASP 3.0 16.6 + - - +
67E PRO* 3.8 5.8 - - + +
69E ALA* 1.3 78.1 - - - +
71E LEU* 1.3 61.2 + - - +
73E LYS* 3.5 9.2 + - + +
74E LEU* 3.1 18.7 + - - +
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Residues in contact with LEU 71 (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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12E LEU* 4.5 14.1 - - + -
56E PHE* 3.7 32.5 - - + -
57E MSE 5.2 7.2 - - - -
67E PRO 2.8 25.1 + - - +
68E TYR* 4.1 9.9 - - + +
70E LEU* 1.3 74.7 - - - +
72E SER* 1.3 59.9 + - - +
74E LEU* 3.1 10.8 + - + +
75E GLU* 2.8 31.9 + - - +
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Residues in contact with SER 72 (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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68E TYR 2.9 20.2 + - - -
69E ALA* 3.7 6.1 - - - -
71E LEU* 1.3 78.1 - - - +
73E LYS* 1.3 62.7 + - - +
75E GLU* 3.8 8.7 - - - +
76E ALA* 2.9 27.1 + - - +
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Residues in contact with LYS 73 (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 LEU* 3.5 30.8 - - + +
69E ALA 2.9 18.4 + - - +
70E LEU* 3.6 9.2 - - + +
72E SER* 1.3 77.6 - - - +
74E LEU* 1.3 61.3 + - - +
76E ALA* 3.5 12.7 + - - +
77E MSE 3.5 26.1 - - + +
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Residues in contact with LEU 74 (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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0C ALA* 6.0 0.2 - - + -
4C ILE* 3.8 25.0 - - + +
8E ARG* 4.1 21.8 - - + +
11E ALA* 4.4 7.4 - - + -
12E LEU* 3.6 41.7 - - + +
15E LEU* 4.1 9.6 - - + -
70E LEU 3.1 10.8 + - - +
71E LEU* 3.1 15.5 + - + +
73E LYS* 1.3 77.8 - - - +
75E GLU* 1.3 63.5 + - + +
77E MSE 3.4 26.5 + - - +
78E THR* 4.5 2.1 + - - -
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Residues in contact with GLU 75 (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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80C SER* 3.1 42.9 + - - -
8E ARG* 5.3 1.4 + - - +
71E LEU 2.8 17.5 + - - +
72E SER* 3.2 8.8 + - - +
74E LEU* 1.3 74.8 - - - +
76E ALA* 1.3 61.8 + - - +
77E MSE 3.0 6.1 + - - -
78E THR* 3.3 21.0 + - - +
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Residues in contact with ALA 76 (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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33D ARG 5.6 1.4 - - - +
72E SER 2.9 17.5 + - - +
73E LYS* 3.8 8.1 - - - +
74E LEU 3.3 0.4 - - - -
75E GLU* 1.3 71.9 - - - +
77E MSE 1.3 56.8 + - + +
78E THR 3.0 11.0 + - - -
79E PRO* 3.7 17.5 - - - +
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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