Contacts of the helix formed by residues 79 - 93 (chain E) in PDB entry 6WNX
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 79 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D LEU 4.6 0.4 - - - +
3D GLN* 3.3 41.5 + - + +
4D ARG* 3.0 30.8 + - - +
6D PHE* 3.7 17.6 - - + -
77E VAL* 5.2 0.4 - - - +
78E ASP* 1.3 72.2 - - - +
80E GLY* 1.3 54.1 + - - +
81E THR 3.3 0.4 - - - -
82E LEU* 3.2 16.7 + - - +
83E PHE* 2.8 35.7 + - - +
108E MET* 5.9 4.1 - - - +
120E THR* 4.1 5.5 + - - +
121E PHE* 3.3 24.4 - - - +
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Residues in contact with GLY 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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2D LEU* 4.2 16.9 + - - -
4D ARG* 3.9 27.8 + - - +
78E ASP* 2.4 16.7 + - - -
79E GLN* 1.3 70.9 - - - +
81E THR* 1.3 60.7 + - - -
83E PHE* 3.2 4.7 + - - +
84E GLU* 3.0 26.6 + - - +
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Residues in contact with THR 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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47E ALA* 6.5 0.2 - - + -
48E ILE* 4.1 13.8 - - + +
51E LYS* 4.9 11.4 - - - +
77E VAL* 3.3 15.7 - - + +
78E ASP* 2.5 49.1 + - - +
80E GLY* 1.3 69.4 - - - +
82E LEU* 1.3 58.6 + - - +
84E GLU* 3.1 10.9 + - + +
85E LEU* 2.9 34.9 + - - +
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Residues in contact with LEU 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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6D PHE* 4.0 14.4 - - + -
75E LEU* 4.5 17.5 - - + -
77E VAL* 4.4 13.7 - - + +
79E GLN* 3.2 19.1 + - + +
81E THR* 1.3 77.3 + - - +
83E PHE* 1.3 63.8 + - - +
85E LEU* 3.1 15.2 + - + +
86E ILE* 2.9 22.0 + - + +
101E THR* 4.0 27.6 - - + +
104E THR* 4.1 15.0 - - - +
105E VAL* 3.8 24.0 - - + -
108E MET* 4.8 13.7 - - + -
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Residues in contact with PHE 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 ARG* 3.9 34.3 - - + -
6D PHE* 4.3 17.5 - + + -
9D ALA* 3.6 32.5 - - + -
10D LEU* 4.2 22.7 - - + -
13D GLN* 4.0 19.7 - - + -
79E GLN 2.8 11.5 + - - +
80E GLY 3.2 8.7 + - - +
82E LEU* 1.3 76.0 - - - +
84E GLU* 1.3 69.5 + - - +
86E ILE* 2.8 31.8 + - + +
87E LEU* 2.9 44.3 + - + +
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Residues in contact with GLU 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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4D ARG* 3.9 13.9 + - - +
43E ASN 5.7 1.0 - - - +
45E ASN* 5.5 5.5 + - - +
48E ILE* 3.6 27.1 - - + +
80E GLY 3.0 18.3 + - - +
81E THR* 3.1 11.6 + - + +
83E PHE* 1.3 93.3 - - - +
85E LEU* 1.3 56.2 + - - +
87E LEU* 3.5 18.6 + - - +
88E ALA* 3.1 28.2 + - - +
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Residues in contact with LEU 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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48E ILE* 4.0 25.8 - - + +
51E LYS* 4.0 29.2 - - + -
52E VAL* 4.8 7.4 - - + -
74E PHE* 5.4 14.4 - - + +
77E VAL* 4.1 20.9 - - + -
81E THR* 2.9 17.5 + - - +
82E LEU* 3.2 20.6 - - + +
83E PHE 3.1 0.2 - - - -
84E GLU* 1.3 75.0 - - - +
86E ILE* 1.3 59.4 + - - +
88E ALA* 3.4 4.0 + - + +
89E ALA* 2.9 30.3 + - - +
97E LEU* 4.6 14.2 - - + +
101E THR* 4.5 14.4 - - + -
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Residues in contact with ILE 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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6D PHE* 3.8 32.5 - - + -
10D LEU* 4.3 15.0 - - + -
18D ILE* 4.1 21.3 - - + -
22D ILE* 5.1 7.0 - - + -
82E LEU* 2.9 22.0 + - + +
83E PHE* 2.8 10.7 + - + +
85E LEU* 1.3 71.9 - - - +
87E LEU* 1.3 66.9 + - - +
89E ALA* 3.3 7.4 + - - +
90E ASN* 3.1 22.2 + - - +
98E LEU* 3.9 16.4 - - + +
101E THR* 3.6 27.6 - - - +
102E CYS* 4.7 2.5 - - - +
105E VAL* 4.2 11.9 - - + -
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Residues in contact with LEU 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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10D LEU* 4.4 6.3 - - + -
13D GLN* 4.0 18.2 - - + +
15D LEU* 3.8 26.1 - - + +
83E PHE* 2.9 58.5 + - + +
84E GLU* 3.5 23.3 - - - +
85E LEU 3.3 0.2 - - - -
86E ILE* 1.3 76.9 - - + +
88E ALA* 1.3 56.8 + - - +
90E ASN* 3.3 6.3 + - - +
91E TYR* 2.9 30.4 + - - +
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Residues in contact with ALA 88 (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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44E VAL* 4.2 21.8 - - + -
48E ILE* 3.8 22.7 - - + -
52E VAL* 5.0 4.3 - - + -
84E GLU 3.1 15.2 + - - +
85E LEU* 3.8 4.5 - - + +
86E ILE 3.3 0.2 - - - -
87E LEU* 1.3 77.5 - - - +
89E ALA* 1.3 54.7 + - - +
91E TYR* 3.2 6.3 + - - +
92E LEU* 2.8 47.6 + - + +
97E LEU* 5.7 0.4 - - + -
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Residues in contact with ALA 89 (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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85E LEU 2.9 18.4 + - - +
86E ILE* 3.6 6.1 - - - +
88E ALA* 1.3 75.1 - - - +
90E ASN* 1.3 53.6 + - - +
92E LEU* 3.4 2.0 + - - +
93E ASP* 2.8 28.4 + - - -
94E ILE* 3.0 17.8 + - - +
97E LEU* 3.8 22.1 - - + +
98E LEU* 3.7 35.8 - - + +
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Residues in contact with ASN 90 (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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15D LEU* 3.6 29.6 - - + +
17D HIS* 4.0 12.7 + - - -
18D ILE* 3.3 25.5 - - + +
86E ILE 3.1 13.0 + - - +
87E LEU* 3.6 10.3 + - - +
89E ALA* 1.3 74.7 - - - +
91E TYR* 1.3 64.4 + - - +
93E ASP* 3.2 14.8 + - - +
98E LEU* 4.0 20.0 - - + +
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Residues in contact with TYR 91 (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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26E THR* 2.6 37.5 + - + +
30E MET* 6.0 2.9 - - - -
40E PRO 5.0 1.2 + - - -
41E LEU* 4.6 10.9 - - + -
42E PRO* 4.0 20.3 - - - +
43E ASN* 3.2 43.8 + - + +
44E VAL* 4.0 15.5 - - + -
87E LEU 2.9 17.0 + - - +
88E ALA* 3.2 7.4 + - - +
90E ASN* 1.3 77.8 - - - +
92E LEU* 1.3 70.1 + - + +
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Residues in contact with LEU 92 (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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24E SER* 2.6 26.3 + - - +
26E THR* 3.0 22.8 + - + -
27E ILE* 4.0 17.3 - - + -
41E LEU* 3.7 29.4 - - + -
44E VAL* 4.9 6.5 - - + -
49E LEU* 5.6 3.6 - - + -
52E VAL* 4.3 22.7 - - + -
88E ALA* 2.8 29.2 + - + +
89E ALA* 5.1 0.2 - - - -
91E TYR* 1.3 89.8 - - + +
93E ASP* 1.3 67.3 + - - +
94E ILE* 3.8 25.1 - - + -
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Residues in contact with ASP 93 (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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23E GLN 3.8 1.2 - - - +
25E VAL* 3.1 50.3 + - + +
26E THR* 3.6 10.5 - - - +
89E ALA 2.8 9.8 + - - -
90E ASN* 3.2 12.9 + - - +
92E LEU* 1.3 82.3 - - - +
94E ILE* 1.3 55.9 + - - +
95E LYS* 4.1 7.4 + - - +
98E LEU* 6.3 1.6 - - - -
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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