Contacts of the helix formed by residues 96 - 110 (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 GLY 96 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55E TRP* 3.6 15.6 - - - -
61E ASP* 4.8 14.6 - - - +
94E ILE 3.6 0.2 + - - -
95E LYS* 1.3 72.6 - - - +
97E LEU* 1.3 53.1 + - - -
98E LEU 3.4 0.4 - - - -
99E ASP* 3.6 17.3 + - - +
100E VAL* 2.8 36.0 + - - +
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Residues in contact with LEU 97 (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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52E VAL* 4.7 18.6 - - + -
55E TRP* 3.4 50.7 - - + +
74E PHE* 4.8 7.0 - - + -
85E LEU* 4.6 14.1 - - + +
88E ALA* 6.1 0.2 - - + -
89E ALA* 3.8 23.1 - - + +
94E ILE* 3.2 33.6 + - + +
95E LYS 3.3 2.4 + - - -
96E GLY* 1.3 71.0 - - - +
98E LEU* 1.3 57.8 + - - +
100E VAL* 3.3 3.7 - - + +
101E THR* 2.6 56.4 + - + +
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Residues in contact with LEU 98 (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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17D HIS* 6.5 0.4 - - + -
18D ILE* 4.4 10.5 - - + -
21D ASN* 6.2 2.7 - - - +
86E ILE* 3.9 37.0 - - + +
89E ALA* 3.7 11.1 - - + +
90E ASN* 4.0 30.5 - - + +
93E ASP* 6.3 1.1 - - - -
94E ILE 3.0 20.2 + - - +
95E LYS* 5.6 1.8 - - + +
97E LEU* 1.3 77.0 - - - +
99E ASP* 1.3 66.9 + - - +
101E THR* 2.7 16.9 + - - -
102E CYS* 3.0 32.7 + - - -
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Residues in contact with ASP 99 (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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25D TYR* 4.2 7.9 + - - -
95E LYS* 3.6 41.4 + - - +
96E GLY* 3.3 22.3 + - - +
97E LEU 3.2 0.4 - - - -
98E LEU* 1.3 86.8 - - - +
100E VAL* 1.3 57.0 + - - +
102E CYS* 3.5 5.2 + - - +
103E LYS* 3.0 53.0 + - - +
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Residues in contact with VAL 100 (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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55E TRP* 4.0 17.0 - - + +
61E ASP* 5.9 0.7 - - - +
68E PRO* 4.3 16.6 - - + -
71E ASP* 3.9 32.5 - - + +
72E GLN* 5.9 0.2 - - - -
74E PHE* 6.1 1.6 - - + -
96E GLY 2.8 19.6 + - - +
97E LEU* 3.3 22.2 - - + +
99E ASP* 1.3 68.0 - - - +
101E THR* 1.3 69.7 + - + +
102E CYS 3.2 0.3 + - - -
103E LYS* 3.2 10.2 + - + +
104E THR* 2.8 49.0 + - + +
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Residues in contact with THR 101 (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 LEU* 4.0 17.2 - - + +
85E LEU* 4.5 15.5 - - + -
86E ILE* 3.6 28.5 - - + +
97E LEU* 2.6 40.3 + - + +
98E LEU* 2.7 19.2 + - - -
100E VAL* 1.3 80.9 - - + +
102E CYS* 1.3 57.6 + - - +
104E THR* 2.2 29.1 + - - -
105E VAL* 3.3 13.7 + - - +
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Residues in contact with CYS 102 (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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18D ILE* 4.1 20.6 - - - -
21D ASN* 5.2 5.2 - - + -
22D ILE* 3.6 37.4 - - + +
25D TYR* 4.2 13.9 - - + +
86E ILE* 4.7 5.6 - - - -
98E LEU* 3.0 36.6 + - - +
99E ASP* 3.7 5.6 - - - +
101E THR* 1.3 76.1 + - - +
103E LYS* 1.3 59.9 + - - +
105E VAL* 3.0 6.8 + - - +
106E ALA* 2.9 26.2 + - - +
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Residues in contact with LYS 103 (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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25D TYR* 3.4 44.9 + - + -
68E PRO* 6.3 3.4 - - + -
99E ASP* 3.0 37.7 + - - +
100E VAL* 3.7 8.7 - - + +
102E CYS* 1.3 74.4 - - - +
104E THR* 1.3 57.7 + - + +
106E ALA* 3.4 10.0 + - - +
107E ASN* 2.9 40.6 + - - +
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Residues in contact with THR 104 (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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71E ASP 5.4 3.8 - - - +
72E GLN* 5.7 4.0 - - - +
75E LEU* 3.6 42.2 - - + +
82E LEU* 4.1 6.5 - - - +
100E VAL* 2.8 35.5 + - + +
101E THR* 2.2 34.8 + - - -
103E LYS* 1.3 73.2 - - - +
105E VAL* 1.3 62.2 + - - +
107E ASN* 3.3 13.1 + - - +
108E MET* 3.3 27.4 + - - +
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Residues in contact with VAL 105 (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* 3.6 50.7 - - + -
22D ILE* 4.1 15.0 - - + -
82E LEU* 3.8 13.0 - - + -
86E ILE* 4.2 6.3 - - + -
101E THR 3.6 12.6 - - - +
102E CYS 3.0 6.8 + - - +
104E THR* 1.3 73.1 + - - +
106E ALA* 1.3 61.6 + - - +
108E MET* 2.8 28.6 + - - +
109E ILE* 3.1 28.2 + - + +
121E PHE* 4.5 9.2 - - + -
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Residues in contact with ALA 106 (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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22D ILE* 3.9 15.2 - - + +
25D TYR* 3.8 35.2 - - + -
26D LEU* 4.0 5.9 - - + +
102E CYS 2.9 12.7 + - - +
103E LYS* 3.5 10.3 - - - +
105E VAL* 1.3 74.8 - - - +
107E ASN* 1.3 58.1 + - - +
109E ILE* 2.9 9.6 + - - +
110E LYS* 2.9 36.4 + - - +
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Residues in contact with ASN 107 (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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103E LYS* 2.9 27.0 + - - +
104E THR* 3.5 11.9 - - - +
105E VAL 3.1 0.2 - - - -
106E ALA* 1.3 74.8 - - - +
108E MET* 1.3 61.1 + - + +
109E ILE 3.3 0.7 + - - -
110E LYS* 3.2 41.1 + - - +
112E LYS* 5.2 1.9 - - - -
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Residues in contact with MET 108 (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* 6.2 1.3 - - - -
75E LEU* 4.1 33.4 - - + -
79E GLN* 5.9 3.8 - - - +
82E LEU* 4.8 13.0 - - + -
104E THR 3.3 14.3 + - - +
105E VAL* 2.8 17.0 + - - +
107E ASN* 1.3 77.9 - - + +
109E ILE* 1.3 56.2 + - - +
112E LYS* 2.7 34.7 + - - +
117E ILE* 4.4 1.6 - - - +
120E THR* 4.3 10.5 - - + +
121E PHE* 4.1 23.1 - - + -
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Residues in contact with ILE 109 (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* 6.3 0.2 - - + -
7D ILE* 4.7 5.8 - - + -
22D ILE* 4.2 16.8 - - + -
23D LEU* 4.8 4.0 - - + -
26D LEU* 3.7 28.3 - - + -
30D SER* 4.9 4.9 - - - +
34D ALA* 5.1 3.6 - - + -
41D TRP* 4.2 26.7 - - + -
105E VAL* 3.6 28.7 - - + +
106E ALA* 2.9 7.4 + - - +
108E MET* 1.3 79.1 - - - +
110E LYS* 1.3 66.5 + - - +
111E GLY 3.5 1.2 + - - -
112E LYS* 3.7 5.6 + - - +
117E ILE* 3.1 28.0 - - + +
121E PHE* 3.8 20.9 - - + -
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Residues in contact with LYS 110 (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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25D TYR* 3.7 27.2 + - - +
26D LEU* 4.0 16.4 - - + -
27D ASP* 4.1 20.2 - - + +
30D SER* 3.9 3.1 - - - -
106E ALA* 2.9 19.7 + - - +
107E ASN* 3.2 37.5 + - - +
109E ILE* 1.3 79.2 - - - +
111E GLY* 1.3 61.6 + - - +
112E LYS* 3.4 8.0 + - - +
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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