Contacts of the helix formed by residues 106 - 129 (chain E) in PDB entry 5WUA
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 LEU 106 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28E VAL* 6.1 4.0 - - + -
31E LEU* 5.0 15.7 - - + +
104E LEU* 3.2 8.0 - - + +
105E HIS* 1.3 77.7 - - - +
107E TYR* 1.3 65.3 + - - +
109E PRO* 3.3 21.4 - - - +
110E ALA* 4.3 2.6 + - - +
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Residues in contact with TYR 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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89E ILE* 6.1 0.7 - - - -
92E GLY* 4.8 20.9 - - - +
95E SER* 6.5 0.4 - - - -
96E ASP* 4.5 22.0 - - + -
103E HIS* 5.4 3.6 - - + -
104E LEU* 3.4 17.4 + - + +
105E HIS 3.2 1.6 - - - -
106E LEU* 1.3 79.4 - - - +
108E MET* 1.3 63.3 + - - +
109E PRO 3.5 0.2 - - - -
110E ALA* 3.9 11.3 + - - +
111E GLY* 3.9 4.7 + - - -
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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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104E LEU 4.4 1.2 + - - +
105E HIS* 3.5 10.6 + - - +
106E LEU 3.3 0.6 - - - -
107E TYR* 1.3 78.7 - - - +
109E PRO* 1.3 55.7 - - - +
111E GLY* 2.5 28.8 + - - +
112E MET* 3.0 12.0 + - + +
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Residues in contact with PRO 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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31E LEU* 4.3 24.2 - - + +
32E ASN* 5.1 3.1 - - - -
34E VAL* 6.1 1.1 - - + -
35E PRO* 5.0 17.1 - - + +
105E HIS 4.2 2.3 - - - +
106E LEU* 3.3 18.2 - - - +
108E MET* 1.3 76.1 - - - +
110E ALA* 1.3 64.5 + - - +
112E MET* 3.3 8.9 + - + +
113E ALA* 3.0 20.5 + - - +
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Residues in contact with ALA 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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85E LEU* 5.2 1.9 - - - +
88E GLU* 4.0 33.4 - - + +
89E ILE* 4.7 6.1 - - + +
106E LEU 4.3 2.5 + - - +
107E TYR 3.9 10.0 + - - +
109E PRO* 1.3 77.5 - - - +
111E GLY* 1.3 64.4 + - - +
113E ALA* 2.8 18.9 + - - +
114E PHE* 2.9 16.1 + - - +
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Residues in contact with GLY 111 (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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89E ILE* 6.1 4.5 - - - +
107E TYR 3.9 2.6 + - - -
108E MET* 2.5 18.4 + - - -
110E ALA* 1.3 75.0 - - - +
112E MET* 1.3 61.9 + - - -
114E PHE* 3.2 5.5 + - - +
115E MET* 3.0 23.7 + - - +
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Residues in contact with MET 112 (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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35E PRO* 5.2 12.8 - - + +
38E PHE* 5.6 1.8 - - + -
39E LEU* 5.7 10.5 - - + +
108E MET* 3.0 9.1 + - + +
109E PRO* 3.6 11.4 - - + +
111E GLY* 1.3 74.9 - - - +
113E ALA* 1.3 64.0 + - - +
115E MET* 3.2 7.7 + - - +
116E ALA* 2.9 21.9 + - - +
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Residues in contact with ALA 113 (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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38E PHE* 4.8 11.7 - - + -
85E LEU* 5.2 3.8 - - + -
109E PRO 3.0 11.5 + - - +
110E ALA* 2.8 19.0 + - - +
112E MET* 1.3 71.1 - - - +
114E PHE* 1.3 55.2 + - - +
116E ALA* 2.6 30.0 + - - +
117E ALA* 3.0 14.9 + - - +
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Residues in contact with PHE 114 (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* 3.4 41.0 - - + +
86E VAL* 4.6 3.6 - - + +
110E ALA 2.9 16.6 + - - +
111E GLY* 4.0 5.2 - - - +
113E ALA* 1.3 72.5 - - - +
115E MET* 1.3 60.1 + - - +
117E ALA* 4.4 3.1 - - - +
118E ILE* 3.9 16.3 + - - +
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Residues in contact with MET 115 (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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111E GLY 3.0 12.5 + - - +
112E MET* 3.4 13.0 - - - +
114E PHE* 1.3 79.6 - - - +
116E ALA* 1.3 64.8 + - - +
118E ILE* 3.4 16.8 - - - +
119E THR* 3.7 5.7 + - - -
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Residues in contact with ALA 116 (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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38E PHE* 4.0 34.5 - - + +
39E LEU* 5.0 1.8 - - - +
41E PHE* 5.8 2.2 - - + -
42E ILE* 4.9 15.9 - - + +
112E MET 2.9 11.8 + - - +
113E ALA 2.6 15.2 + - - +
115E MET* 1.3 70.2 - - - +
117E ALA* 1.3 67.2 + - - +
119E THR* 2.9 18.2 + - - -
120E SER* 2.9 10.3 + - - -
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Residues in contact with ALA 117 (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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81E LEU* 6.0 6.7 - - + -
82E LEU* 6.2 4.3 - - - +
113E ALA 3.0 9.8 + - - +
114E PHE* 5.1 3.6 - - - +
116E ALA* 1.3 79.1 - - - +
118E ILE* 1.3 64.8 + - - +
120E SER* 2.9 26.7 + - - -
121E VAL* 3.1 6.8 + - - +
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Residues in contact with ILE 118 (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* 6.5 0.7 - - - -
114E PHE 3.9 12.1 + - - +
115E MET* 3.4 13.9 + - - +
116E ALA 3.0 0.2 - - - -
117E ALA* 1.3 79.7 - - - +
119E THR* 1.3 64.3 + - - +
120E SER 3.1 0.2 + - - -
121E VAL* 3.2 13.7 + - - +
122E VAL* 3.4 8.1 + - - +
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Residues in contact with THR 119 (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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42E ILE* 5.3 12.6 - - - -
45E PRO* 5.9 4.9 - - - -
115E MET 3.7 5.0 + - - -
116E ALA* 2.9 13.1 + - - -
118E ILE* 1.3 76.2 - - - +
120E SER* 1.3 55.3 + - - +
122E VAL* 2.6 32.0 + - - +
123E TYR* 2.9 13.6 + - - +
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Residues in contact with SER 120 (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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41E PHE* 6.3 3.1 - - - -
116E ALA 2.9 7.1 + - - -
117E ALA* 2.9 28.0 + - - -
119E THR* 1.3 75.9 - - - +
121E VAL* 1.3 60.9 + - - -
123E TYR* 3.2 6.6 + - - +
124E TYR* 3.0 19.8 + - - +
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Residues in contact with VAL 121 (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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78E THR* 5.0 16.8 - - - -
117E ALA 3.1 6.5 + - - +
118E ILE* 3.5 9.9 - - - +
120E SER* 1.3 77.7 - - - +
122E VAL* 1.3 62.6 + - - +
124E TYR* 3.0 14.0 + - - +
125E HIS* 2.9 19.1 + - - +
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Residues in contact with VAL 122 (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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118E ILE 3.4 3.0 + - - +
119E THR* 2.6 29.5 + - - +
121E VAL* 1.3 73.6 - - - +
123E TYR* 1.3 52.6 + - - +
125E HIS* 2.6 30.5 + - + +
126E ASN* 2.9 13.2 + - - +
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Residues in contact with TYR 123 (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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45E PRO* 4.6 20.9 - - + -
49E ILE* 5.7 9.0 - - + -
119E THR 2.9 10.3 + - - +
120E SER* 3.8 8.3 - - - +
122E VAL* 1.3 74.4 - - - +
124E TYR* 1.3 63.6 + - - +
126E ASN* 3.8 5.8 - - - +
127E ILE* 2.9 28.2 + - - +
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Residues in contact with TYR 124 (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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120E SER 3.0 11.4 + - - +
121E VAL* 3.0 18.2 + - - +
123E TYR* 1.3 76.7 - - - +
125E HIS* 1.3 56.0 + - - +
127E ILE* 4.5 3.6 - - - -
128E GLU* 3.1 34.3 + - + +
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Residues in contact with HIS 125 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121E VAL 2.9 9.8 + - - +
122E VAL* 2.6 23.6 + - - +
124E TYR* 1.3 72.8 - - - +
126E ASN* 1.3 56.8 + - - +
127E ILE 3.1 0.2 - - - -
129E THR* 3.0 35.4 + - - +
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Residues in contact with ASN 126 (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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49E ILE* 5.1 15.3 - - + -
122E VAL 2.9 10.8 + - - +
123E TYR* 3.8 5.2 - - - +
125E HIS* 1.3 77.3 - - - +
127E ILE* 1.3 58.0 + - - +
129E THR* 5.1 1.1 - - - -
130E SER* 3.2 22.0 - - - -
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Residues in contact with ILE 127 (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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123E TYR 2.9 17.9 + - - +
124E TYR* 4.0 4.0 - - - +
126E ASN* 1.3 78.0 - - - +
128E GLU* 1.3 60.3 + - - +
130E SER* 2.7 24.2 + - - -
131E ASN 2.9 20.5 + - - +
133E PRO* 6.0 3.8 - - + -
136E LEU* 3.8 29.2 - - + -
137E ILE 5.3 1.3 - - - +
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Residues in contact with GLU 128 (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 LEU* 5.0 9.4 - - - +
68E PHE* 4.2 28.2 + - + +
124E TYR* 3.1 15.1 + - + +
125E HIS* 5.5 0.4 - - - -
127E ILE* 1.3 78.0 - - - +
129E THR* 1.3 54.3 + - - +
131E ASN* 2.6 28.1 + - - +
133E PRO* 5.9 4.3 - - - -
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Residues in contact with THR 129 (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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64E THR 3.6 20.1 - - - +
65E TRP* 4.9 4.1 - - - -
66E LEU* 5.1 12.1 + - - +
125E HIS* 3.0 22.0 + - - +
126E ASN* 5.1 0.9 - - - -
128E GLU* 1.3 78.6 - - - +
130E SER* 1.3 57.2 + - - +
131E ASN* 3.2 0.7 + - - +
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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
------------------------------------------------------------
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