Contacts of the helix formed by residues 131 - 146 (chain E) in PDB entry 4ADV
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 ASN 131 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A C 3.2 30.5 + - - +
19A A 3.5 26.7 - - - +
129E SER* 3.0 5.2 - - - +
130E THR* 1.3 76.5 + - - +
132E PRO* 1.3 71.0 - - - +
133E ILE* 3.2 15.4 - - - +
134E ASN* 2.7 49.3 + - + +
135E VAL* 2.9 30.4 + - - +
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Residues in contact with PRO 132 (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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10A A 5.2 4.7 - - - +
15E ILE* 4.1 24.0 - - + -
16E ALA* 5.3 9.2 - - + -
18E ASN* 5.2 9.0 - - - +
35E LEU* 3.9 4.7 - - + -
109E ALA* 4.5 2.9 - - + +
130E THR 3.1 7.1 - - - +
131E ASN* 1.3 90.0 - - - +
133E ILE* 1.3 74.5 + - + +
134E ASN 2.9 1.4 + - - -
135E VAL* 3.4 11.7 - - + -
136E VAL* 2.9 29.3 + - - +
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Residues in contact with ILE 133 (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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17A U 4.9 3.1 - - - +
18A C 3.6 28.3 - - - +
1078A U 5.7 0.2 - - - +
1079A G 5.5 3.6 - - - +
18E ASN* 5.0 7.4 - - - +
35E LEU* 3.4 11.3 - - + +
47E PHE* 5.1 1.8 - - + -
49E TYR* 3.2 49.1 - - + +
131E ASN* 3.2 13.4 - - - +
132E PRO* 1.3 83.7 - - + +
134E ASN* 1.3 62.5 + - - +
136E VAL* 3.2 6.7 - - - +
137E ARG* 2.9 32.0 + - - +
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Residues in contact with ASN 134 (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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18A C 3.4 5.3 + - - -
19A A 2.5 29.6 + - - +
88E HIS* 4.0 18.8 + - - +
89E THR* 3.0 33.9 + - - +
91E SER* 4.1 8.1 - - - -
131E ASN* 2.7 23.3 + - + +
133E ILE* 1.3 85.5 - - - +
135E VAL* 1.3 50.4 + - - +
136E VAL 2.9 5.2 - - - -
137E ARG* 2.7 16.6 + - - +
138E ALA* 2.7 32.7 + - - +
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Residues in contact with VAL 135 (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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10A A 5.7 0.7 - - - +
91E SER* 3.1 19.5 - - - +
93E VAL* 4.3 5.0 - - + +
109E ALA* 3.2 24.8 - - + +
110E MET* 4.1 17.1 + - + +
126E ALA* 4.3 11.2 - - + -
129E SER 3.1 28.3 - - - +
130E THR* 3.9 11.0 - - - +
131E ASN 2.9 24.2 + - - +
132E PRO* 3.4 9.2 - - + -
134E ASN* 1.3 72.0 - - - +
136E VAL* 1.3 51.8 + - - +
138E ALA* 3.8 2.5 - - - +
139E THR* 2.7 37.2 + - - +
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Residues in contact with VAL 136 (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 ILE* 4.7 1.8 - - + -
35E LEU* 3.5 20.0 - - + -
37E VAL* 3.6 18.8 - - + -
47E PHE* 4.0 17.3 - - + -
109E ALA* 3.6 14.1 - - + -
113E VAL* 3.4 22.4 - - + +
132E PRO 2.9 25.2 + - - +
133E ILE 3.2 18.4 - - - +
134E ASN 2.8 0.8 + - - -
135E VAL* 1.3 80.1 - - - +
137E ARG* 1.3 62.5 + - + +
139E THR* 2.7 15.6 + - - -
140E ILE* 3.5 15.3 - - + +
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Residues in contact with ARG 137 (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 PHE* 3.5 41.6 - - + -
88E HIS* 4.0 32.6 + - + +
133E ILE* 2.9 30.1 + - - +
134E ASN* 2.7 34.3 + - - +
136E VAL* 1.3 72.7 - - + +
138E ALA* 1.3 54.5 + - - +
139E THR 2.9 5.6 - - - -
140E ILE* 3.6 8.7 - - + +
141E ASP* 2.8 40.4 + - - +
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Residues in contact with ALA 138 (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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86E GLY* 3.6 17.8 - - - +
87E VAL* 4.0 3.8 + - - -
88E HIS* 3.9 28.5 - - + +
91E SER* 3.5 27.8 - - - +
93E VAL* 3.5 16.6 - - + +
134E ASN 2.7 16.7 + - - +
135E VAL 4.0 0.9 - - - +
136E VAL 3.5 0.2 - - - -
137E ARG* 1.3 73.4 - - - +
139E THR* 1.3 59.5 + - - +
141E ASP* 4.0 1.8 + - - +
142E GLY* 3.5 12.5 + - - -
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Residues in contact with THR 139 (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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93E VAL* 3.6 20.2 - - + -
95E MET* 3.4 29.9 - - + +
110E MET* 3.5 24.6 - - + -
113E VAL* 3.8 17.6 - - - +
135E VAL 2.7 16.9 + - - +
136E VAL* 2.7 17.5 + - - -
138E ALA* 1.3 76.9 - - - +
140E ILE* 1.3 57.4 + - - -
141E ASP 3.2 1.1 - - - -
142E GLY* 2.9 17.2 + - - -
143E LEU* 3.1 18.3 + - - +
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Residues in contact with ILE 140 (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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37E VAL* 5.6 0.7 - - + -
45E VAL* 4.8 10.1 - - + -
46E GLY* 4.5 7.4 - - - +
47E PHE* 3.3 51.6 - - + +
71E ILE* 3.8 27.4 - - + +
113E VAL* 4.8 11.7 - - + -
136E VAL* 3.5 16.6 - - + +
137E ARG* 3.1 7.7 + - + +
139E THR* 1.3 79.4 + - - +
141E ASP* 1.3 62.6 + - - +
143E LEU* 3.4 13.6 + - + +
144E GLU* 2.8 33.9 + - - +
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Residues in contact with ASP 141 (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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86E GLY* 4.9 4.7 - - - -
87E VAL 4.4 7.3 - - - +
88E HIS* 4.0 26.2 - - - +
137E ARG* 2.8 22.7 + - - +
138E ALA* 4.1 6.3 - - - +
140E ILE* 1.3 79.4 - - - +
142E GLY* 1.3 64.6 + - - +
144E GLU* 3.4 21.4 + - - +
145E ASN* 3.3 27.1 + - - +
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Residues in contact with GLY 142 (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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84E VAL* 3.0 39.3 - - - +
85E LYS 4.5 0.7 - - - -
86E GLY* 4.1 19.0 - - - -
95E MET* 5.2 1.8 - - - -
138E ALA 3.5 5.9 + - - -
139E THR* 2.9 10.7 + - - -
141E ASP* 1.3 78.4 - - - +
143E LEU* 1.3 55.5 + - - -
145E ASN* 3.0 17.0 + - - +
146E MET 3.1 0.2 + - - -
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Residues in contact with LEU 143 (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 VAL* 5.1 7.0 - - + -
73E VAL* 3.5 41.9 - - + +
74E ALA 4.8 0.7 + - - -
75E LEU* 5.3 0.7 - - + -
80E LEU* 3.8 11.9 - - + -
84E VAL* 4.1 0.8 - - - +
95E MET* 4.2 8.3 - - - -
113E VAL* 5.1 3.4 - - + +
114E LEU* 3.7 32.5 - - + -
117E ALA* 5.5 2.0 - - + -
119E VAL* 4.9 4.0 - - + -
139E THR* 3.1 24.4 + - - +
140E ILE* 3.5 20.0 - - + +
142E GLY* 1.3 68.7 - - - +
144E GLU* 1.3 61.5 + - - +
145E ASN 2.9 5.2 - - - -
146E MET* 3.0 44.5 + - - +
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Residues in contact with GLU 144 (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 ILE* 3.3 30.7 - - + +
72E ASN 5.8 1.6 - - - -
73E VAL* 5.7 0.2 - - - -
140E ILE* 2.8 21.5 + - - +
141E ASP* 3.5 25.0 - - - +
142E GLY 3.1 0.2 - - - -
143E LEU* 1.3 76.1 - - - +
145E ASN* 1.3 65.0 + - - +
146E MET 5.3 0.2 - - - -
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Residues in contact with ASN 145 (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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84E VAL* 4.3 9.2 - - + -
85E LYS 5.4 5.5 + - - +
141E ASP* 3.3 13.8 + - - +
142E GLY* 3.0 10.0 + - - +
143E LEU 2.9 0.4 - - - -
144E GLU* 1.3 91.5 - - - +
146E MET* 1.3 66.4 + - - +
147E ASN* 2.7 24.6 + - - -
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Residues in contact with MET 146 (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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73E VAL* 3.5 23.3 - - + -
74E ALA* 3.8 21.6 - - + +
75E LEU* 4.3 2.5 - - + -
80E LEU* 3.4 44.4 - - + -
81E GLN* 2.8 42.3 + - + +
82E HIS 4.6 0.4 - - - +
84E VAL* 3.7 26.7 - - + +
142E GLY 3.1 5.5 + - - -
143E LEU* 3.0 32.2 + - - +
144E GLU 5.3 0.3 - - - +
145E ASN* 1.3 73.3 - - - +
147E ASN* 1.3 60.0 + - - +
148E SER 3.4 3.3 + - - -
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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