Contacts of the helix formed by residues 123 - 141 (chain E) in PDB entry 3J8B
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 PHE 123 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91E ILE 4.4 5.9 + - - +
121E HIS* 3.2 15.0 - - + +
122E GLY* 1.3 78.0 - - - +
124E ARG* 1.3 65.7 + - - +
125E GLN* 3.3 3.1 - - + +
126E GLU* 3.5 16.6 + - + +
127E TYR* 3.3 21.5 + - - +
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Residues in contact with ARG 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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122E GLY 4.2 1.2 + - - -
123E PHE* 1.3 68.5 - - - +
125E GLN* 1.3 60.9 + - - +
127E TYR* 3.4 7.1 + - - +
128E LEU* 2.9 30.1 + - - +
157E LEU* 3.9 27.6 - - + +
159E PRO* 5.8 5.4 - - + -
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Residues in contact with GLN 125 (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 PHE* 3.3 3.0 - - + +
124E ARG* 1.3 78.0 - - - +
126E GLU* 1.3 57.9 + - - +
128E LEU* 3.2 8.2 + - - +
129E ASP* 2.9 29.1 + - - +
157E LEU 5.5 0.4 - - - -
159E PRO* 6.5 0.7 - - + -
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Residues in contact with GLU 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E ILE* 4.4 16.4 - - + +
121E HIS* 6.1 3.1 - - + -
123E PHE* 3.5 19.0 + - + +
124E ARG 3.3 0.6 - - - -
125E GLN* 1.3 77.0 - - - +
127E TYR* 1.3 58.8 + - - +
129E ASP* 3.2 8.1 + - - +
130E THR* 2.9 27.7 + - - -
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Residues in contact with TYR 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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91E ILE* 4.3 18.1 - - + +
92E VAL* 5.4 2.9 - - - +
123E PHE 3.3 11.3 + - - +
124E ARG* 3.7 10.1 - - - +
125E GLN 3.3 0.2 - - - -
126E GLU* 1.3 78.6 - - - +
128E LEU* 1.3 57.2 + - - +
130E THR* 3.2 8.9 + - - -
131E LEU* 2.9 28.3 + - - +
157E LEU* 4.8 9.0 - - + -
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Residues in contact with LEU 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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124E ARG 2.9 18.4 + - - +
125E GLN* 3.4 7.9 - - - +
127E TYR* 1.3 78.0 - - - +
129E ASP* 1.3 57.0 + - - +
131E LEU* 3.2 7.8 + - - +
132E TYR* 2.9 29.3 + - - +
154E PHE* 4.6 13.1 - - + +
157E LEU* 4.3 21.3 - - + +
158E VAL* 5.8 1.1 - - - -
164E ASN* 6.4 1.3 - - + -
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Residues in contact with ASP 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E GLN 2.9 14.0 + - - +
126E GLU* 3.2 11.6 + - - +
128E LEU* 1.3 76.2 - - - +
130E THR* 1.3 52.6 + - - +
132E TYR* 3.2 7.9 + - - +
133E ARG* 2.5 40.1 + - + +
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Residues in contact with THR 130 (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 LEU* 5.5 2.1 - - - +
87E GLU* 5.4 2.9 - - - -
88E THR* 4.0 32.5 - - - -
91E ILE* 5.1 3.1 - - - -
126E GLU 2.9 14.0 + - - -
127E TYR* 3.2 11.6 + - - -
129E ASP* 1.3 75.7 - - - +
131E LEU* 1.3 58.2 + - - +
133E ARG* 3.7 6.3 - - - +
134E TYR* 2.8 31.4 + - - +
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Residues in contact with LEU 131 (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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127E TYR 2.9 12.9 + - - +
128E LEU* 3.6 7.9 - - - +
130E THR* 1.3 76.8 - - - +
132E TYR* 1.3 58.0 + - - +
134E TYR* 3.5 5.4 + - - +
135E ALA* 3.0 21.5 + - - +
150E TYR* 3.1 31.4 - - - +
153E PHE* 4.5 7.6 - - + -
154E PHE* 4.1 21.5 - - + +
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Residues in contact with TYR 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E LEU 2.9 17.9 + - - +
129E ASP* 3.4 7.6 - - - +
131E LEU* 1.3 77.0 - - - +
133E ARG* 1.3 57.7 + - - +
135E ALA* 3.1 8.6 + - - +
136E LYS* 2.8 28.1 + - - +
150E TYR 5.1 0.4 - - - -
151E LEU* 5.6 1.8 - - - +
154E PHE* 5.2 4.6 - - + +
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Residues in contact with ARG 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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84E LEU* 5.8 7.8 - - + +
129E ASP* 2.5 22.2 + - + +
130E THR* 3.2 7.2 + - - +
132E TYR* 1.3 72.7 - - - +
134E TYR* 1.3 58.7 + - - +
136E LYS* 3.4 7.9 + - - +
137E PHE* 2.9 29.1 + - - +
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Residues in contact with TYR 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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84E LEU* 5.5 10.4 - - + +
130E THR 2.8 18.0 + - - +
131E LEU* 3.7 6.5 - - - +
133E ARG* 1.3 74.2 - - - +
135E ALA* 1.3 58.4 + - - +
137E PHE* 3.7 6.3 - - - +
138E GLN* 2.9 31.5 + - - +
150E TYR* 3.9 16.3 - - + +
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Residues in contact with ALA 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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131E LEU 3.0 15.1 + - - +
132E TYR* 3.1 12.3 - - - +
134E TYR* 1.3 75.3 - - - +
136E LYS* 1.3 65.9 + - - +
138E GLN 3.4 0.7 + - - -
139E TYR* 2.9 26.2 + - - +
147E ALA* 3.6 30.5 - - - +
150E TYR* 4.2 2.4 - - - +
151E LEU* 3.8 17.5 - - + +
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Residues in contact with LYS 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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132E TYR 2.8 15.7 + - - +
133E ARG* 3.7 9.4 - - - +
134E TYR 3.4 0.2 - - - -
135E ALA* 1.3 75.0 - - - +
137E PHE* 1.3 57.0 + - - +
139E TYR* 3.2 5.5 + - - +
140E GLU* 3.0 33.7 + - - +
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Residues in contact with PHE 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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80E GLN* 5.9 7.6 - - + -
81E LEU* 6.5 0.4 - - - -
84E LEU* 6.0 5.6 - - + -
133E ARG 2.9 17.9 + - - +
134E TYR* 3.7 7.9 - - - +
135E ALA 3.2 0.2 - - - -
136E LYS* 1.3 77.6 - - - +
138E GLN* 1.3 60.0 + - - +
140E GLU* 4.1 4.3 - - - +
141E CYS* 3.0 28.3 + - - +
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Residues in contact with GLN 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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134E TYR 2.9 18.2 + - - +
137E PHE* 1.3 75.8 - - - +
139E TYR* 1.3 62.8 + - - +
141E CYS* 3.3 7.0 + - - +
142E GLY 2.9 4.9 + - - -
143E ASN* 2.8 47.4 + - + +
146E GLY* 4.2 4.7 - - - -
147E ALA* 3.6 17.3 - - - +
150E TYR* 6.2 0.2 - - + -
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Residues in contact with TYR 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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135E ALA 2.9 19.5 + - - +
136E LYS* 3.6 6.1 - - - +
138E GLN* 1.3 76.5 - - - +
140E GLU* 1.3 55.1 + - - +
142E GLY* 2.7 27.1 + - - -
143E ASN 4.7 1.6 - - - +
144E TYR* 5.6 1.1 - - - +
147E ALA* 3.6 15.2 - - + +
175E SER* 6.5 0.2 - - - -
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Residues in contact with GLU 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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48E THR* 5.4 2.1 - - - -
49E ASN* 3.5 19.0 + - + +
50E MET* 3.4 24.3 + - - +
136E LYS 3.0 17.0 + - - +
137E PHE* 4.2 3.8 - - - +
139E TYR* 1.3 75.6 - - - +
141E CYS* 1.3 60.2 + - - +
142E GLY 3.0 1.1 + - - -
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Residues in contact with CYS 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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49E ASN* 3.9 14.4 - - + +
50E MET* 4.1 11.4 - - - +
51E VAL 5.1 0.7 + - - -
52E ASP* 5.6 4.5 - - - +
77E VAL* 6.0 5.8 - - + -
137E PHE 3.0 22.6 + - - +
138E GLN* 3.4 9.2 - - - +
140E GLU* 1.3 75.6 - - - +
142E GLY* 1.3 60.8 + - - +
143E ASN* 3.3 6.4 + - + +
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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