Contacts of the helix formed by residues 125 - 139 (chain E) in PDB entry 6N0M
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 CYS 125 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E ALA* 3.3 21.4 + - + +
123E HIS 3.0 2.4 - - - +
124E GLN* 1.3 71.8 - - - +
126E SER* 1.3 65.2 + - - +
127E TYR* 3.1 4.3 - - - -
128E LEU* 3.0 34.9 + - - -
129E VAL* 2.8 22.5 + - - +
208E SER* 3.7 14.6 - - - +
211E VAL* 4.1 18.2 - - - -
212E PHE* 3.8 24.2 - - + -
312E MET* 3.7 5.3 - - - -
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Residues in contact with SER 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E GLN 3.0 10.8 + - - -
125E CYS* 1.3 71.1 - - - +
127E TYR* 1.3 64.2 + - - +
129E VAL* 4.3 2.2 - - - -
130E GLY* 2.8 22.3 + - - -
212E PHE* 5.2 0.4 - - - -
218E PRO* 5.8 4.8 - - - +
312E MET* 3.6 21.7 - - - +
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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
----------------------------------------------------------
77E ASP* 3.1 23.4 - - - +
78E ASN 3.3 0.9 + - - -
79E LEU* 3.1 30.5 + - + -
125E CYS* 3.1 1.5 - - - -
126E SER* 1.3 84.2 + - - +
128E LEU* 1.3 73.9 + - + +
130E GLY* 3.8 0.3 - - - -
131E SER* 3.0 29.4 + - - -
211E VAL* 3.7 26.5 - - + -
216E ILE* 3.4 21.5 - - + +
217E LEU 3.2 28.9 - - - -
218E PRO* 3.7 24.0 - - + +
219E GLU* 3.0 28.4 + - - -
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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
----------------------------------------------------------
79E LEU* 4.5 8.7 - - + -
116E ALA 5.1 0.2 - - - +
120E ALA* 3.6 16.1 - - + +
125E CYS* 3.0 16.5 + - - -
127E TYR* 1.3 89.8 - - + +
129E VAL* 1.3 66.8 + - - +
131E SER* 4.2 4.9 - - - +
132E HIS* 3.1 54.7 + - + +
204E CYS* 3.8 12.3 - - + +
207E LEU* 3.6 31.9 - - + +
208E SER* 3.5 29.2 - - - +
211E VAL* 4.0 3.8 - - + -
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Residues in contact with VAL 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E ILE* 3.9 22.2 - - + +
120E ALA* 3.8 4.9 - - + -
121E ALA* 3.8 28.3 - - + +
125E CYS 2.8 19.5 + - - +
126E SER* 4.0 2.7 - - - +
128E LEU* 1.3 77.1 - - - +
130E GLY* 1.3 52.5 + - - +
132E HIS* 3.6 0.3 - - - -
133E MET* 2.6 60.5 + - + +
311E ASP* 6.0 0.7 - - - +
312E MET* 3.8 32.5 - - + -
315E PHE* 4.9 3.8 - - + -
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Residues in contact with GLY 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E SER 2.8 19.0 + - - -
127E TYR 3.8 0.2 - - - -
129E VAL* 1.3 75.0 - - - +
131E SER* 1.3 68.6 + - - +
133E MET* 3.1 10.7 + - - +
134E ALA* 2.9 23.0 + - - +
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Residues in contact with SER 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E ASP* 5.4 4.3 + - - -
127E TYR* 3.0 27.8 + - - -
128E LEU* 3.7 10.3 - - - +
130E GLY* 1.3 77.7 - - - +
132E HIS* 1.3 69.3 + - - -
134E ALA* 2.9 6.2 + - - +
135E GLU* 2.9 45.7 + - - +
219E GLU* 5.9 1.8 - - - -
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Residues in contact with HIS 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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97E HIS* 5.1 2.9 - - - -
101E LEU* 3.5 34.9 - - + +
113E HIS* 3.3 32.8 + - - +
116E ALA* 3.1 29.5 - - + +
117E ILE* 3.9 9.2 - - + -
128E LEU* 3.1 41.7 + - + +
131E SER* 1.3 81.7 + - - +
133E MET* 1.3 57.7 + - - +
135E GLU* 3.6 18.7 + - - +
136E PHE* 2.6 36.9 + - - +
204E CYS* 4.1 6.5 - - - -
207E LEU* 5.9 1.4 - - - +
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Residues in contact with MET 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E ILE* 3.8 11.5 - - - +
129E VAL* 2.6 43.4 + - + +
130E GLY* 3.2 11.2 - - - +
132E HIS* 1.3 70.9 - - - +
134E ALA* 1.3 62.8 + - - +
136E PHE* 3.3 3.5 - - - +
137E LEU* 3.1 28.1 + - + +
146E LEU* 3.5 33.4 - - + +
311E ASP* 3.7 24.9 - - - +
315E PHE* 4.2 24.7 - - + -
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Residues in contact with ALA 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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130E GLY 2.9 10.8 + - - +
131E SER* 3.4 8.3 - - - +
133E MET* 1.3 75.8 - - - +
135E GLU* 1.3 53.4 + - + +
137E LEU* 2.9 16.3 + - - +
138E GLN* 2.8 49.2 + - + +
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Residues in contact with GLU 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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97E HIS* 5.4 2.8 + - - -
102E HIS* 3.4 28.0 + - - -
113E HIS* 3.6 28.8 + - + +
131E SER* 2.9 34.6 + - - +
132E HIS* 3.6 15.0 + - - +
134E ALA* 1.3 72.7 - - + +
136E PHE* 1.3 65.5 + - - +
138E GLN* 3.9 12.5 - - + +
139E THR* 3.1 28.2 + - - +
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Residues in contact with PHE 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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110E SER* 3.3 32.3 - - - -
113E HIS* 3.9 11.6 - - + +
114E TYR* 4.1 8.3 - + + -
117E ILE* 4.2 7.0 - - + -
132E HIS 2.6 23.7 + - - +
133E MET 3.3 3.8 - - - +
135E GLU* 1.3 74.6 - - - +
137E LEU* 1.3 61.6 + - + +
139E THR* 3.3 7.7 - - - +
141E GLY* 2.8 50.7 + - - -
142E ASP 3.4 26.0 - - - -
143E PRO* 4.6 0.9 - - + -
145E TRP* 3.5 34.3 - + + -
146E LEU* 3.3 37.7 - - + -
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Residues in contact with LEU 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E MET* 3.1 13.9 + - + +
134E ALA* 2.9 14.7 + - - +
136E PHE* 1.3 74.9 - - + +
138E GLN* 1.3 66.8 + - - +
139E THR 3.2 0.7 + - - -
140E GLY* 3.2 12.1 + - - -
141E GLY 3.7 11.3 + - - +
143E PRO* 3.9 33.7 - - + -
146E LEU* 3.6 29.8 - - + -
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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 ALA* 2.8 38.5 + - + +
135E GLU* 3.9 10.8 - - + +
137E LEU* 1.3 76.1 - - - +
139E THR* 1.3 57.8 + - - +
140E GLY 3.5 3.1 + - - -
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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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109E SER* 3.4 24.3 + - - -
110E SER* 3.5 31.6 + - - +
113E HIS* 3.9 7.4 - - + -
135E GLU 3.1 22.3 + - - +
136E PHE 3.3 9.4 - - - +
137E LEU 3.1 0.4 - - - -
138E GLN* 1.3 76.5 - - - +
140E GLY* 1.3 54.5 + - - +
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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