Contacts of the helix formed by residues 122 - 138 (chain D) in PDB entry 6E7P
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 ARG 122 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A PRO 2.9 24.7 + - - -
141A ASP* 3.6 21.7 + - - +
142A VAL 2.7 17.3 + - - +
143A SER 3.3 17.7 + - - +
144A LEU* 3.5 25.8 - - + +
121D THR* 1.3 73.7 - - - +
123D GLU* 1.3 61.9 + - - +
124D GLN 3.4 0.2 - - - -
125D LEU* 3.5 6.2 + - - +
126D TYR* 3.2 30.4 + - + -
225D PHE* 3.2 44.1 - - + -
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Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ASP 5.3 0.3 - - - +
142A VAL* 3.8 20.2 - - - +
121D THR* 3.2 27.2 + - - +
122D ARG* 1.3 78.9 + - - +
124D GLN* 1.3 65.4 + - + +
125D LEU 3.2 0.9 - - - -
126D TYR* 3.8 12.9 - - + +
127D GLN* 3.2 36.6 + - + +
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Residues in contact with GLN 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LEU* 5.7 0.5 - - - +
118D ALA 4.4 2.2 - - - +
119D ALA* 3.3 17.5 - - + +
120D TYR* 2.5 43.3 + - - +
121D THR* 2.8 32.1 + - + +
123D GLU* 1.3 78.5 - - + +
125D LEU* 1.3 58.1 + - - +
127D GLN* 4.1 5.4 - - - +
128D ALA* 3.2 27.2 + - - +
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 4.5 2.2 - - + -
119D ALA* 4.4 12.1 - - + +
121D THR 4.0 9.0 + - - +
122D ARG 3.5 11.5 + - - +
123D GLU 3.2 0.6 - - - -
124D GLN* 1.3 78.5 - - - +
126D TYR* 1.3 63.7 + - - +
128D ALA* 3.5 1.1 + - - +
129D ILE* 3.2 35.1 + - + +
223D LEU* 3.8 15.9 - - + -
225D PHE* 3.6 28.3 - - + -
228D LEU* 4.5 5.6 - - + -
231D VAL* 5.8 1.6 - - + -
262D PHE* 3.6 36.8 - - + -
271D ILE* 3.7 30.5 - - + -
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Residues in contact with TYR 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D ARG* 3.2 29.3 + - + -
123D GLU* 3.6 10.1 + - + +
124D GLN 3.4 0.4 - - - -
125D LEU* 1.3 78.1 - - - +
127D GLN* 1.3 63.6 + - + +
129D ILE* 3.3 5.5 + - + +
130D PHE* 3.1 61.1 + + + -
221D LEU* 4.1 16.5 + - + -
222D THR* 4.3 3.1 - - - +
223D LEU* 3.7 35.2 + - + -
225D PHE* 3.8 29.1 - + - -
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Residues in contact with GLN 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LEU* 3.6 25.0 - - + +
123D GLU* 3.2 25.8 + - + +
124D GLN* 4.4 5.4 - - - +
126D TYR* 1.3 78.3 - - + +
128D ALA* 1.3 60.0 + - - +
130D PHE* 4.1 7.1 - - + +
131D HIS* 3.3 25.8 + - - +
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Residues in contact with ALA 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D PHE 4.9 2.4 - - - +
106D LEU* 6.0 0.2 - - - -
107D LEU* 4.4 19.4 + - + +
119D ALA* 5.4 0.2 - - + -
124D GLN 3.2 20.0 + - - +
125D LEU* 3.9 3.8 - - + +
126D TYR 3.2 0.8 - - - -
127D GLN* 1.3 78.4 - - - +
129D ILE* 1.3 62.2 + - - +
131D HIS* 4.3 1.6 - - - +
132D ALA* 3.4 20.8 + - - +
262D PHE* 3.7 27.7 - - + -
273D ILE* 4.4 12.1 - - + -
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Residues in contact with ILE 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LEU* 3.2 24.2 + - + +
126D TYR* 3.3 8.3 + - + +
128D ALA* 1.3 76.2 - - - +
130D PHE* 1.3 77.8 + - + +
132D ALA* 3.2 13.8 + - - +
133D VAL* 3.2 14.4 + - + +
165D LEU* 4.2 28.7 - - + -
221D LEU* 5.0 5.2 - - + -
223D LEU* 4.1 31.0 - - + -
231D VAL* 4.5 16.4 - - + -
233D ILE* 4.6 8.0 - - + +
262D PHE* 4.0 24.5 - - + -
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Residues in contact with PHE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D TYR* 3.1 53.2 + + + +
127D GLN* 4.6 5.8 - - + +
129D ILE* 1.3 89.3 - - + +
131D HIS* 1.3 58.4 + - - +
133D VAL* 3.2 6.1 + - + +
134D ASP* 3.0 42.9 + - - +
218D TYR* 4.5 22.4 - + - -
219D LYS* 4.4 43.3 - - + +
221D LEU* 4.7 10.3 - - + -
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Residues in contact with HIS 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU 4.2 9.2 + - - -
105D PHE 4.6 2.9 - - - -
106D LEU 4.3 5.7 + - - -
107D LEU* 3.6 49.3 - - + +
127D GLN 3.3 18.7 + - - +
128D ALA 4.3 2.7 - - - +
129D ILE 3.3 0.4 - - - -
130D PHE* 1.3 78.8 - - - +
132D ALA* 1.3 61.6 + - - +
134D ASP* 4.3 7.4 - - - +
135D GLN* 3.4 48.2 + - + +
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Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D PHE* 3.7 32.9 - - - +
128D ALA 3.4 12.9 + - - +
129D ILE 3.2 11.6 + - - +
131D HIS* 1.3 80.8 - - - +
133D VAL* 1.3 60.6 + - - +
136D TYR* 3.8 16.3 + - - +
163D LEU* 5.2 0.9 - - - +
233D ILE* 4.3 15.7 - - + +
235D PHE* 5.8 2.9 - - - -
260D ILE* 4.3 19.1 - - + +
262D PHE* 5.5 1.1 - - + -
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Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ILE* 3.4 15.7 - - + +
130D PHE* 3.2 7.2 + - - +
132D ALA* 1.3 77.6 - - - +
134D ASP* 1.3 59.9 + - - +
136D TYR* 3.0 6.1 + - - +
137D LEU* 3.0 32.6 + - + +
163D LEU* 4.0 26.0 - - + -
165D LEU* 3.9 27.6 - - + -
195D VAL* 5.0 6.3 - - + -
218D TYR* 3.6 38.6 - - + +
233D ILE* 4.8 6.5 - - + -
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Residues in contact with ASP 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D PHE* 3.0 30.8 + - - +
131D HIS* 4.2 8.1 + - - +
133D VAL* 1.3 76.0 - - - +
135D GLN* 1.3 65.9 + - + +
137D LEU* 3.2 9.2 + - - +
138D ALA* 3.1 24.3 + - - +
218D TYR* 3.0 26.5 + - - -
219D LYS* 4.3 12.3 + - - -
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Residues in contact with GLN 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C THR* 5.6 3.8 - - - +
104D LEU* 3.3 41.3 + - + +
105D PHE* 4.0 13.0 - - + -
131D HIS* 3.4 37.2 + - + +
132D ALA 4.6 0.2 - - - +
133D VAL 3.3 0.4 - - - -
134D ASP* 1.3 78.8 - - + +
136D TYR* 1.3 63.3 + - - +
138D ALA* 3.3 6.3 + - - +
139D LEU* 3.2 28.5 + - + +
142D VAL* 3.8 28.8 - - - +
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Residues in contact with TYR 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D PHE* 4.2 10.2 - + + -
132D ALA 3.8 12.1 + - - +
133D VAL 3.0 10.9 + - - +
135D GLN* 1.3 80.8 - - - +
137D LEU* 1.3 68.8 + - + +
138D ALA 3.3 0.3 + - - -
139D LEU* 3.7 7.1 + - + +
149D TYR* 2.8 63.5 + + - +
150D VAL* 5.3 1.6 + - - +
162D GLY* 4.0 17.2 + - - -
163D LEU* 3.5 41.7 - - + -
195D VAL* 5.1 1.1 - - + -
196D ASP 5.3 0.4 - - - -
197D PRO* 4.1 19.1 - - + +
235D PHE* 3.7 41.4 - + + +
236D ARG 5.0 2.6 + - - -
237D LEU* 4.8 5.8 - - + -
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D VAL* 3.0 20.7 + - + +
134D ASP* 3.2 9.8 + - - +
136D TYR* 1.3 84.2 - - + +
138D ALA* 1.3 58.0 + - + +
139D LEU 3.6 0.6 + - - -
140D PRO* 5.2 1.4 - - - +
149D TYR* 4.2 6.7 + - - -
195D VAL* 4.3 20.0 - - + -
196D ASP 4.3 4.0 - - - +
197D PRO* 4.4 3.8 - - + -
198D PRO* 3.9 37.5 - - + +
216D SER 5.9 0.7 - - - +
218D TYR* 3.4 37.0 - - + +
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D ASP 3.1 15.1 + - - +
135D GLN* 3.3 8.5 + - - +
136D TYR 3.2 0.4 - - - -
137D LEU* 1.3 80.5 - - + +
139D LEU* 1.3 61.9 + - - +
140D PRO* 3.6 4.0 - - - -
141D ASP* 3.4 18.8 + - + +
142D VAL* 3.3 27.7 + - + +
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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
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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