Contacts of the helix formed by residues 119 - 132 (chain C) in PDB entry 1EJI
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 SER 119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117C PRO* 3.0 2.4 + - - +
118C TYR* 1.3 81.0 - - - +
120C GLY* 1.3 64.1 + - - +
122C PRO* 3.3 16.5 - - - +
123C ALA* 3.2 21.5 + - - +
256C HIS* 4.3 5.5 - - - -
263C ARG* 5.2 0.3 + - - -
264C ALA 3.6 10.2 + - - -
265C GLY* 3.8 9.3 - - - -
502C PLG 2.6 26.7 + - - -
118D TYR* 3.9 13.1 + - - -
303D GLY 4.9 0.3 + - - -
305D HIS* 3.3 21.3 + - - -
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Residues in contact with GLY 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C SER* 1.3 77.2 + - - +
121C SER* 1.3 66.2 + - - +
123C ALA* 3.0 18.0 + - - +
124C ASN* 3.2 13.9 + - - -
253C THR 4.8 2.7 - - - -
254C THR* 3.4 18.1 - - - +
264C ALA 4.1 0.6 + - - -
265C GLY* 4.8 0.2 - - - -
502C PLG 3.1 28.8 + - - -
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Residues in contact with SER 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C GLY* 1.3 70.4 - - - +
122C PRO* 1.3 71.7 - - - +
124C ASN* 3.1 9.6 + - - +
125C PHE* 3.0 23.7 + - - +
148C HIS* 4.0 7.8 - - - -
150C THR* 3.3 32.7 - - - +
502C PLG 3.1 16.2 + - - -
300D LEU 3.7 18.6 - - - -
301D GLN 3.9 1.1 + - - -
302D GLY* 3.5 17.3 + - - -
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Residues in contact with PRO 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C PRO* 4.7 1.1 - - - -
118C TYR* 4.3 11.7 - - + +
119C SER* 3.3 34.3 - - - +
121C SER* 1.3 96.9 - - - +
123C ALA* 1.3 62.5 + - - +
125C PHE* 3.4 6.7 + - + +
126C ALA* 2.9 25.5 + - - +
300C LEU* 5.6 0.5 - - - +
301C GLN* 4.3 9.2 - - + +
502C PLG 4.2 0.2 - - - +
118D TYR* 3.8 25.4 - - + -
300D LEU 5.4 3.8 - - - +
301D GLN* 5.6 0.7 - - + -
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Residues in contact with ALA 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C PRO* 3.8 20.1 - - + +
119C SER 3.2 10.7 + - - +
120C GLY* 3.0 12.0 + - - +
122C PRO* 1.3 77.6 - - - +
124C ASN* 1.3 64.1 + - - +
126C ALA* 3.2 6.2 - - - +
127C VAL* 3.2 18.7 + - - +
252C THR* 4.4 7.9 - - - -
253C THR 4.9 1.8 - - - +
266C MSE 4.2 12.3 - - - +
267C ILE* 3.2 28.0 - - + +
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Residues in contact with ASN 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C GLY 3.2 7.0 + - - -
121C SER 3.1 6.8 + - - +
123C ALA* 1.3 74.7 - - - +
125C PHE* 1.3 67.6 + - - +
127C VAL* 2.8 16.8 + - - +
128C TYR* 3.0 40.9 + - + +
150C THR* 3.1 23.8 + - - +
151C HIS* 4.3 0.2 + - - -
226C MSE 3.4 9.8 - - - +
228C ASP* 2.8 22.5 + - - +
252C THR* 2.7 31.3 + - - -
502C PLG 3.9 11.5 - - - -
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Residues in contact with PHE 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C SER 3.0 14.1 + - - +
122C PRO* 3.9 6.7 - - + +
124C ASN* 1.3 75.9 - - - +
126C ALA* 1.3 56.6 + - - +
128C TYR* 3.4 12.9 + + - +
129C THR* 2.8 51.0 + - - -
150C THR* 5.9 0.2 - - - -
162C ALA* 4.0 23.8 - - + -
163C THR* 4.8 5.6 - - - -
166C PHE* 3.7 31.6 - + - -
167C PHE* 3.8 22.7 - + - -
300C LEU* 3.8 20.4 - - + -
125D PHE* 4.3 13.5 - + - -
166D PHE* 3.9 18.4 - + - -
300D LEU* 4.7 8.5 - - + +
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Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C PRO* 5.6 0.9 - - + -
122C PRO 2.9 13.1 + - - +
123C ALA* 3.2 12.6 - - - +
125C PHE* 1.3 79.1 - - - +
127C VAL* 1.3 57.5 + - - +
129C THR* 3.4 0.5 + - - -
130C ALA* 3.0 21.8 + - - +
267C ILE* 3.9 13.9 - - + -
292C ILE* 5.5 1.1 - - - -
295C ALA* 3.4 13.3 - - - +
296C VAL* 4.1 18.4 - - + +
300C LEU* 3.6 22.0 - - + +
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Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C ALA 3.4 13.5 - - - +
124C ASN 2.8 8.2 + - - +
126C ALA* 1.3 74.8 - - - +
128C TYR* 1.3 60.8 + - - +
130C ALA* 3.0 5.5 + - - +
131C LEU* 2.7 54.5 + - + +
197C LEU* 4.3 7.4 - - + -
226C MSE 4.0 20.4 - - + -
250C VAL* 4.3 9.4 - - + -
252C THR* 3.8 13.2 - - + -
267C ILE* 3.7 31.0 - - + -
292C ILE* 4.7 5.6 - - + -
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Residues in contact with TYR 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ASN* 3.0 33.9 + - + +
125C PHE* 3.8 11.4 - + - +
127C VAL* 1.3 76.7 - - - +
129C THR* 1.3 59.1 + - - +
132C VAL* 2.7 34.0 + - - +
133C GLU 3.1 8.3 + - - -
138C ILE* 3.8 20.6 - - + -
150C THR* 2.7 31.4 + - - -
151C HIS* 4.0 1.0 - - - -
163C THR* 3.5 26.0 - - + -
167C PHE* 3.5 25.1 - + + -
197C LEU* 4.3 13.5 - - + -
199C ILE* 3.4 25.3 - - + +
226C MSE 3.6 26.3 - - + +
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Residues in contact with THR 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C PHE* 2.8 47.0 + - - -
126C ALA 3.5 5.2 - - - -
128C TYR* 1.3 79.8 - - - +
130C ALA* 1.3 60.8 + - - +
133C GLU* 4.0 15.5 + - - +
134C PRO* 5.5 0.9 - - - +
167C PHE* 4.1 7.8 - - - -
295C ALA* 4.4 9.0 - - + -
299C GLY* 6.4 0.4 - - - -
300C LEU* 3.8 17.6 - - + +
162D ALA* 5.7 0.7 - - + -
165D ILE* 4.9 15.7 - - + -
166D PHE* 3.4 22.8 - - + -
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Residues in contact with ALA 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C ALA 3.0 10.8 + - - +
127C VAL 3.7 2.7 - - - +
129C THR* 1.3 80.8 - - - +
131C LEU* 1.3 61.0 + - + +
133C GLU* 4.7 9.1 - - - +
291C LEU* 3.5 41.9 - - + +
292C ILE* 3.7 13.9 - - + +
295C ALA* 3.4 26.2 - - + -
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Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C VAL* 2.7 40.6 + - + +
130C ALA* 1.3 82.4 - - + +
132C VAL* 1.3 61.4 + - - +
133C GLU* 3.8 4.6 - - - +
196C LYS* 3.5 21.0 + - - +
197C LEU* 4.6 10.3 - - + -
224C TYR* 4.1 34.0 - - + -
250C VAL* 4.1 13.5 - - + -
288C LEU* 3.6 33.7 - - + -
291C LEU* 4.0 23.1 - - + -
292C ILE* 4.4 8.1 - - + -
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C TYR* 2.7 23.9 + - - +
131C LEU* 1.3 75.1 - - - +
133C GLU* 1.3 73.4 + - - +
136C GLY* 3.3 39.2 - - - +
137C ARG 4.1 3.8 - - - +
138C ILE* 3.8 25.6 - - + -
167C PHE* 3.6 9.6 - - + -
196C LYS* 3.2 24.4 + - + +
197C LEU* 3.9 29.8 - - + -
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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