Contacts of the helix formed by residues 119 - 132 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A PRO* 3.1 2.2 + - - +
118A TYR* 1.3 81.7 - - - +
120A GLY* 1.3 64.3 + - - +
122A PRO* 3.2 15.4 - - - +
123A ALA* 3.2 19.8 + - - +
256A HIS* 4.2 7.3 - - - -
263A ARG* 5.2 0.7 + - - +
264A ALA 3.6 10.2 + - - -
265A GLY* 3.8 9.3 - - - -
500A PLG 2.5 24.5 + - - -
118B TYR* 4.0 13.0 + - - -
303B GLY 5.2 0.3 + - - -
305B HIS* 3.4 21.5 + - - -
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Residues in contact with GLY 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A SER* 1.3 69.3 + - - +
121A SER* 1.3 66.5 + - - -
123A ALA* 3.0 18.5 + - - +
124A ASN* 3.2 13.3 + - - -
253A THR 4.8 2.2 - - - -
254A THR* 3.5 25.9 - - - +
265A GLY* 4.8 0.9 - - - -
500A PLG 2.9 31.3 + - - -
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Residues in contact with SER 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLY* 1.3 70.9 - - - +
122A PRO* 1.3 71.1 - - - +
124A ASN* 3.2 6.6 + - - +
125A PHE* 3.0 23.3 + - - +
148A HIS* 4.0 2.4 - - - -
150A THR* 3.4 32.3 - - - +
500A PLG 3.1 25.1 + - - -
300B LEU 3.7 19.7 - - - -
301B GLN 3.9 1.6 + - - -
302B GLY* 3.5 15.3 + - - -
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Residues in contact with PRO 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A PRO* 4.7 1.6 - - + -
118A TYR* 4.3 5.6 - - + +
119A SER* 3.2 34.1 - - - +
120A GLY 3.8 0.2 - - - +
121A SER* 1.3 96.1 - - - +
123A ALA* 1.3 61.4 + - - +
125A PHE* 3.4 5.7 + - + +
126A ALA* 2.9 25.0 + - - +
300A LEU* 5.4 0.7 - - - +
301A GLN* 4.3 17.0 - - + +
118B TYR* 3.9 24.9 - - + -
300B LEU 5.5 2.7 - - - +
301B GLN* 5.8 0.7 - - + -
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A PRO* 3.8 18.5 - - + +
119A SER 3.2 10.2 + - - +
120A GLY* 3.0 12.8 + - - +
122A PRO* 1.3 77.0 - - - +
124A ASN* 1.3 63.5 + - - +
126A ALA* 3.2 15.5 - - - +
127A VAL* 3.2 8.8 + - - +
252A THR* 4.4 8.1 - - - -
253A THR 4.9 1.3 - - - +
266A MSE 4.2 12.6 - - - +
267A ILE* 3.3 30.6 - - + +
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Residues in contact with ASN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLY 3.2 6.1 + - - +
121A SER 3.2 7.2 + - - +
123A ALA* 1.3 74.2 - - - +
125A PHE* 1.3 68.6 + - - +
127A VAL* 2.8 16.5 + - - +
128A TYR* 3.0 37.8 + - + +
150A THR* 2.8 26.1 + - - +
151A HIS* 4.2 1.4 + - - -
226A MSE 3.6 6.5 - - - +
228A ASP* 2.8 24.1 + - - +
252A THR* 2.8 32.0 + - - -
500A PLG 3.8 10.9 - - - -
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Residues in contact with PHE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A SER 3.0 13.8 + - - +
122A PRO* 3.9 5.6 - - + +
124A ASN* 1.3 78.1 - - - +
126A ALA* 1.3 57.5 + - - +
128A TYR* 3.8 12.1 - + - +
129A THR* 2.8 51.3 + - - -
150A THR* 5.8 0.2 - - - -
162A ALA* 4.0 23.6 - - + -
163A THR* 4.8 5.6 - - - -
166A PHE* 3.8 28.5 - + - -
167A PHE* 3.9 18.4 - + - -
300A LEU* 3.7 20.4 - - + -
125B PHE* 4.3 12.8 - + - -
166B PHE* 3.7 24.5 - + - -
300B LEU* 4.8 5.8 - - + -
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A PRO* 5.7 0.7 - - + -
122A PRO 2.9 15.2 + - - +
123A ALA* 3.2 11.9 - - - +
124A ASN 3.0 0.2 - - - -
125A PHE* 1.3 78.0 - - - +
127A VAL* 1.3 56.3 + - - +
129A THR* 3.5 2.8 + - - -
130A ALA* 3.0 27.7 + - - +
267A ILE* 3.9 15.3 - - + -
292A ILE* 5.3 2.1 - - - +
295A ALA* 3.5 4.5 - - - +
296A VAL* 4.1 18.2 - - + -
300A LEU* 3.5 21.9 - - + +
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Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ALA 3.5 13.5 - - - +
124A ASN 2.8 13.1 + - - +
126A ALA* 1.3 70.9 - - - +
128A TYR* 1.3 60.6 + - - +
130A ALA* 3.1 4.5 + - - +
131A LEU* 2.8 53.9 + - + +
197A LEU* 4.2 7.4 - - + -
226A MSE 3.9 20.6 - - - -
250A VAL* 4.2 9.4 - - + -
252A THR* 3.8 13.2 - - + -
267A ILE* 3.7 30.7 - - + -
292A ILE* 4.7 5.8 - - + -
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Residues in contact with TYR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ASN* 3.0 28.9 + - + +
125A PHE* 3.8 10.8 - + - +
127A VAL* 1.3 76.0 - - - +
129A THR* 1.3 60.3 + - - +
132A VAL* 2.7 32.9 + - - +
133A GLU 3.0 8.1 + - - -
138A ILE* 3.7 18.4 - - + -
150A THR* 2.4 31.0 + - - -
151A HIS* 3.6 6.6 - - - -
163A THR* 3.5 27.4 - - + -
167A PHE* 3.5 25.0 - + + -
197A LEU* 4.4 12.1 - - + -
199A ILE* 3.2 28.9 - - + +
226A MSE 3.7 21.4 - - + +
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Residues in contact with THR 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PHE* 2.8 45.7 + - - -
126A ALA 3.5 5.2 - - - -
128A TYR* 1.3 78.6 - - - +
130A ALA* 1.3 59.9 - - - +
133A GLU* 4.0 16.1 + - - +
134A PRO* 5.5 0.7 - - - +
167A PHE* 3.8 7.1 - - - -
295A ALA* 4.1 15.0 - - + -
299A GLY* 6.2 1.1 - - - -
300A LEU* 3.8 14.4 - - + +
162B ALA* 5.7 0.4 - - + -
165B ILE* 4.7 17.5 - - + -
166B PHE* 3.6 18.6 - - + -
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ALA 3.0 18.3 + - - +
127A VAL 3.1 2.9 + - - +
129A THR* 1.3 79.7 - - - +
131A LEU* 1.3 63.7 + - - +
133A GLU* 4.6 8.8 - - - +
291A LEU* 3.4 49.9 - - + +
292A ILE* 3.7 15.0 - - + +
295A ALA* 3.5 8.7 - - + -
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A VAL* 2.8 39.3 + - + +
130A ALA* 1.3 82.6 - - + +
132A VAL* 1.3 61.0 + - - +
133A GLU* 4.5 4.2 - - - +
196A LYS* 3.6 20.7 + - - +
197A LEU* 4.6 10.8 - - + -
224A TYR* 4.1 34.0 - - + -
250A VAL* 4.1 13.0 - - + -
288A LEU* 3.6 33.9 - - + -
291A LEU* 3.9 26.0 - - + -
292A ILE* 4.4 8.3 - - + -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A TYR* 2.7 27.8 + - - +
131A LEU* 1.3 76.8 - - - +
133A GLU* 1.3 75.6 + - - +
136A GLY* 3.3 38.6 - - - +
137A ARG 4.0 2.9 - - - +
138A ILE* 3.8 25.8 - - + -
167A PHE* 3.7 9.6 - - + -
196A LYS* 3.2 24.4 + - + +
197A LEU* 3.9 25.4 - - + -
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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