Contacts of the helix formed by residues 136 - 150 (chain B) in PDB entry 1X7O
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 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B PRO* 3.6 0.7 - - - +
135B THR* 1.3 77.4 + - - +
137B PRO* 1.3 67.4 - - - +
138B GLY* 3.5 5.7 + - - -
139B ASN* 3.1 50.4 + - - +
140B ILE* 3.4 14.6 + - - +
162B ALA* 4.4 2.5 - - - -
234B GLU* 3.5 7.2 + - - +
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Residues in contact with PRO 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B THR 3.6 8.5 - - - +
136B SER* 1.3 81.9 - - - +
138B GLY* 1.3 65.5 + - - +
140B ILE* 3.0 23.7 + - + +
141B GLY 3.1 11.3 + - - -
162B ALA* 3.9 11.0 - - + -
163B ASP 4.3 2.9 - - - +
166B ASP* 3.7 44.2 - - + +
168B LYS* 4.3 18.2 - - + +
169B SER* 3.3 18.1 - - - +
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Residues in contact with GLY 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B SER* 3.2 5.6 + - - -
137B PRO* 1.3 81.2 - - - +
139B ASN* 1.3 61.2 + - - +
142B SER* 3.2 13.7 + - - -
168B LYS* 4.1 14.7 - - - +
172B SER* 3.1 26.7 + - - -
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Residues in contact with ASN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B PHE* 3.8 17.7 - - + -
136B SER* 3.1 24.6 + - - +
137B PRO 3.2 0.4 - - - -
138B GLY* 1.3 74.4 - - - +
140B ILE* 1.3 65.8 + - - +
142B SER* 3.6 5.1 - - - -
143B ILE* 3.0 29.1 + - - +
234B GLU* 3.0 37.8 + - - +
262B ASN* 3.0 26.6 + - - +
263B ALA* 4.5 3.8 - - - +
264B ALA* 4.1 12.3 - - + +
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Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B PHE* 4.2 10.3 - - + -
134B PRO* 4.0 26.5 - - + -
136B SER 3.4 8.0 + - - +
137B PRO* 3.0 12.8 + - + +
139B ASN* 1.3 75.8 - - - +
141B GLY* 1.3 63.9 + - - +
143B ILE* 3.2 4.7 + - - +
144B ILE* 3.0 38.2 + - + +
155B LEU* 4.2 3.8 - - + +
157B VAL* 4.2 13.0 - - + -
162B ALA* 3.4 42.0 - - + +
163B ASP 4.2 7.0 - - - +
164B VAL* 4.0 17.7 - - + +
169B SER* 3.7 11.0 - - - +
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Residues in contact with GLY 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B PRO 3.1 7.9 + - - -
140B ILE* 1.3 77.7 - - - +
142B SER* 1.3 57.0 + - - +
144B ILE* 3.1 6.5 + - - +
145B ARG 3.0 23.6 + - - -
169B SER* 3.3 22.9 + - - -
172B SER* 3.3 15.0 - - - -
173B SER* 3.2 20.4 - - - -
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Residues in contact with SER 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ASN* 4.8 7.6 - - - +
265A ASN* 3.0 23.7 + - - +
138B GLY 3.2 20.1 + - - -
139B ASN* 3.6 5.6 - - - -
140B ILE 3.2 0.2 - - - -
141B GLY* 1.3 77.7 - - - +
143B ILE* 1.3 61.5 + - - +
145B ARG* 3.2 6.4 + - - +
146B SER* 3.1 24.3 + - - -
172B SER* 3.3 12.6 + - - -
264B ALA* 3.7 14.6 - - - +
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Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B VAL* 4.0 27.8 - - + -
131B PHE* 3.5 35.9 - - + -
139B ASN 3.0 15.7 + - - +
140B ILE 3.8 3.8 - - - +
142B SER* 1.3 72.4 - - - +
144B ILE* 1.3 59.1 + - - +
146B SER* 4.0 5.6 - - - +
147B ALA* 2.8 29.5 + - + +
155B LEU* 4.4 12.3 - - + -
231B ILE* 4.3 9.2 - - + -
263B ALA 4.1 2.9 - - - +
264B ALA* 3.7 24.9 - - - +
267B ALA* 3.9 24.9 - - + -
271B LEU* 5.2 3.1 - - + -
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Residues in contact with ILE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ILE* 3.0 34.4 + - + +
141B GLY* 3.1 13.7 + - - +
143B ILE* 1.3 77.2 - - - +
145B ARG* 1.3 62.2 + - - +
147B ALA* 3.4 5.4 + - - +
148B ASP* 3.0 23.2 + - - +
155B LEU* 3.4 20.2 - - + -
164B VAL* 4.3 4.5 - - + -
169B SER* 4.6 2.2 - - - +
173B SER* 4.1 4.5 - - - -
176B SER* 3.6 32.3 - - - +
177B LEU* 3.7 18.8 - - + +
180B LEU* 4.0 12.6 - - + +
182B ALA* 3.9 22.4 - - + -
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Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLU 5.2 7.9 + - - -
259A SER* 3.4 9.9 + - - +
260A SER* 3.0 44.2 + - - +
261A LEU* 3.5 14.4 + - - -
262A ASN* 3.4 34.9 + - - +
141B GLY 3.0 10.5 + - - +
142B SER* 3.2 10.1 + - - +
144B ILE* 1.3 77.0 - - - +
146B SER* 1.3 57.4 + - - +
148B ASP* 3.6 0.3 - - - +
149B ALA* 2.9 26.2 + - - +
172B SER 3.8 14.7 + - - +
173B SER 3.6 13.9 - - - +
174B THR* 3.5 29.1 + - - +
176B SER* 3.7 10.3 - - - +
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LEU* 3.5 24.1 - - - +
262A ASN 5.6 0.3 + - - -
265A ASN* 3.5 13.7 + - - -
142B SER 3.1 11.1 + - - -
143B ILE* 4.0 7.2 - - - -
145B ARG* 1.3 74.6 - - - +
147B ALA* 1.3 65.8 + - - +
150B LEU* 3.0 32.0 + - - +
267B ALA* 6.3 0.4 - - - -
268B THR* 2.7 35.9 + - - -
271B LEU* 4.7 5.3 - - - +
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B VAL* 4.8 9.4 - - + -
143B ILE* 2.8 23.5 + - + +
144B ILE* 3.8 2.7 - - - +
146B SER* 1.3 73.6 - - - +
148B ASP* 1.3 63.1 + - - +
150B LEU 3.8 0.2 - - - -
151B GLY 3.4 2.4 + - - -
152B ALA* 2.9 48.5 + - + +
154B GLY 5.1 2.0 - - - +
155B LEU* 5.6 1.6 - - + -
180B LEU* 4.1 19.3 - - + -
271B LEU* 4.3 13.8 - - + +
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Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ALA* 3.9 9.2 - - - +
258A ALA* 5.7 1.6 - - - +
259A SER* 3.1 16.5 + - - -
144B ILE 3.0 17.2 + - - +
145B ARG 3.6 4.3 - - - +
147B ALA* 1.3 79.6 - - - +
149B ALA* 1.3 61.7 + - - +
150B LEU 3.4 0.2 + - - -
151B GLY* 3.6 6.6 + - - -
152B ALA 4.8 1.3 - - - +
176B SER* 3.0 22.1 + - - +
179B SER* 2.8 34.3 + - - +
180B LEU* 3.9 19.1 - - + +
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A MSE 3.5 28.4 - - - -
255A ALA* 2.8 30.2 + - - +
256A GLY 5.9 0.7 - - - +
259A SER* 3.6 20.8 + - - +
260A SER 3.7 11.9 - - - +
261A LEU* 3.9 12.6 - - + -
145B ARG 2.9 20.5 + - - +
148B ASP* 1.3 75.0 - - - +
150B LEU* 1.3 59.5 + - - +
151B GLY 3.4 0.2 - - - -
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ILE* 3.8 28.9 - - + -
253A PRO 4.0 11.4 - - - +
254A MSE 4.3 7.2 - - + -
255A ALA* 4.5 1.3 - - - +
261A LEU* 4.3 10.1 - - + -
127B LEU* 4.3 6.9 - - - +
146B SER* 3.0 21.6 + - - +
147B ALA 3.8 0.4 - - - +
148B ASP 3.3 0.2 - - - -
149B ALA* 1.3 77.9 - - - +
151B GLY* 1.3 59.4 + - - +
152B ALA 3.4 4.4 + - - -
268B THR* 3.8 28.5 - - + +
271B LEU* 3.8 28.0 - - + +
272B TYR* 4.0 8.3 - - + +
275B VAL* 3.1 35.4 - - + +
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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