Contacts of the helix formed by residues 183 - 193 (chain A) in PDB entry 4IVR
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 THR 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A ALA* 4.3 19.0 - - + +
177A TYR* 4.1 0.7 - - - -
182A MET* 1.3 82.4 - - - +
184A PRO* 1.3 70.1 - - - +
185A GLN* 3.4 18.3 + - - +
186A ALA* 3.1 27.5 + - + +
187A VAL* 3.2 15.9 + - - +
92B GLY 4.9 1.4 + - - -
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Residues in contact with PRO 184 (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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177A TYR* 3.6 34.9 - - + +
183A THR* 1.3 81.9 - - - +
185A GLN* 1.3 71.4 + - - +
187A VAL* 3.2 7.7 + - + +
188A LEU* 2.9 33.8 + - - +
291A LEU 5.6 0.2 - - - +
292A PHE* 4.8 6.4 - - + -
294A ALA* 4.5 0.7 - - + -
296A GLU* 3.6 28.0 - - + +
297A LEU* 3.6 33.0 - - + -
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Residues in contact with GLN 185 (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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183A THR* 3.4 10.7 - - - +
184A PRO* 1.3 90.2 - - - +
186A ALA* 1.3 58.6 + - - +
188A LEU* 3.3 4.3 + - - +
189A ALA* 2.8 27.4 + - - +
296A GLU* 4.0 19.7 + - - +
297A LEU* 3.9 8.5 - - + -
308A PHE* 3.6 25.6 - - + -
87B TYR* 4.0 14.9 + - - +
90B VAL 5.3 0.6 + - - -
91B LEU 3.0 25.9 + - - +
92B GLY* 3.3 27.0 + - - +
93B ALA* 5.1 1.0 - - - +
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Residues in contact with ALA 186 (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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122A THR* 4.4 22.0 - - + +
182A MET* 4.3 15.5 - - + -
183A THR* 3.1 20.9 + - + +
185A GLN* 1.3 76.2 - - - +
187A VAL* 1.3 66.9 + - - +
189A ALA* 3.1 9.2 + - - +
190A PHE* 2.9 28.9 + - - -
126B ILE* 5.1 4.5 - - + -
127B THR* 5.8 3.8 - - - +
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Residues in contact with VAL 187 (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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169A LEU 4.3 0.3 - - - +
170A LEU* 4.7 3.6 - - + +
173A PRO* 3.7 24.5 - - + +
174A ALA* 4.3 18.6 - - + +
177A TYR* 3.9 14.4 - - + -
182A MET* 3.6 18.4 - - + -
183A THR 3.2 17.3 + - - +
184A PRO* 3.2 10.5 + - + +
186A ALA* 1.3 76.8 - - - +
188A LEU* 1.3 58.5 + - - +
190A PHE* 3.3 8.9 + - - +
191A VAL* 2.9 29.9 + - + +
292A PHE* 3.9 25.4 - - + -
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Residues in contact with LEU 188 (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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184A PRO 2.9 15.5 + - - +
185A GLN* 3.6 5.2 - - - +
186A ALA 3.2 0.2 - - - -
187A VAL* 1.3 75.1 - - - +
189A ALA* 1.3 53.4 + - - +
191A VAL* 3.0 14.7 + - + +
192A ALA* 2.7 35.6 + - - +
292A PHE* 3.5 31.4 - - + -
297A LEU* 4.0 21.5 - - + -
304A LEU* 6.0 0.2 - - + -
308A PHE* 3.8 38.4 - - + +
311A ALA* 4.1 19.1 - - + +
312A LEU* 4.0 18.8 - - + -
130B MET* 4.5 8.3 - - + -
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Residues in contact with ALA 189 (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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185A GLN 2.8 15.5 + - - +
186A ALA* 3.1 9.4 + - - +
188A LEU* 1.3 72.0 - - - +
190A PHE* 1.3 65.0 + - - +
192A ALA* 3.3 11.6 + - - +
193A LEU* 3.4 21.5 + - + +
87B TYR* 5.4 0.2 - - - +
126B ILE* 3.6 27.8 - - + +
127B THR* 5.4 1.1 - - - +
130B MET* 3.6 33.5 - - + +
133B ALA* 5.6 0.3 - - - +
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Residues in contact with PHE 190 (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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122A THR* 3.5 41.1 - - + -
125A GLN* 3.9 25.4 - - + -
126A ILE* 3.7 32.3 - - + -
168A ALA 4.0 5.8 - - - -
169A LEU* 3.1 34.0 - - + +
173A PRO* 3.4 29.4 - - + -
182A MET* 4.5 7.2 - - - -
186A ALA 2.9 14.9 + - - -
187A VAL* 3.3 7.6 - - - +
189A ALA* 1.3 79.1 - - - +
191A VAL* 1.3 62.5 + - - +
193A LEU* 3.0 18.6 + - + +
194A ILE* 3.5 8.5 + - - +
126B ILE* 4.4 14.4 - - + -
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Residues in contact with VAL 191 (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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169A LEU 3.9 6.3 - - - +
170A LEU* 3.8 28.7 - - + -
187A VAL* 2.9 23.5 + - + +
188A LEU* 3.0 24.2 + - + +
190A PHE* 1.3 74.3 - - - +
192A ALA* 1.3 64.0 + - - +
194A ILE* 3.1 26.4 + - + +
292A PHE* 4.9 2.7 - - + -
311A ALA* 3.3 28.7 - - + +
314A VAL* 3.9 6.4 - - + +
315A LEU* 4.0 23.8 - - + +
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Residues in contact with ALA 192 (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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188A LEU 2.7 17.5 + - - +
189A ALA* 3.6 9.6 - - - +
190A PHE 3.2 0.4 - - - -
191A VAL* 1.3 73.7 - - - +
193A LEU* 1.3 62.3 + - - +
194A ILE 3.4 3.3 + - - +
311A ALA* 4.8 3.4 - - + -
314A VAL* 4.4 11.5 - - + +
318A ARG* 5.5 0.3 + - - -
130B MET 4.8 0.4 - - - +
133B ALA* 4.3 9.5 - - + +
134B VAL* 3.4 41.7 - - + +
137B ALA* 4.3 16.3 - - - +
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Residues in contact with LEU 193 (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 ILE* 5.5 0.2 - - + -
169A LEU* 3.7 7.9 - - + +
189A ALA* 3.4 19.1 - - + +
190A PHE* 3.0 15.3 + - + +
192A ALA* 1.3 76.5 - - - +
194A ILE* 1.3 66.0 + - - +
195A PRO* 3.2 9.5 - - - +
126B ILE* 4.5 20.4 - - + -
133B ALA* 3.7 26.5 - - + -
169B LEU* 4.1 22.2 - - + -
193B LEU* 3.7 54.3 - - + +
195B PRO* 5.4 4.3 - - + -
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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