Contacts of the helix formed by residues 176 - 188 (chain A) in PDB entry 5J1T
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 HIS 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A PHE* 5.8 3.0 + - + +
141A ALA* 3.5 31.3 + - + +
144A ILE* 3.6 26.7 - - + +
147A TYR* 6.3 1.6 - - + -
174A LYS 3.8 0.8 + - - -
175A MET* 1.3 76.2 - - - +
177A ALA* 1.3 70.6 + - + +
178A GLY* 2.9 26.6 + - - -
179A LEU* 2.9 29.6 + - + +
180A ILE* 3.1 11.3 + - - +
435B PHE* 3.3 41.7 - + + -
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Residues in contact with ALA 177 (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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175A MET 3.3 4.7 + - - -
176A HIS* 1.3 78.1 + - + +
178A GLY* 1.3 57.5 + - - +
180A ILE* 3.3 13.4 + - - +
181A ASP* 2.9 33.4 + - - +
252A PHE* 4.0 17.2 - - + -
435B PHE* 3.7 14.1 - - + +
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Residues in contact with GLY 178 (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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144A ILE* 3.6 20.8 - - - +
148A LYS* 4.9 6.2 + - - +
176A HIS* 2.9 12.1 + - - -
177A ALA* 1.3 79.4 - - - +
179A LEU* 1.3 61.9 + - - +
181A ASP* 3.5 14.6 + - - +
182A ALA* 3.2 19.9 + - - +
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Residues in contact with LEU 179 (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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138A PHE* 3.5 49.1 - - + -
144A ILE* 3.6 10.2 - - + +
147A TYR* 3.9 11.4 - - + -
148A LYS* 3.5 43.3 - - + +
151A LEU* 4.1 11.4 - - + -
175A MET* 3.7 19.0 - - + +
176A HIS* 2.9 19.5 + - + +
178A GLY* 1.3 75.7 - - - +
180A ILE* 1.3 63.9 + - - +
182A ALA* 3.1 17.7 + - + +
183A ILE* 3.5 10.2 + - - +
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Residues in contact with ILE 180 (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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172A MET* 3.2 40.6 - - + +
175A MET* 4.0 34.3 - - + +
176A HIS 3.1 8.6 + - - +
177A ALA* 3.3 11.9 + - - +
179A LEU* 1.3 74.4 - - - +
181A ASP* 1.3 65.7 + - - +
183A ILE* 3.0 29.1 + - + +
184A LYS* 3.3 7.9 + - - +
205A PHE* 6.0 0.2 - - + -
252A PHE* 3.8 17.0 - - + -
253A TRP* 3.4 31.6 - - + -
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Residues in contact with ASP 181 (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 ALA* 2.9 19.0 + - - +
178A GLY* 3.5 16.6 - - - +
179A LEU 3.3 0.2 - - - -
180A ILE* 1.3 75.8 - - - +
182A ALA* 1.3 61.7 + - - +
184A LYS* 2.8 49.8 + - + +
185A PRO* 3.7 5.4 - - - +
252A PHE* 3.4 10.9 - - - -
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Residues in contact with ALA 182 (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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148A LYS* 3.7 35.9 - - + +
151A LEU* 5.7 1.1 - - + -
152A GLN* 3.8 23.8 + - + +
178A GLY 3.2 8.9 + - - +
179A LEU* 3.1 16.3 + - + +
180A ILE 3.1 0.8 - - - -
181A ASP* 1.3 79.6 - - - +
183A ILE* 1.3 61.1 + - + +
185A PRO* 3.8 9.5 - - - +
186A PHE* 4.1 9.7 - - - -
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Residues in contact with ILE 183 (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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151A LEU* 3.7 30.7 - - + -
152A GLN* 6.1 0.7 - - + -
155A ILE* 3.9 17.7 - - + -
169A PHE* 3.9 28.7 - - + -
175A MET* 4.9 3.4 - - + -
179A LEU 3.5 4.2 + - - +
180A ILE* 3.0 27.9 + - + +
182A ALA* 1.3 78.8 - - + +
184A LYS* 1.3 67.0 + - - +
185A PRO* 3.3 3.8 - - - -
186A PHE* 3.0 31.0 + - + +
187A LEU* 3.6 16.5 + - + +
203A PHE* 5.0 1.8 - - + -
205A PHE* 4.0 25.4 - - + -
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Residues in contact with LYS 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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180A ILE* 3.3 14.7 + - + +
181A ASP* 2.8 40.0 + - - +
183A ILE* 1.3 76.8 - - - +
185A PRO* 1.4 66.5 - - + +
187A LEU* 3.0 27.9 + - + +
188A ASP* 3.5 10.3 + - - +
252A PHE* 2.8 59.5 + - - +
253A TRP* 4.8 4.5 - - + -
254A HIS 5.5 1.6 - - - +
262A LEU* 3.8 22.1 - - + +
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Residues in contact with PRO 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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181A ASP 3.7 9.4 - - - +
182A ALA 3.8 9.6 - - - +
183A ILE 3.4 4.3 - - - -
184A LYS* 1.4 94.1 - - + +
186A PHE* 1.3 63.4 + - + +
187A LEU 3.2 0.7 + - - -
188A ASP* 3.4 9.4 + - + +
190A TYR* 3.5 32.9 - - + +
193A VAL* 3.6 26.1 - - + +
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Residues in contact with PHE 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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95A PRO* 3.2 18.4 - - - +
152A GLN* 4.2 29.2 - - + -
155A ILE* 3.8 36.8 - - + -
156A ARG* 4.8 4.5 - - + -
182A ALA 4.1 14.1 - - - -
183A ILE* 3.0 26.2 + - + +
185A PRO* 1.3 78.1 - - + +
187A LEU* 1.3 58.3 + - - +
188A ASP 3.4 1.0 + - - +
193A VAL* 4.3 13.5 - - + -
198A TYR* 3.4 60.9 - + + +
203A PHE* 3.8 20.4 - + + -
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Residues in contact with LEU 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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94A LYS* 2.9 33.8 + - - +
95A PRO* 3.6 6.7 - - - +
97A THR* 3.9 11.2 - - + +
183A ILE* 3.6 19.1 - - + +
184A LYS* 3.0 18.1 + - - +
186A PHE* 1.3 77.6 - - - +
188A ASP* 1.3 60.9 + - - +
203A PHE* 3.3 48.7 - - + -
205A PHE* 3.8 23.8 - - + -
253A TRP* 3.9 20.9 - - + -
262A LEU* 4.1 18.6 - - + -
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Residues in contact with ASP 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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94A LYS* 4.1 4.3 - - - -
95A PRO* 3.4 17.0 - - - +
184A LYS 3.5 5.3 + - - +
185A PRO* 3.4 5.9 + - - +
186A PHE 3.4 0.9 - - - +
187A LEU* 1.3 81.7 - - - +
189A TYR* 1.3 76.9 + - - +
190A TYR* 3.2 38.2 + - + +
198A TYR* 6.0 0.2 - - - +
199A GLN* 5.3 0.2 - - - +
255A SER* 2.7 24.7 + - - -
256A SER* 2.9 33.3 + - - -
257A LEU* 3.9 5.3 + - - +
262A LEU* 3.4 16.1 - - + +
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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