Contacts of the helix formed by residues 173 - 184 (chain A) in PDB entry 5JEI
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 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A LEU 6.1 0.7 - - - +
13A GLU* 5.9 0.2 - - - -
59A GLY 5.8 2.7 - - - +
138A LEU* 3.5 10.5 - - - -
171A VAL* 3.4 7.4 - - - +
172A ARG* 1.3 85.2 - - + +
174A THR* 1.3 65.0 + - - +
175A ALA* 3.5 9.3 + - - +
176A GLU* 2.7 44.2 + - - +
177A GLY 3.1 9.4 + - - -
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Residues in contact with THR 174 (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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13A GLU* 2.7 34.1 + - - +
138A LEU* 3.9 5.1 - - - +
173A THR* 1.3 73.6 - - - +
175A ALA* 1.3 64.9 + - - +
177A GLY* 3.0 2.6 + - - -
178A VAL* 2.9 30.4 + - + +
190A TYR* 4.1 11.9 + - + -
192A LEU* 4.0 26.7 - - + -
196A MET* 4.2 10.1 - - + -
200A ILE* 5.0 3.1 - - + -
301A FWD 3.2 18.0 - - - -
312A EDO 4.3 10.3 - - - -
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Residues in contact with ALA 175 (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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173A THR* 3.2 9.0 + - - +
174A THR* 1.3 78.1 - - - +
176A GLU* 1.3 58.4 + - + +
178A VAL* 3.4 6.3 + - - +
179A ALA* 2.9 29.3 + - - +
312A EDO 3.7 30.4 - - - +
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Residues in contact with GLU 176 (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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171A VAL* 4.1 14.4 - - + +
172A ARG* 2.9 51.7 + - - +
173A THR* 2.7 39.5 + - - +
175A ALA* 1.3 75.7 - - + +
177A GLY* 1.3 59.7 + - - +
179A ALA* 3.4 6.2 + - - +
180A ARG* 2.9 29.1 + - - +
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Residues in contact with GLY 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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171A VAL* 3.7 22.6 - - - +
173A THR 3.1 7.5 + - - -
174A THR 3.0 7.3 + - - -
176A GLU* 1.3 75.4 - - - +
178A VAL* 1.3 61.2 + - - +
180A ARG* 3.2 4.7 + - - +
181A VAL* 3.0 27.9 + - - +
188A TYR* 4.2 1.1 - - - -
190A TYR* 3.9 21.1 - - - -
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Residues in contact with VAL 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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114A MET* 3.9 23.8 - - + -
174A THR* 2.9 27.9 + - + +
175A ALA* 3.7 7.9 - - - +
177A GLY* 1.3 76.6 - - - +
179A ALA* 1.3 63.1 + - - +
181A VAL* 3.2 3.5 + - - +
182A ARG* 2.9 59.9 + - + +
190A TYR* 4.4 0.6 - - + -
192A LEU* 5.1 1.1 - - + -
200A ILE* 3.8 39.7 - - + -
208A THR* 4.8 1.1 - - + -
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Residues in contact with ALA 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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175A ALA 2.9 18.7 + - - +
176A GLU* 3.8 7.6 - - - +
178A VAL* 1.3 77.7 - - - +
180A ARG* 1.3 57.0 + - - +
182A ARG* 3.2 8.6 + - - +
183A LYS* 2.9 55.8 + - - +
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Residues in contact with ARG 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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134A ALA* 5.5 2.4 - - - +
167A PRO* 4.2 16.2 + - - +
168A SER 2.9 31.3 + - - -
169A VAL* 3.7 22.2 + - - +
170A PHE 4.0 8.1 + - - -
171A VAL* 4.2 9.6 - - + +
176A GLU 2.9 18.1 + - - +
177A GLY* 3.6 5.6 - - - +
178A VAL 3.2 0.2 - - - -
179A ALA* 1.3 73.9 - - - +
181A VAL* 1.3 65.1 + - - +
183A LYS* 3.4 4.2 + - - +
184A SER* 2.7 39.8 + - - +
188A TYR* 3.5 40.2 - - + +
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Residues in contact with VAL 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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114A MET* 4.1 11.7 - - + +
115A ILE* 3.8 6.5 - - - -
116A LYS* 3.3 45.9 - - + +
177A GLY 3.0 18.9 + - - +
178A VAL 3.5 7.4 - - - +
180A ARG* 1.3 78.4 - - - +
182A ARG* 1.3 62.3 + - - +
183A LYS 3.3 0.3 + - - -
184A SER* 3.5 8.3 + - - -
185A LYS 4.3 1.6 + - - -
186A GLY 4.8 0.2 + - - -
188A TYR* 3.8 23.4 - - + +
190A TYR* 3.5 31.9 - - + +
208A THR* 4.1 12.1 - - + -
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Residues in contact with ARG 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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116A LYS* 3.7 22.1 - - - +
178A VAL* 2.9 40.4 + - - +
179A ALA* 3.2 8.9 + - - +
181A VAL* 1.3 77.5 - - - +
183A LYS* 1.3 62.4 + - + +
185A LYS 4.6 1.7 + - - -
200A ILE* 3.9 22.6 + - - +
203A ARG* 3.9 12.1 + - - +
204A LYS 3.6 18.4 + - - -
205A PRO* 3.6 20.3 - - - +
206A CYS* 4.7 0.6 - - - +
207A ASP* 2.8 35.1 + - - +
208A THR* 4.0 12.3 + - + +
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Residues in contact with LYS 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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179A ALA* 2.9 38.0 + - - +
180A ARG* 4.3 3.6 - - - +
182A ARG* 1.3 80.4 - - + +
184A SER* 1.3 59.2 + - - +
185A LYS* 3.4 23.3 + - - +
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Residues in contact with SER 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 ARG* 2.7 35.0 + - - +
181A VAL 3.5 3.8 + - - -
183A LYS* 1.3 78.5 - - - +
185A LYS* 1.3 65.8 + - - +
186A GLY 3.2 2.0 - - - -
187A LYS* 2.9 26.8 + - - +
188A TYR* 3.7 24.6 - - - +
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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