Contacts of the helix formed by residues 168 - 177 (chain A) in PDB entry 2I2X
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 GLY 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A MET 3.0 0.2 + - - -
167A GLY* 1.3 69.2 - - - -
169A LYS* 1.3 63.6 + - - +
170A GLU* 3.2 14.4 + - - +
172A PHE 3.0 18.9 + - - -
187A SER* 3.3 14.6 - - - -
191A LEU* 4.0 11.0 - - - -
222A GLN* 3.1 18.6 + - - -
459A TYR* 2.9 19.0 + - - -
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Residues in contact with LYS 169 (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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131A GLU* 3.6 25.4 + - - -
136A LEU* 4.2 5.6 - - + +
166A MET* 2.9 54.8 + - + +
167A GLY 3.2 1.4 + - - -
168A GLY* 1.3 76.9 - - - +
170A GLU* 1.3 58.3 + - - +
172A PHE* 3.3 4.8 + - - +
173A ASP* 2.9 51.1 + - - +
221A ALA* 4.2 20.0 - - + +
222A GLN* 4.3 7.6 - - + +
135B VAL* 3.7 10.9 - - - +
159B ARG* 4.4 1.8 - - - +
500B B13 3.4 34.3 + - + +
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Residues in contact with GLU 170 (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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136A LEU* 3.4 23.2 - - + +
168A GLY* 3.2 17.7 - - - -
169A LYS* 1.3 76.7 - - - +
171A VAL* 1.3 88.7 + - + +
173A ASP* 3.7 7.3 + - - +
174A TYR* 3.5 19.4 + - - +
191A LEU* 4.2 0.5 - - - +
451A VAL* 4.2 6.3 - - + +
453A VAL* 4.1 22.5 - - + +
454A PHE* 3.8 32.0 - - + +
455A LYS 4.7 2.3 + - - -
458A ASN* 4.9 1.0 + - - -
459A TYR* 2.7 31.8 + - - -
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Residues in contact with VAL 171 (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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170A GLU* 1.3 92.9 + - + +
172A PHE* 1.3 60.5 + - - +
174A TYR* 3.5 5.2 + - - +
175A ALA* 2.8 26.9 + - - +
183A GLY* 4.4 5.4 - - - +
186A TYR* 4.4 5.8 - - + -
187A SER* 4.0 15.9 - - - -
191A LEU* 4.0 10.3 - - + -
447A TYR* 3.7 46.2 - - + -
451A VAL* 4.9 4.9 - - + -
454A PHE* 3.8 31.2 - - + -
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Residues in contact with PHE 172 (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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168A GLY 3.0 18.8 + - - +
169A LYS 3.6 2.7 - - - +
171A VAL* 1.3 76.9 - - - +
173A ASP* 1.3 70.5 + - - +
175A ALA* 3.2 2.4 + - - -
176A VAL* 2.7 68.2 + - + +
184A LEU* 3.9 17.5 - - + -
187A SER* 3.4 13.7 - - - +
188A ILE* 4.1 13.0 - - + -
221A ALA 3.9 3.6 - - - -
222A GLN* 3.0 56.5 - - + -
225A THR* 3.7 17.9 - - + -
226A ALA* 3.7 17.7 - - + -
246A ALA* 4.9 0.2 - - + -
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Residues in contact with ASP 173 (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 LYS* 2.9 35.7 + - - +
170A GLU* 3.9 6.9 - - - +
171A VAL 3.4 0.2 - - - -
172A PHE* 1.3 94.4 - - - +
174A TYR* 1.3 62.5 + - - +
176A VAL* 3.8 9.8 - - - +
177A LEU* 3.3 27.1 - - + +
221A ALA 4.6 3.3 - - - +
225A THR* 4.5 3.3 - - - +
137B ASP* 5.0 4.4 - - + +
138B ILE* 4.8 5.7 - - + +
500B B13 3.4 34.4 + - - +
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Residues in contact with TYR 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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170A GLU 3.5 10.0 + - - +
171A VAL 3.5 6.9 + - - +
172A PHE 3.2 0.2 - - - -
173A ASP* 1.3 80.0 - - - +
175A ALA* 1.3 67.3 + - - +
176A VAL 3.4 0.5 + - - -
177A LEU* 3.5 4.7 + - - -
178A ARG* 2.9 73.0 + - - +
180A ASP* 4.5 6.1 - - - -
447A TYR* 4.1 18.8 - + - -
450A GLU* 2.4 53.8 + - + +
451A VAL* 3.7 30.3 - - + -
103B ASP* 4.9 3.4 + - - -
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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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171A VAL* 2.8 21.7 + - + +
172A PHE* 3.8 3.6 - - - +
174A TYR* 1.3 76.9 - - + +
176A VAL* 1.3 58.9 + - - +
178A ARG* 3.0 17.2 + - - -
179A ASN* 3.4 0.7 + - - -
180A ASP* 3.3 47.9 + - + +
183A GLY* 3.9 22.9 - - - -
184A LEU* 3.9 6.9 - - + +
447A TYR* 5.4 0.2 - - - +
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Residues in contact with VAL 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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172A PHE* 2.7 59.7 + - + +
173A ASP* 3.8 10.3 - - - +
175A ALA* 1.3 72.7 - - - +
177A LEU* 1.3 66.5 + - + +
178A ARG 3.1 1.1 + - - -
179A ASN* 4.2 2.8 + - - +
184A LEU* 3.9 11.9 - - + +
225A THR* 5.1 0.9 - - + -
226A ALA* 4.1 7.6 - - + -
229A ILE* 3.9 21.9 - - + +
238A LEU* 3.8 41.4 - - + +
242A ILE* 5.7 1.1 - - + -
246A ALA* 6.1 0.2 - - + -
96B PRO* 4.1 3.6 - - - +
138B ILE* 5.8 1.6 - - + -
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Residues in contact with LEU 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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173A ASP* 3.3 18.6 + - + +
174A TYR* 3.5 1.2 + - - -
175A ALA 3.2 1.2 - - - -
176A VAL* 1.3 92.6 - - + +
178A ARG* 1.3 77.1 + - - +
229A ILE* 4.3 9.6 - - + -
95B LEU* 4.4 17.3 - - + -
96B PRO* 3.1 28.4 - - + +
99B MET* 3.3 39.1 - - + +
138B ILE* 4.3 29.4 - - + -
141B ASN* 4.6 18.8 - - + +
142B ILE* 5.8 1.3 - - + -
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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