Contacts of the helix formed by residues 168 - 177 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166I MET 3.1 0.6 + - - -
167I GLY* 1.3 68.5 - - - -
169I LYS* 1.3 58.0 + - - +
170I GLU* 3.2 14.8 - - - -
172I PHE* 3.1 23.4 + - - +
187I SER* 3.2 18.6 - - - -
191I LEU* 3.8 11.9 - - - -
222I GLN* 2.9 16.3 + - - -
459I TYR* 2.8 17.8 + - - -
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Residues in contact with LYS 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I GLU* 4.0 12.3 + - - -
136I LEU* 4.0 13.0 - - + +
166I MET* 2.9 54.7 + - + +
167I GLY 3.2 1.4 + - - -
168I GLY* 1.3 78.5 - - - +
170I GLU* 1.3 58.9 + - - +
172I PHE* 3.8 2.9 - - - +
173I ASP* 3.0 47.5 + - - +
221I ALA* 4.0 21.5 - - + +
222I GLN* 4.2 8.7 - - + +
135J VAL* 4.6 8.1 - - - +
137J ASP* 5.8 1.2 + - - -
159J ARG* 5.2 3.8 - - - +
500J B13 3.3 36.5 + - + +
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Residues in contact with GLU 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I LEU* 3.4 23.6 - - + +
168I GLY* 3.2 16.3 - - - -
169I LYS* 1.3 78.7 - - - +
171I VAL* 1.3 87.8 + - + +
173I ASP* 3.5 6.5 + - - +
174I TYR* 3.4 17.7 + - - +
191I LEU* 4.2 0.9 - - - +
451I VAL* 4.3 6.7 - - + +
453I VAL* 4.4 21.3 - - + +
454I PHE* 3.9 36.6 - - + +
455I LYS 5.0 0.7 + - - -
458I ASN* 4.9 3.6 + - - -
459I TYR* 2.6 30.5 + - - -
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Residues in contact with VAL 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170I GLU* 1.3 90.9 + - + +
172I PHE* 1.3 60.1 + - - +
174I TYR* 3.0 9.4 + - - +
175I ALA* 2.9 25.7 + - - +
183I GLY* 4.0 10.3 - - - +
186I TYR* 4.3 4.7 - - + -
187I SER* 3.7 21.5 - - - -
191I LEU* 4.0 9.9 - - + -
447I TYR* 4.0 43.7 - - + -
451I VAL* 4.9 5.4 - - + -
454I PHE* 3.9 29.4 - - + -
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Residues in contact with PHE 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168I GLY 3.1 19.1 + - - +
169I LYS 3.8 3.4 - - - +
171I VAL* 1.3 75.8 - - - +
173I ASP* 1.3 69.9 + - - +
174I TYR 3.0 0.5 + - - -
175I ALA* 3.0 3.9 + - - +
176I VAL* 2.8 63.8 + - + +
184I LEU* 4.0 17.5 - - + -
187I SER* 3.4 12.6 - - - +
188I ILE* 4.0 11.9 - - + -
221I ALA 3.7 10.8 - - - -
222I GLN* 2.8 49.8 - - + +
225I THR* 3.5 24.9 - - + -
226I ALA* 3.7 13.2 - - + -
246I ALA* 5.0 0.9 - - + -
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Residues in contact with ASP 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169I LYS* 3.0 35.5 + - - +
170I GLU* 3.9 7.4 - - - +
171I VAL 3.4 0.2 - - - -
172I PHE* 1.3 93.1 - - - +
174I TYR* 1.3 60.1 + - - +
176I VAL* 3.7 9.3 - - - +
177I LEU* 3.5 24.6 - - - +
221I ALA 4.5 3.3 - - - +
225I THR* 4.3 2.6 - - - +
137J ASP* 5.5 2.0 - - + +
138J ILE* 3.4 26.9 - - + +
141J ASN* 6.3 1.1 - - - +
500J B13 3.8 20.1 + - - +
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Residues in contact with TYR 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170I GLU 3.4 9.4 + - - +
171I VAL 3.0 8.9 + - - +
172I PHE 3.0 0.6 - - - -
173I ASP* 1.3 80.7 - - - +
175I ALA* 1.3 69.9 + - - +
176I VAL 3.5 0.3 + - - -
177I LEU 3.6 5.0 + - - -
178I ARG* 3.1 69.9 + - + +
180I ASP* 4.6 4.9 - - - -
447I TYR* 4.2 18.2 - + - -
450I GLU* 2.9 49.8 + - + +
451I VAL* 3.6 28.0 - - + -
103J ASP* 4.6 3.2 + - - -
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Residues in contact with ALA 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171I VAL* 2.9 16.8 + - + +
172I PHE* 3.8 1.1 - - - +
174I TYR* 1.3 81.1 - - + +
176I VAL* 1.3 63.8 + - - +
178I ARG* 3.1 11.1 + - - -
179I ASN* 3.3 0.9 + - - -
180I ASP* 3.2 44.9 + - + +
183I GLY* 3.8 15.0 - - - +
184I LEU* 3.6 22.1 - - + +
447I TYR* 5.5 0.2 - - + -
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Residues in contact with VAL 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172I PHE* 2.8 63.6 + - + +
173I ASP* 3.7 11.2 - - - +
175I ALA* 1.3 73.9 - - - +
177I LEU* 1.3 67.5 + - + +
178I ARG 3.2 1.1 + - - -
179I ASN* 4.1 4.0 + - - +
184I LEU* 4.0 12.8 - - + +
226I ALA* 4.0 18.8 - - + -
229I ILE* 4.1 20.1 - - + +
238I LEU* 3.4 32.6 - - + +
242I ILE* 5.9 0.8 - - + +
96J PRO* 4.3 1.0 - - - +
138J ILE* 4.5 2.5 - - + -
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Residues in contact with LEU 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173I ASP 3.5 16.6 - - - +
174I TYR 3.9 8.5 - - - +
175I ALA 3.1 1.0 - - - -
176I VAL* 1.3 94.1 - - + +
178I ARG* 1.3 66.9 - - - +
179I ASN 3.8 0.9 - - - -
229I ILE* 4.3 16.2 - - + -
237I ASN 6.0 0.2 - - - +
95J LEU* 4.4 10.7 - - + +
96J PRO* 3.2 14.1 - - - +
99J MET* 3.1 39.2 - - + +
138J ILE* 4.5 13.7 - - + -
141J ASN* 4.8 14.8 - - + +
142J ILE* 4.2 35.2 - - + -
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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