Contacts of the helix formed by residues 168 - 177 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166E MET 3.1 0.2 + - - -
167E GLY* 1.3 70.3 - - - -
169E LYS* 1.3 57.6 + - - +
170E GLU* 3.1 8.5 - - - +
171E VAL 3.4 0.2 + - - -
172E PHE* 2.8 31.5 + - - +
187E SER* 3.4 19.2 - - - -
191E LEU* 3.9 8.7 - - - -
222E GLN* 3.2 8.2 + - - -
459E TYR* 2.9 23.2 + - - -
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Residues in contact with LYS 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E GLU* 3.5 14.6 + - - -
136E LEU* 3.7 22.8 - - + +
166E MET* 2.9 41.9 + - + +
167E GLY 3.3 1.6 + - - -
168E GLY* 1.3 75.7 - - - +
170E GLU* 1.3 55.0 + - - +
172E PHE* 3.3 5.9 + - - +
173E ASP* 2.8 55.7 + - - +
221E ALA* 4.3 19.7 - - + +
222E GLN* 3.8 7.1 - - - +
459E TYR* 4.4 0.2 + - - -
135F VAL* 3.7 23.4 - - - +
159F ARG* 4.3 2.6 - - - +
500F B13 3.7 27.4 + - + +
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Residues in contact with GLU 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E LEU* 3.8 21.1 - - + +
168E GLY* 3.1 8.3 - - - -
169E LYS* 1.3 74.8 - - - +
171E VAL* 1.3 97.0 + - + +
173E ASP* 3.7 6.9 + - - +
174E TYR* 3.5 18.9 + - - +
451E VAL* 4.3 7.0 - - + +
453E VAL* 4.8 17.4 - - + +
454E PHE* 3.3 28.5 - - + +
455E LYS 4.9 1.2 + - - -
458E ASN* 5.2 1.2 + - - -
459E TYR* 2.4 42.8 + - - -
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Residues in contact with VAL 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E GLU* 1.3 101.4 + - + +
172E PHE* 1.3 67.6 + - - +
174E TYR* 3.2 7.3 + - - +
175E ALA* 3.1 20.4 + - - +
183E GLY* 4.3 7.0 - - - +
186E TYR* 4.3 4.5 - - + -
187E SER* 3.9 17.5 - - - -
191E LEU* 3.6 15.5 - - + -
447E TYR* 3.8 40.8 - - + -
451E VAL* 4.8 4.0 - - + -
454E PHE* 3.9 22.9 - - + -
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Residues in contact with PHE 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E GLY 2.8 19.5 + - - +
169E LYS 3.4 4.9 - - - +
171E VAL* 1.3 76.8 - - - +
173E ASP* 1.3 64.7 + - - +
175E ALA* 3.1 4.2 + - - +
176E VAL* 2.9 62.9 + - + +
184E LEU* 4.5 9.4 - - + -
187E SER* 3.4 11.1 - - - +
188E ILE* 3.9 20.2 - - + -
221E ALA 3.8 11.4 - - - -
222E GLN* 2.9 58.6 - - + +
225E THR* 3.8 20.6 - - + -
226E ALA* 3.8 11.4 - - + -
246E ALA* 5.0 0.9 - - + -
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Residues in contact with ASP 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E LYS* 2.8 44.4 + - - +
170E GLU* 3.9 7.3 + - - +
171E VAL 3.4 0.4 - - - -
172E PHE* 1.3 86.3 - - - +
174E TYR* 1.3 61.0 + - - +
176E VAL* 3.5 9.7 - - - +
177E LEU* 3.3 24.4 - - - +
221E ALA 5.2 0.8 - - - +
225E THR* 4.5 0.2 - - - +
137F ASP* 6.0 1.3 - - + -
138F ILE* 3.4 14.7 - - + +
500F B13 3.2 34.8 + - - +
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Residues in contact with TYR 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E GLU 3.5 6.7 + - - +
171E VAL 3.2 7.4 + - - +
172E PHE 3.2 0.6 - - - -
173E ASP* 1.3 78.8 - - - +
175E ALA* 1.3 67.3 + - - +
177E LEU* 3.6 5.1 + - - -
178E ARG* 2.7 78.8 + - - +
180E ASP* 5.0 4.7 - - + -
447E TYR* 4.5 14.4 - + - -
450E GLU* 2.9 48.2 + - + +
451E VAL* 3.5 34.1 - - + -
103F ASP* 4.8 2.8 + - - -
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Residues in contact with ALA 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E VAL* 3.1 16.1 + - + +
172E PHE 3.8 2.9 - - - +
174E TYR* 1.3 78.9 - - + +
176E VAL* 1.3 66.0 + - - +
177E LEU 3.0 2.7 - - - -
178E ARG* 3.0 12.8 + - - -
179E ASN* 3.4 1.4 + - - -
180E ASP* 3.3 45.2 + - + +
183E GLY* 3.8 23.6 - - - -
184E LEU* 3.8 6.1 - - + +
447E TYR* 5.4 0.4 - - + -
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Residues in contact with VAL 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E PHE* 2.9 50.1 + - + +
173E ASP* 3.5 16.8 - - - +
175E ALA* 1.3 76.8 - - - +
177E LEU* 1.3 75.7 + - + +
178E ARG 3.5 1.0 + - - -
179E ASN* 4.3 2.5 + - - +
184E LEU* 3.8 13.2 - - + +
226E ALA* 4.2 17.5 - - + -
229E ILE* 4.0 15.3 - - + +
238E LEU* 3.4 35.0 - - + +
242E ILE* 6.2 0.7 - - + -
96F PRO* 4.4 1.0 - - - +
138F ILE* 4.9 2.5 - - + -
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Residues in contact with LEU 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E ASP 3.3 18.4 - - - +
174E TYR* 3.6 8.5 + - - +
175E ALA 3.0 1.4 - - - -
176E VAL* 1.3 93.3 - - + +
178E ARG* 1.3 69.5 + - - +
179E ASN 3.8 0.9 - - - -
229E ILE* 4.2 16.2 - - + -
95F LEU* 4.2 21.0 - - + +
96F PRO* 3.2 26.2 - - - +
99F MET* 3.3 31.5 - - + +
138F ILE* 4.5 23.1 - - + -
141F ASN* 4.9 19.1 - - + +
142F ILE* 5.5 1.6 - - + -
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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