Contacts of the helix formed by residues 180 - 187 (chain E) in PDB entry 1I3O
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 180 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173E TRP* 4.2 0.7 - - - +
178E HIS 5.9 0.2 - - - -
179E LEU* 1.3 78.9 - - - +
181E PRO* 1.3 77.1 - - - +
182E ARG* 3.9 7.1 + - - +
183E GLU* 3.1 25.9 + - - +
184E LEU* 3.3 12.8 + - - +
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Residues in contact with PRO 181 (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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167E LEU* 3.9 12.8 - - + +
170E PHE* 3.3 56.3 - - + +
173E TRP* 3.7 19.1 - - + -
180E THR* 1.3 86.8 - - + +
182E ARG* 1.3 53.2 + - - +
184E LEU* 2.9 3.3 + - - +
185E ALA* 2.6 36.4 + - - +
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Residues in contact with ARG 182 (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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163E GLU* 4.6 12.0 + - - +
167E LEU* 3.6 38.8 - - + +
180E THR* 3.3 7.2 + - - +
181E PRO* 1.3 78.9 - - + +
183E GLU* 1.3 57.6 + - - +
185E ALA* 3.9 0.7 - - - +
186E SER* 2.8 32.7 + - - -
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Residues in contact with GLU 183 (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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179E LEU* 3.4 12.8 - - + +
180E THR* 3.1 19.5 + - - +
182E ARG* 1.3 78.1 - - - +
184E LEU* 1.3 63.0 + - - +
186E SER* 3.5 6.2 + - - -
187E ALA* 3.3 15.4 + - - +
215E ARG* 2.3 43.5 + - - +
216E ALA* 2.8 30.2 + - + +
217E TRP 4.5 1.6 + - - +
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Residues in contact with LEU 184 (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 PHE* 3.4 26.9 - - + -
173E TRP* 3.2 39.0 - - + +
179E LEU* 3.4 30.3 - - + -
180E THR 3.3 12.3 + - - +
181E PRO 2.9 5.3 + - - +
183E GLU* 1.3 75.2 - - - +
185E ALA* 1.3 63.2 + - - +
187E ALA* 3.1 6.8 + - - -
189E LEU* 2.8 37.1 + - + +
198E VAL* 4.1 4.3 - - + -
210E TRP* 3.9 28.7 - - + -
216E ALA* 4.0 5.8 - - + -
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Residues in contact with ALA 185 (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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163E GLU* 3.9 7.0 - - + -
166E ARG* 2.6 48.3 + - + +
167E LEU* 3.7 28.0 - - + +
170E PHE* 4.5 2.0 - - + -
181E PRO 2.6 20.0 + - - +
182E ARG* 3.9 1.8 - - - +
184E LEU* 1.3 72.9 - - - +
186E SER* 1.3 55.4 + - - +
188E GLY* 2.9 11.4 + - - -
189E LEU 3.3 12.1 + - - +
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Residues in contact with SER 186 (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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163E GLU* 3.0 20.1 + - - -
166E ARG* 4.7 0.4 - - - +
182E ARG 2.8 19.5 + - - -
183E GLU* 3.8 7.6 - - - -
184E LEU 3.2 0.2 - - - -
185E ALA* 1.3 77.0 - - - +
187E ALA* 1.3 56.1 + - - +
188E GLY 3.1 2.1 + - - -
229E PHE* 4.0 14.0 - - - -
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Residues in contact with ALA 187 (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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183E GLU 3.3 13.9 + - - +
184E LEU 3.1 6.5 + - - +
185E ALA 3.1 1.2 - - - -
186E SER* 1.3 75.4 - - - +
188E GLY* 1.3 59.4 + - - +
189E LEU* 3.2 7.0 + - + +
216E ALA* 3.8 6.7 - - + -
217E TRP* 3.7 39.3 - - + +
220E HIS* 2.8 34.2 + - - +
229E PHE* 3.5 11.8 - - - -
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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