Contacts of the helix formed by residues 215 - 224 (chain F) 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 ARG 215 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180F THR* 5.6 3.0 - - - +
183F GLU* 2.4 40.0 + - - +
213F GLY* 3.1 23.7 + - - +
214F ASP* 1.3 87.6 + - - +
216F ALA* 1.3 69.5 + - - +
217F TRP* 3.4 4.3 - - + +
218F SER* 3.2 19.7 + - - +
219F GLU* 3.0 20.3 + - - +
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Residues in contact with ALA 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F GLU* 3.9 20.7 + - + +
184F LEU* 3.3 30.2 - - + +
187F ALA* 3.8 18.4 - - + -
189F LEU* 4.6 1.5 - - + +
210F TRP* 3.9 17.0 - - - -
214F ASP 3.6 3.0 + - - -
215F ARG* 1.3 78.2 - - - +
217F TRP* 1.3 59.6 + - - +
219F GLU* 3.1 3.3 + - - +
220F HIS* 2.9 27.5 + - - +
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Residues in contact with TRP 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F GLU* 5.6 0.4 - - - +
187F ALA* 3.7 20.3 - - + +
215F ARG* 3.4 3.9 - - + +
216F ALA* 1.3 79.9 - - - +
218F SER* 1.3 94.5 + - - +
220F HIS* 3.2 15.8 + - + +
221F ARG* 3.2 55.9 + - + +
229F PHE* 6.1 4.5 - + - -
230F VAL* 5.4 12.8 + - + +
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Residues in contact with SER 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215F ARG* 3.2 22.6 + - - +
217F TRP* 1.3 102.4 - - - +
219F GLU* 1.3 67.4 + - - +
221F ARG* 3.5 10.7 + - - +
222F ARG* 3.1 22.8 + - - +
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Residues in contact with GLU 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207F LEU* 4.2 4.7 - - + +
210F TRP* 3.8 24.9 - - + -
214F ASP* 4.0 33.1 - - + +
215F ARG 3.0 14.8 + - - +
216F ALA 3.5 7.2 - - - +
218F SER* 1.3 77.2 + - - +
220F HIS* 1.3 67.6 + - - +
222F ARG* 2.9 42.9 + - - -
223F HIS* 3.2 39.9 + - + +
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Residues in contact with HIS 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ZN 2.0 37.5 - - - -
187F ALA* 2.9 28.5 + - - +
189F LEU* 3.8 14.4 - - + +
200F CYS* 3.5 18.7 - - + +
207F LEU* 3.9 11.2 - - + +
216F ALA 2.9 14.6 + - - +
217F TRP* 3.2 16.8 + - + +
219F GLU* 1.3 77.6 - - - +
221F ARG* 1.3 57.5 + - - +
224F PHE* 3.0 35.9 + + + +
227F CYS* 4.3 1.1 - - - -
229F PHE* 4.3 8.1 - + - -
230F VAL* 3.9 16.3 - - + +
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Residues in contact with ARG 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F TRP* 3.2 50.0 + - - +
218F SER* 3.6 12.8 + - - +
220F HIS* 1.3 78.2 - - - +
222F ARG* 1.3 66.9 + - - +
223F HIS 3.3 0.4 - - - -
224F PHE 3.7 1.6 - - - -
225F PRO* 2.9 32.2 - - + +
230F VAL* 3.3 33.9 - - + -
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Residues in contact with ARG 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F ASP* 5.4 0.8 + - - -
218F SER 3.1 17.1 + - - +
219F GLU* 2.9 33.5 + - - +
221F ARG* 1.3 83.1 - - + +
223F HIS* 1.3 98.2 + - - +
225F PRO* 3.8 7.3 - - - +
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Residues in contact with HIS 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ALA* 3.6 15.4 - - - +
207F LEU* 4.1 16.8 - - + +
219F GLU* 3.2 34.0 + - - +
222F ARG* 1.3 114.0 + - - +
224F PHE* 1.3 95.8 + - + +
225F PRO* 3.5 3.8 - - - -
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Residues in contact with PHE 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B MET* 3.0 29.2 - - + +
317B ALA* 4.2 8.5 - - + -
203F CYS* 4.2 6.3 - - - -
205F GLY* 3.4 34.3 - - - -
206F LYS 3.6 11.7 - - - -
207F LEU* 3.6 27.1 - - + -
220F HIS* 3.0 29.5 + + + +
221F ARG 3.5 2.9 - - - -
223F HIS* 1.3 98.0 - - + +
225F PRO* 1.3 57.5 - - - +
226F ASN 3.0 11.0 + - - -
227F CYS* 3.0 27.6 + - + +
230F VAL* 3.5 7.8 - - - +
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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