Contacts of the helix formed by residues 211 - 223 (chain F) in PDB entry 4ILW
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 LEU 211 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124F LEU* 4.5 9.9 - - + -
129F VAL* 4.0 34.8 - - + +
132F ALA* 4.0 21.5 - - + -
133F ILE* 4.6 6.7 - - + -
162F PHE* 4.0 17.0 - - + -
196F PHE* 3.8 32.1 - - + -
202F TRP* 3.7 28.3 - - + -
203F THR 3.2 15.4 + - - +
209F THR 3.2 3.2 + - - -
210F ASN* 1.3 71.2 - - - +
212F PHE* 1.3 51.5 + - - +
214F VAL* 3.3 0.7 + - - -
215F ALA* 2.7 38.8 + - - +
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Residues in contact with PHE 212 (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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132F ALA* 3.8 22.7 - - + +
135F LYS* 3.7 43.5 - - + -
136F ALA* 3.7 20.6 - - - +
139F VAL* 3.8 17.9 - - + -
203F THR 5.0 0.2 + - - -
210F ASN* 3.3 8.5 - - - +
211F LEU* 1.3 79.2 - - - +
213F LEU* 1.3 83.1 + - + +
215F ALA* 3.7 2.0 - - - +
216F ALA* 2.8 33.8 + - + +
245F LEU* 3.8 26.0 - - + -
248F PHE* 3.9 26.0 - + + -
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Residues in contact with LEU 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210F ASN* 3.1 16.0 - - + +
212F PHE* 1.3 90.4 - - + +
214F VAL* 1.3 62.9 + - - +
216F ALA* 3.5 5.4 + - - +
217F HIS* 3.3 17.7 + - - +
234F LEU* 3.7 12.3 - - + +
239F TYR* 3.6 28.9 - - + +
240F ASN* 4.5 7.3 - - - +
241F SER* 3.8 40.4 - - - +
242F PHE* 4.3 10.5 - - - +
244F GLU 4.5 2.2 - - - +
245F LEU* 3.7 25.6 - - + -
248F PHE* 4.0 20.0 - - + -
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Residues in contact with VAL 214 (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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2B SER* 3.7 17.0 - - - +
180F LEU* 4.3 8.5 - - + -
181F ALA* 3.7 30.5 - - + -
196F PHE* 3.8 9.4 - - + -
202F TRP* 3.8 22.4 - - + -
209F THR* 4.1 11.9 - - + -
210F ASN 3.2 16.7 + - - +
211F LEU 3.9 0.7 - - - +
213F LEU* 1.3 73.8 - - - +
215F ALA* 1.3 67.3 + - - +
217F HIS* 3.2 7.2 + - - +
218F GLU* 3.0 21.5 + - + +
239F TYR* 4.1 15.3 - - + -
240F ASN* 5.2 2.0 - - - +
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Residues in contact with ALA 215 (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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133F ILE* 4.4 16.6 - - + -
136F ALA* 3.8 14.6 - - + -
194F ILE* 4.4 1.6 - - + +
196F PHE* 3.7 26.8 - - + -
211F LEU 2.7 23.4 + - - +
212F PHE* 3.7 3.8 - - - +
214F VAL* 1.3 72.6 - - - +
216F ALA* 1.3 57.8 + - - +
218F GLU* 3.7 2.7 - - - +
219F LEU* 2.8 37.8 + - + +
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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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136F ALA* 3.5 22.1 - - + +
139F VAL* 4.9 4.9 - - + -
140F TRP* 2.8 31.7 + - - +
212F PHE* 2.8 25.5 + - + +
213F LEU* 3.6 7.0 - - - +
215F ALA* 1.3 76.7 - - - +
217F HIS* 1.3 63.1 + - - +
219F LEU* 4.5 0.2 - - - -
220F GLY 3.3 5.2 + - - -
234F LEU* 3.6 20.4 - - + -
248F PHE* 5.3 1.6 - - + -
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Residues in contact with HIS 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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1B CYS 2.9 5.8 + - - -
2B SER* 3.3 20.6 - - - +
213F LEU 3.3 10.3 + - - +
214F VAL* 3.2 8.6 + - - +
216F ALA* 1.3 78.4 - - - +
218F GLU* 1.3 72.9 + - - +
220F GLY* 3.0 10.6 + - - -
221F HIS* 3.1 2.8 + - - -
227F HIS* 3.5 16.8 - + - -
234F LEU* 2.8 33.4 + - + +
235F MET* 3.4 34.8 - - + +
236F TYR 3.9 7.4 - - - -
237F PRO* 3.9 2.0 + - + -
240F ASN* 3.3 10.2 + - - +
301F ZN 2.0 37.7 - - - -
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Residues in contact with GLU 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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1B CYS 3.0 21.4 + - - -
2B SER* 2.5 42.0 + - - +
181F ALA* 3.4 18.8 - - + +
182F HIS* 3.5 11.1 - - - -
183F ALA* 3.4 16.4 - - + +
194F ILE* 3.8 26.7 - - + -
196F PHE* 4.8 0.4 - - + -
214F VAL* 3.0 20.2 + - + +
215F ALA 4.0 2.7 - - - +
217F HIS* 1.3 79.5 - - - +
219F LEU* 1.3 64.3 + - - +
221F HIS* 3.0 22.5 + - - +
222F SER* 3.0 10.0 + - - -
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Residues in contact with LEU 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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133F ILE* 4.5 5.6 - - + +
136F ALA* 3.8 25.4 - - + +
137F LEU* 3.6 41.1 - - + +
140F TRP* 3.8 12.1 - - + +
148F PHE* 5.4 2.7 - - + -
158F ILE* 4.1 26.2 - - + -
160F ILE* 5.1 3.1 - - + -
194F ILE* 3.6 21.0 - - + +
215F ALA* 2.8 24.0 + - + +
216F ALA 3.7 4.9 - - - +
218F GLU* 1.3 77.6 - - - +
220F GLY* 1.3 56.3 + - - +
222F SER* 3.1 5.1 + - - -
223F LEU* 2.9 33.3 + - + +
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Residues in contact with GLY 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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140F TRP* 3.6 23.0 - - - +
216F ALA 3.3 6.5 + - - -
217F HIS 3.0 11.5 + - - -
219F LEU* 1.3 75.9 - - - +
221F HIS* 1.3 54.6 + - - +
223F LEU* 3.3 5.5 + - - +
224F GLY 3.2 5.4 + - - -
225F LEU* 2.8 41.4 + - - +
235F MET* 4.0 6.3 - - - -
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Residues in contact with HIS 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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1B CYS 3.2 11.8 + - - -
69B SER* 4.6 0.7 - - - -
70B ALA* 3.7 29.3 - - + +
183F ALA* 4.0 11.4 - - + -
184F TYR 4.1 2.9 - - - +
185F PRO* 3.4 15.8 - - - +
217F HIS* 3.1 12.7 + + - -
218F GLU* 3.0 18.0 + - - +
220F GLY* 1.3 71.3 - - - +
222F SER* 1.3 66.0 + - - +
223F LEU 3.0 0.2 - - - -
224F GLY* 2.9 13.7 + - - -
225F LEU 3.0 25.0 + - - +
226F PHE* 4.0 8.2 - - - -
227F HIS* 3.1 19.3 + + - -
235F MET* 3.6 10.1 - - + -
301F ZN 2.2 36.3 - - - -
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Residues in contact with SER 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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108F TRP* 2.8 24.7 + - - -
158F ILE* 4.2 16.1 - - - +
183F ALA* 4.4 0.7 - - - +
184F TYR 3.4 11.9 + - - -
185F PRO 4.2 0.2 - - - -
186F PRO* 3.3 12.1 - - - +
192F GLY* 2.6 29.0 + - - -
193F ASP 4.2 0.7 + - - -
194F ILE* 3.4 21.7 - - - +
218F GLU 3.0 7.4 + - - -
219F LEU* 3.3 13.5 - - - -
221F HIS* 1.3 75.5 - - - +
223F LEU* 1.3 57.7 + - - +
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Residues in contact with LEU 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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106F PRO 4.0 0.3 - - - +
108F TRP* 4.0 8.5 - - + +
113F LEU* 3.8 28.9 - - + -
140F TRP* 3.8 37.7 - - + -
146F LEU* 4.1 13.5 - - + -
148F PHE* 3.9 20.6 - - + -
158F ILE* 4.7 4.5 - - + -
186F PRO* 3.6 5.8 - - - +
219F LEU* 2.9 17.9 + - + +
220F GLY 3.7 5.6 - - - +
221F HIS 3.0 0.6 - - - -
222F SER* 1.3 80.4 - - - +
224F GLY* 1.3 55.4 + - - +
225F LEU 3.8 0.4 - - - -
258F ILE* 4.0 22.0 - - + -
261F LEU* 3.7 4.0 - - - +
262F TYR* 2.5 32.2 + - + +
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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