Contacts of the helix formed by residues 204 - 221 (chain B) in PDB entry 4FDI
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 ASN 204 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B PRO 4.8 1.4 + - - -
202B GLU* 4.3 6.1 - - - +
203B ALA* 1.3 76.9 - - - +
205B LEU* 1.3 63.9 + - - +
206B THR 3.3 2.5 - - - -
207B GLN* 3.1 14.8 + - + +
208B ILE* 3.1 32.7 + - + +
242B SER* 4.1 15.3 - - - -
243B LYS 4.9 0.7 + - - -
601B NAG 1.4 71.7 + - - +
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PHE* 5.4 2.7 - - + -
180B VAL* 5.0 2.9 - - + -
190B TYR* 3.7 33.9 - - + -
194B PHE* 4.0 29.8 - - + -
195B PRO 4.8 2.5 - - - +
196B ILE* 3.9 24.2 - - + -
203B ALA* 3.3 8.3 + - + -
204B ASN* 1.3 79.1 - - - +
206B THR* 1.3 58.2 + - - +
208B ILE* 3.3 10.9 + - + +
209B TYR* 2.9 53.1 + - + +
240B TYR* 3.3 32.7 - - + +
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Residues in contact with THR 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ALA 5.0 0.8 + - - -
204B ASN 3.3 0.6 - - - -
205B LEU* 1.3 73.7 - - - +
207B GLN* 1.3 60.2 + - - +
209B TYR* 3.4 9.8 + - - +
210B LEU* 2.8 28.3 + - - +
230B TRP* 4.7 6.9 - - + -
232B VAL* 5.1 5.2 - - + +
234B ALA* 3.4 27.2 - - - +
240B TYR* 3.5 7.7 + - - -
260B GLU* 3.8 36.5 + - + +
261B ILE* 4.2 19.2 - - + +
264B SER* 3.8 13.9 - - - +
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Residues in contact with GLN 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ASN* 3.1 13.3 + - + +
206B THR* 1.3 75.7 - - - +
208B ILE* 1.3 60.2 + - + +
210B LEU* 3.3 21.6 + - - +
211B GLN* 2.9 29.3 + - - +
242B SER* 3.9 15.3 - - - +
245B PHE* 3.8 14.6 - - - -
260B GLU* 2.7 37.3 + - - +
263B ASP* 5.4 2.2 + - - -
264B SER* 4.4 8.1 + - - -
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PHE* 3.4 35.9 - - + -
182B ARG* 5.8 0.4 - - - +
194B PHE* 4.2 27.1 - - + -
204B ASN* 3.1 28.3 + - + +
205B LEU* 3.5 11.4 - - + +
207B GLN* 1.3 75.5 - - + +
209B TYR* 1.3 57.5 + - + +
211B GLN* 3.2 8.4 + - - +
212B GLU* 2.8 34.3 + - + +
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Residues in contact with TYR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 3.7 25.8 - - + +
139B GLY* 4.0 24.8 - - - -
160B PHE* 4.0 30.7 - + - -
161B GLY* 4.4 6.8 - - - -
162B SER 4.8 0.5 + - - -
180B VAL* 5.5 1.2 - - - +
190B TYR* 3.3 22.7 + - - -
205B LEU* 2.9 36.4 + - + +
206B THR* 3.6 7.4 - - - +
208B ILE* 1.3 73.7 - - - +
210B LEU* 1.3 64.3 + - - +
212B GLU* 3.4 1.4 + - - -
213B ALA 3.1 12.6 + - - -
230B TRP* 2.9 18.4 + - + -
232B VAL* 3.7 32.5 - - + -
233B ASP* 4.0 12.0 + - - -
240B TYR* 3.8 19.7 + - - -
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B THR 2.8 20.7 + - - +
207B GLN* 3.5 24.0 - - - +
208B ILE 3.3 0.2 - - - -
209B TYR* 1.3 73.9 - - - +
211B GLN* 1.3 58.0 + - - +
213B ALA* 3.0 5.4 + - - +
214B LEU* 2.9 52.2 + - + +
230B TRP* 4.0 8.4 - - - +
263B ASP* 5.7 0.7 - - - +
264B SER* 3.5 42.8 - - - +
267B LYS* 3.8 28.0 - - + -
268B ILE* 3.8 14.8 - - + -
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Residues in contact with GLN 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLN 2.9 14.7 + - - +
208B ILE* 3.5 10.8 - - - +
210B LEU* 1.3 76.0 - - - +
212B GLU* 1.3 66.1 + - - +
214B LEU* 3.3 19.6 + - - +
215B ASP* 2.7 65.6 + - - +
218B LYS* 4.8 5.7 - - - +
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LYS* 2.9 33.8 + - - +
138B VAL* 3.8 20.4 - - + -
160B PHE* 3.7 27.4 - - + +
182B ARG* 2.8 40.4 + - - -
208B ILE* 2.8 25.2 + - + +
209B TYR* 3.7 6.7 - - - +
210B LEU 3.3 0.2 - - - -
211B GLN* 1.3 79.2 - - - +
213B ALA* 1.3 62.1 + - - +
215B ASP* 4.0 7.6 - - - +
216B PHE* 3.1 24.8 + - - +
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 4.4 2.4 - - - +
209B TYR 3.1 4.4 + - - -
210B LEU 3.0 9.4 + - - +
212B GLU* 1.3 74.0 - - - +
214B LEU* 1.3 65.2 + - - +
216B PHE* 3.3 4.8 + - - +
217B ILE* 3.0 29.9 + - + +
228B LEU* 3.7 19.2 - - + +
230B TRP* 3.5 31.9 - - + +
268B ILE* 4.0 17.0 - - + -
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Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 2.9 47.7 + - + +
211B GLN* 3.9 23.8 - - - +
213B ALA* 1.3 75.4 - - - +
215B ASP* 1.3 63.6 + - - +
217B ILE* 3.2 3.5 + - + -
218B LYS* 2.9 39.4 + - - +
267B LYS* 4.1 23.3 - - + +
268B ILE* 4.1 10.8 - - + -
271B LEU* 3.6 27.3 - - + +
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Residues in contact with ASP 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LYS* 5.9 0.4 - - - +
211B GLN* 2.7 51.9 + - - +
212B GLU* 4.0 9.4 - - - +
214B LEU* 1.3 78.0 - - - +
216B PHE* 1.3 62.1 + - - +
218B LYS* 3.4 13.8 + - - +
219B ARG* 3.0 39.3 + - + +
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Residues in contact with PHE 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL* 3.5 28.9 - - + -
135B SER 4.6 0.2 - - - -
136B LYS* 3.7 44.0 - - + -
158B GLU* 3.7 23.8 - - - -
212B GLU 3.1 20.7 + - - +
213B ALA* 3.6 4.9 - - - +
215B ASP* 1.3 76.1 - - - +
217B ILE* 1.3 64.4 + - - +
219B ARG* 3.3 13.5 + - - +
220B GLN* 3.0 43.8 + - + +
226B PHE* 3.7 25.6 - + + -
227B PHE 3.8 14.4 - - - -
228B LEU* 4.1 16.2 - - + -
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Residues in contact with ILE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.3 7.4 - - + -
213B ALA* 3.0 21.9 + - + +
214B LEU* 3.6 5.4 - - - +
216B PHE* 1.3 76.0 - - + +
218B LYS* 1.3 64.1 + - - +
221B ALA* 3.0 26.1 + - + +
226B PHE* 4.0 30.3 - - + -
228B LEU* 4.2 14.1 - - + -
268B ILE* 4.0 26.9 - - + +
271B LEU* 3.9 13.9 - - + -
272B LEU* 3.9 22.7 - - + -
275B LEU* 3.7 20.2 - - + -
277B VAL* 5.1 0.7 - - + -
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Residues in contact with LYS 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B GLN* 4.8 4.8 - - - +
214B LEU* 2.9 34.2 + - - +
215B ASP* 3.7 15.8 + - - +
217B ILE* 1.3 76.4 - - - +
219B ARG* 1.3 63.0 - - + +
221B ALA* 3.9 11.3 + - - +
223B HIS* 5.2 1.4 - - - -
271B LEU* 3.8 34.5 - - + -
275B LEU* 4.3 15.5 - - + +
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Residues in contact with ARG 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B LYS* 3.6 14.1 - - - +
158B GLU* 2.8 44.0 + - - -
215B ASP* 3.0 25.0 + - + +
216B PHE* 3.6 20.9 - - - +
217B ILE 3.2 0.4 - - - -
218B LYS* 1.3 78.6 - - + +
220B GLN* 1.3 82.2 + - - +
221B ALA 3.6 0.2 - - - -
223B HIS* 3.7 19.4 - - - +
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Residues in contact with GLN 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL* 3.7 32.8 - - + +
158B GLU* 4.2 1.2 + - - -
216B PHE* 3.0 42.8 + - + +
219B ARG* 1.3 104.8 + - - +
221B ALA* 1.3 60.2 + - - +
223B HIS* 2.9 21.4 + - - +
224B HIS* 2.9 36.4 + - - +
226B PHE* 3.8 24.7 - - + -
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Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASN* 6.1 0.2 - - - -
217B ILE* 3.0 19.5 + - + +
218B LYS 4.3 6.7 - - - +
219B ARG 3.6 0.8 - - - -
220B GLN* 1.3 74.7 - - - +
222B ARG* 1.3 68.3 + - + +
223B HIS* 3.1 18.9 - - - -
224B HIS 5.0 0.7 - - - -
226B PHE* 5.0 5.8 - - + -
275B LEU* 4.0 27.1 - - + -
277B VAL* 5.0 16.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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