Contacts of the helix formed by residues 208 - 222 (chain B) in PDB entry 1F5Q
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 TYR 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B ASP* 3.7 20.9 - - + -
169B ASN* 4.1 16.5 + - - +
170B ILE* 3.9 22.1 - - + +
173B LEU* 5.4 4.7 - - - +
203B THR 3.8 13.7 - - - -
204B MET* 3.3 21.4 + - + +
207B LYS* 1.3 104.2 + - + +
209B ASP* 1.3 64.8 + - - +
210B TYR* 3.1 40.8 - + + -
211B TYR* 3.6 13.1 - - + +
212B GLU* 3.5 21.2 + - - +
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Residues in contact with ASP 209 (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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207B LYS 4.9 0.9 - - - +
208B TYR* 1.3 73.3 + - - +
210B TYR* 1.3 68.3 + - + +
211B TYR 3.1 2.2 - - - -
212B GLU* 3.4 13.9 + - - +
213B ASN* 3.1 35.2 + - - +
128D LYS* 5.0 10.3 + - - +
131D THR* 5.4 3.5 - - - +
135D LYS* 4.7 13.0 + - - -
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Residues in contact with TYR 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 4.2 1.8 - - + -
160B MET* 3.8 30.0 - - + +
161B HIS 5.0 2.7 - - - +
162B ALA* 3.3 21.9 - - + +
163B PRO* 3.6 15.7 - - + -
166B ASP* 2.5 39.4 + - - +
170B ILE* 3.6 6.9 - - - +
204B MET* 3.6 20.4 - - + -
208B TYR* 3.1 28.3 - + + -
209B ASP* 1.3 80.1 - - + +
211B TYR* 1.3 75.2 + - - +
213B ASN* 4.0 5.3 - - - +
214B ARG* 3.2 37.7 + - - +
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Residues in contact with TYR 211 (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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160B MET* 4.0 15.7 - - + +
197B LEU* 4.3 2.3 + - + -
200B MET* 4.1 14.8 - - + -
201B HIS* 2.7 45.4 + + - +
204B MET* 3.6 46.7 - - + +
205B ASN* 3.7 29.4 - - + -
206B GLN 4.8 0.2 - - - -
208B TYR* 3.6 12.2 + - + +
209B ASP 3.1 0.4 - - - -
210B TYR* 1.3 84.8 - - - +
212B GLU* 1.3 64.4 + - + +
213B ASN 3.1 0.3 + - - -
214B ARG 3.2 0.3 + - - -
215B ILE* 2.9 74.9 + - + +
229B LEU* 4.3 0.7 - - - +
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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
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205B ASN* 6.2 1.3 - - - +
206B GLN* 4.1 13.7 - - + +
208B TYR 3.5 12.7 + - - +
209B ASP* 3.4 12.9 + - - +
211B TYR* 1.3 88.1 - - + +
213B ASN* 1.3 63.9 + - - +
215B ILE* 4.3 10.9 - - - +
216B ASP* 5.2 3.6 - - - +
127D ASP* 3.6 37.9 - - + +
128D LYS* 3.9 18.7 + - - +
131D THR* 2.3 39.0 + - - +
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Residues in contact with ASN 213 (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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209B ASP* 3.1 27.5 + - - +
210B TYR* 4.0 6.3 - - - +
212B GLU* 1.3 87.8 + - - +
214B ARG* 1.3 66.2 + - + +
215B ILE 3.8 0.4 - - - -
216B ASP* 5.3 2.0 + - - +
217B GLY 5.8 0.2 + - - -
128D LYS* 4.1 25.1 + - - +
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Residues in contact with ARG 214 (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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159B ILE* 3.9 10.3 + - - -
160B MET* 3.5 47.8 + - + +
161B HIS* 3.7 26.8 + - - +
210B TYR* 3.2 24.8 + - - +
213B ASN* 1.3 85.0 - - + +
215B ILE* 1.3 64.9 + - - +
216B ASP 3.2 3.4 + - - -
217B GLY* 3.3 5.1 + - - +
218B VAL* 3.1 26.5 + - + +
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Residues in contact with ILE 215 (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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160B MET* 4.0 15.7 - - + +
197B LEU* 3.8 24.5 - - + -
201B HIS* 5.3 1.3 - - + +
211B TYR* 2.9 53.6 + - + +
212B GLU* 4.3 11.7 - - - +
214B ARG* 1.3 76.6 - - - +
216B ASP* 1.3 69.1 + - - +
218B VAL* 4.3 2.7 - - + -
219B CYS* 3.0 47.3 + - - -
229B LEU* 4.3 10.3 - - + -
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Residues in contact with ASP 216 (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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212B GLU 5.2 3.3 - - - +
213B ASN 5.3 2.6 + - - +
214B ARG 3.2 1.2 - - - -
215B ILE* 1.3 88.6 - - - +
217B GLY* 1.3 58.5 + - - +
219B CYS* 3.7 5.0 - - - +
220B LYS* 2.9 31.7 + - - +
226B LYS* 4.4 19.9 - - - +
127D ASP* 5.0 6.6 - - - +
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Residues in contact with GLY 217 (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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21B ARG* 5.5 0.9 - - - -
214B ARG* 3.3 6.5 + - - +
216B ASP* 1.3 75.8 - - - +
218B VAL* 1.3 66.8 + - - +
220B LYS* 3.1 7.6 + - - +
221B SER* 2.8 27.5 + - - -
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Residues in contact with VAL 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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21B ARG* 4.9 3.8 - - - +
24B ILE* 6.5 0.2 - - + -
156B ILE* 4.9 8.1 - - + -
159B ILE* 4.3 27.6 - - + -
160B MET* 3.9 21.1 - - + -
197B LEU* 4.2 20.9 - - + -
214B ARG* 3.1 22.1 + - + +
215B ILE* 3.7 6.5 - - + +
217B GLY* 1.3 75.3 - - - +
219B CYS* 1.3 64.2 + - - +
221B SER* 2.7 24.4 + - - -
222B LEU* 3.2 29.4 + - + +
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Residues in contact with CYS 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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197B LEU* 4.4 12.6 - - - -
215B ILE* 3.0 45.6 + - - +
216B ASP* 3.7 6.7 - - - +
218B VAL* 1.3 76.6 - - - +
220B LYS* 1.3 55.7 + - - +
222B LEU* 3.1 4.5 + - - +
223B TYR 3.0 8.8 + - - -
224B ILE* 2.6 60.4 + - + +
225B THR 5.2 2.5 - - - -
226B LYS* 6.0 1.1 - - - -
229B LEU* 4.1 17.3 - - - -
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Residues in contact with LYS 220 (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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216B ASP 2.9 18.0 + - - +
217B GLY* 3.4 9.2 - - - +
219B CYS* 1.3 78.1 - - - +
221B SER* 1.3 61.1 + - - +
223B TYR* 3.1 21.5 + - - +
224B ILE 4.1 6.9 + - - +
225B THR* 6.5 0.2 - - - +
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Residues in contact with SER 221 (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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21B ARG* 2.9 46.4 + - - -
25B TYR* 5.1 6.1 + - - -
217B GLY 2.8 16.5 + - - -
218B VAL* 2.7 20.3 + - - +
220B LYS* 1.3 73.1 - - - +
222B LEU* 1.3 62.2 + - - +
223B TYR* 3.4 13.4 + - - -
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Residues in contact with LEU 222 (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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21B ARG* 4.1 13.2 - - - +
24B ILE* 3.6 37.9 - - + -
25B TYR* 4.7 8.7 - - + -
28B GLU* 5.7 5.1 - - + +
156B ILE* 5.8 1.8 - - + -
193B VAL* 4.5 17.0 - - + -
197B LEU* 4.2 17.7 - - + -
218B VAL* 3.2 32.5 + - + +
219B CYS 3.1 4.1 + - - +
220B LYS 3.1 0.6 - - - -
221B SER* 1.3 84.1 - - - +
223B TYR* 1.3 78.9 + - - +
224B ILE* 3.3 17.9 + - + +
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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