Contacts of the helix formed by residues 208 - 222 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166D ASP* 3.0 33.5 + - - -
169D ASN* 3.8 19.2 + - - +
170D ILE* 3.9 18.0 - - + +
173D LEU* 5.7 1.2 - - - +
203D THR 3.9 18.3 + - - -
204D MET* 3.2 26.6 + - + +
206D GLN 3.8 0.6 + - - -
207D LYS* 1.3 108.1 + - + +
209D ASP* 1.3 65.6 + - - +
210D TYR* 3.4 20.6 - + + -
211D TYR* 3.5 18.8 - - + +
212D GLU* 3.2 25.1 + - - +
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Residues in contact with ASP 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D TYR* 1.3 69.3 - - - +
210D TYR* 1.3 91.8 + - - +
211D TYR 3.2 0.2 + - - -
212D GLU* 3.4 10.8 + - - +
213D ASN* 3.1 35.3 + - - +
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Residues in contact with TYR 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D LEU* 4.4 2.2 - - + -
160D MET* 3.5 32.5 - - + +
161D HIS 4.7 3.8 - - - +
162D ALA* 3.2 23.5 - - + +
163D PRO* 3.2 23.6 - - + -
166D ASP* 2.8 38.4 + - - +
170D ILE* 3.8 4.5 - - - +
204D MET* 3.5 21.1 - - + -
208D TYR* 3.4 18.3 - + + -
209D ASP* 1.3 95.8 - - - +
211D TYR* 1.3 71.8 + - - +
213D ASN* 4.0 4.2 - - - +
214D ARG* 3.1 44.2 + - - +
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Residues in contact with TYR 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D MET* 3.9 22.0 - - + -
197D LEU* 4.6 1.7 + - + -
200D MET* 4.6 8.1 - - + -
201D HIS* 2.8 40.0 + - - +
204D MET* 3.8 31.4 - - + -
205D ASN* 3.2 52.7 - - + -
206D GLN 4.6 0.7 - - - -
208D TYR* 3.4 13.6 + - + +
209D ASP 3.1 0.4 - - - -
210D TYR* 1.3 81.4 - - - +
212D GLU* 1.3 59.7 + - - +
214D ARG 3.2 0.3 + - - -
215D ILE* 2.8 78.9 + - + +
229D LEU* 4.4 0.3 - - - +
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Residues in contact with GLU 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D ASN* 5.1 7.0 - - - +
206D GLN* 4.9 16.3 - - - +
208D TYR 3.2 13.8 + - - +
209D ASP* 3.8 8.9 - - - +
211D TYR* 1.3 87.2 - - + +
213D ASN* 1.3 67.2 + - - +
215D ILE* 4.4 11.6 - - - +
216D ASP* 4.6 7.4 - - - +
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Residues in contact with ASN 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D ASP* 3.1 29.5 + - - +
210D TYR* 4.2 5.3 - - - +
211D TYR 3.3 0.2 - - - -
212D GLU* 1.3 85.9 - - - +
214D ARG* 1.3 72.0 + - + +
216D ASP* 4.9 6.7 + - - +
217D GLY 5.4 0.9 + - - -
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Residues in contact with ARG 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ILE* 4.2 7.3 + - - -
160D MET* 3.8 38.9 + - + +
161D HIS* 3.6 32.9 + - - +
210D TYR* 3.1 33.0 + - - +
213D ASN* 1.3 88.6 - - + +
215D ILE* 1.3 66.6 + - - +
216D ASP 2.8 5.4 + - - -
217D GLY* 3.1 12.7 + - - +
218D VAL* 3.2 16.1 + - + +
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Residues in contact with ILE 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D MET* 3.5 9.0 - - + +
197D LEU* 3.8 24.7 - - + -
201D HIS* 5.3 1.1 - - + +
205D ASN* 5.5 2.0 - - - +
211D TYR* 2.8 67.1 + - + +
212D GLU* 4.4 10.5 - - - +
214D ARG* 1.3 71.7 - - - +
216D ASP* 1.3 72.5 + - - +
218D VAL* 4.3 2.9 - - + -
219D CYS* 3.0 44.3 + - - -
229D LEU* 4.2 9.9 - - + -
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Residues in contact with ASP 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D GLU 4.6 9.9 - - - +
213D ASN 5.2 5.7 - - - +
214D ARG 2.8 6.0 + - - +
215D ILE* 1.3 83.7 - - - +
217D GLY* 1.3 61.7 + - - +
219D CYS* 3.8 4.8 - - - +
220D LYS* 3.2 33.1 + - - +
226D LYS* 4.6 15.9 - - - +
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Residues in contact with GLY 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ARG* 5.1 1.4 + - - -
213D ASN 5.4 0.8 + - - -
214D ARG* 3.1 6.2 + - - +
216D ASP* 1.3 76.5 - - - +
218D VAL* 1.3 64.1 + - - +
220D LYS* 3.8 7.6 - - - +
221D SER* 3.1 25.6 + - - -
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Residues in contact with VAL 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ARG* 5.2 4.3 - - - +
156D ILE* 4.8 9.0 - - + -
159D ILE* 4.6 18.8 - - + -
160D MET* 3.9 22.2 - - + -
197D LEU* 4.4 20.9 - - + -
214D ARG* 3.2 22.1 + - + +
215D ILE* 3.8 6.5 - - + +
217D GLY* 1.3 78.0 - - - +
219D CYS* 1.3 62.8 - - - +
221D SER* 2.6 22.6 + - - +
222D LEU* 3.3 26.2 + - + +
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Residues in contact with CYS 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D LEU* 4.7 6.7 - - - -
215D ILE* 3.0 48.6 + - - +
216D ASP* 3.8 5.6 - - - +
218D VAL* 1.3 78.5 - - - +
220D LYS* 1.3 57.2 + - - +
222D LEU* 3.3 4.3 + - - -
223D TYR 3.2 3.6 + - - -
224D ILE* 2.7 62.1 + - + +
225D THR 5.2 3.4 - - - +
226D LYS* 6.0 1.8 - - - -
229D LEU* 3.9 18.4 - - - -
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Residues in contact with LYS 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D ASP* 3.2 23.0 + - - +
217D GLY* 3.9 7.9 - - - +
218D VAL 3.2 0.2 - - - -
219D CYS* 1.3 75.7 - - - +
221D SER* 1.3 64.2 + - - +
222D LEU 3.0 2.0 - - - -
223D TYR* 3.1 20.3 + - - +
224D ILE 4.3 4.9 - - - +
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Residues in contact with SER 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ARG* 3.3 35.5 + - - -
25D TYR* 4.8 8.4 + - - -
217D GLY 3.1 14.6 + - - -
218D VAL* 2.6 22.9 + - - +
220D LYS* 1.3 76.9 - - - +
222D LEU* 1.3 64.1 + - - +
223D TYR* 3.4 15.3 - - - -
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Residues in contact with LEU 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ARG* 4.9 4.3 - - - +
24D ILE* 3.5 43.5 - - + -
25D TYR* 4.2 19.1 - - + -
28D GLU* 4.5 16.3 - - + +
156D ILE* 6.1 2.5 - - + -
191D ARG* 6.1 0.2 - - - -
193D VAL* 4.6 7.0 - - + -
197D LEU* 4.2 17.0 - - + -
218D VAL* 3.3 33.6 + - + +
219D CYS 3.3 1.6 + - - +
220D LYS 3.0 0.8 - - - -
221D SER* 1.3 84.4 - - - +
223D TYR* 1.3 75.7 + - - +
224D ILE* 3.3 22.9 - - + +
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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