Contacts of the helix formed by residues 205 - 223 (chain B) in PDB entry 3UFJ
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 SER 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B SER* 1.3 88.0 + - - +
206B LYS* 1.3 70.7 + - - +
207B GLU 2.9 0.7 - - - -
208B PHE* 2.6 29.6 + - - +
209B ARG* 3.2 14.5 + - - +
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Residues in contact with LYS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B SER* 4.8 3.6 - - - +
205B SER* 1.3 78.7 - - - +
207B GLU* 1.3 64.4 + - + +
209B ARG* 3.3 8.6 + - - +
210B GLU* 3.1 22.8 + - - +
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Residues in contact with GLU 207 (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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193B VAL* 4.5 11.6 - - + +
195B ARG* 3.3 46.2 + - - +
203B LEU* 2.2 45.8 - - + +
204B SER* 2.7 16.4 + - - +
205B SER 2.7 4.0 + - - -
206B LYS* 1.3 78.2 - - + +
208B PHE* 1.3 57.1 + - + +
210B GLU* 3.3 8.3 + - - +
211B GLY* 2.9 25.1 + - - -
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Residues in contact with PHE 208 (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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139B ILE* 4.2 23.1 - - + -
192B MET* 3.9 27.5 - - + +
193B VAL* 4.1 18.2 - - + -
200B SER* 4.8 4.7 - - - -
203B LEU* 3.7 28.3 - - + -
204B SER* 3.9 17.3 - - - -
205B SER* 2.6 29.4 + - - +
207B GLU* 1.3 73.7 - - - +
209B ARG* 1.3 58.1 + - + +
211B GLY* 2.8 19.6 + - - -
212B GLY* 2.8 14.9 + - - -
237B ILE* 4.9 16.2 - - + -
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Residues in contact with ARG 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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205B SER* 3.2 12.6 + - - +
206B LYS* 3.7 9.4 - - - +
208B PHE* 1.3 79.7 - - + +
210B GLU* 1.3 62.0 + - - +
212B GLY* 3.5 1.7 + - - -
213B ARG* 3.2 21.7 + - - +
241B GLU* 4.5 25.0 - - + +
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Residues in contact with GLU 210 (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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206B LYS 3.1 13.1 + - - +
207B GLU* 3.6 9.9 - - - +
209B ARG* 1.3 75.7 - - - +
211B GLY* 1.3 57.2 + - - +
213B ARG* 3.4 8.1 - - - +
214B ILE* 3.1 25.6 + - - +
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B MET* 3.4 27.5 - - - +
193B VAL* 5.1 2.5 - - - -
207B GLU 2.9 11.0 + - - -
208B PHE* 2.8 9.2 + - - -
210B GLU* 1.3 75.1 - - - +
212B GLY* 1.3 51.1 + - - -
214B ILE* 2.9 8.6 + - - +
215B LEU* 2.6 36.6 + - - +
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Residues in contact with GLY 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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192B MET* 3.8 21.0 - - - -
208B PHE 2.8 15.2 + - - -
209B ARG* 4.0 2.0 - - - -
211B GLY* 1.3 70.5 - - - -
213B ARG* 1.3 52.6 - - - +
215B LEU* 3.4 4.6 - - - +
216B VAL* 2.6 38.3 + - - +
238B PHE* 4.6 13.5 - - - -
241B GLU* 6.4 2.0 - - - -
242B VAL* 6.4 0.7 - - - -
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Residues in contact with ARG 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 ARG 3.2 13.1 + - - +
210B GLU* 3.4 13.2 - - - +
211B GLY 3.1 0.2 - - - -
212B GLY* 1.3 76.0 - - - +
214B ILE* 1.3 61.1 + - - +
216B VAL* 3.9 5.2 - - - +
217B GLN* 3.3 23.0 + - - +
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Residues in contact with ILE 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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192B MET 5.4 2.0 - - - +
210B GLU 3.1 13.1 + - - +
211B GLY* 2.9 13.3 + - - +
213B ARG* 1.3 70.2 - - - +
215B LEU* 1.3 68.5 + - - +
217B GLN* 3.5 6.5 + - - +
218B LYS* 3.2 18.2 + - - +
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ILE* 4.9 27.4 - - + -
190B THR* 5.1 7.9 - - + -
191B ASN 5.0 12.6 - - - +
192B MET* 5.0 8.2 + - - -
211B GLY 2.6 17.4 + - - +
212B GLY* 3.4 12.6 - - - +
214B ILE* 1.3 67.9 - - - +
216B VAL* 1.3 71.6 + - - +
217B GLN 2.7 2.3 + - - -
218B LYS* 2.7 20.1 + - + +
219B LEU* 3.1 14.3 + - + -
229B PHE* 6.2 2.0 - - + -
238B PHE* 5.1 10.1 - - + -
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Residues in contact with VAL 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 GLY 2.6 21.7 + - - +
213B ARG* 3.9 5.6 - - - +
215B LEU* 1.3 73.2 - - - +
217B GLN* 1.3 50.5 + - - +
219B LEU* 3.1 7.1 + - - +
220B GLN* 2.7 55.0 + - - +
238B PHE* 5.1 12.7 - - + -
242B VAL* 6.0 2.9 - - + -
259B ILE* 4.9 5.1 - - + +
260B PRO* 5.4 11.0 - - + -
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Residues in contact with GLN 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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213B ARG 3.3 10.3 + - - +
214B ILE* 3.6 11.4 - - - +
215B LEU 2.7 3.8 + - - -
216B VAL* 1.3 75.6 - - - +
218B LYS* 1.3 64.0 + - - +
220B GLN* 2.9 17.3 + - - +
221B LYS* 2.9 20.9 + - - +
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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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126B ASP* 5.7 2.9 - - - +
128B LEU* 4.8 17.5 - - + -
190B THR* 6.3 2.5 - - + -
214B ILE 3.2 9.0 + - - +
215B LEU* 2.7 15.4 + - + +
217B GLN* 1.3 73.8 - - - +
219B LEU* 1.3 55.6 + - - +
221B LYS* 2.9 22.1 + - - +
222B TYR* 2.9 25.0 + - + -
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Residues in contact with LEU 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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137B ILE* 6.4 2.5 - - + -
215B LEU* 3.1 14.9 + - + +
216B VAL* 3.6 8.5 - - - +
218B LYS* 1.3 72.5 - - - +
220B GLN* 1.3 55.6 + - - +
221B LYS 3.0 5.2 - - - -
222B TYR* 4.4 2.0 - - - +
223B GLN* 2.7 34.8 + - - +
224B PRO* 3.8 13.2 - - + +
259B ILE* 4.4 28.3 - - + -
262B THR* 5.4 0.7 - - - -
264B THR* 4.9 1.2 + - - -
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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
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216B VAL* 2.7 41.9 + - - +
217B GLN* 2.9 14.1 + - - +
219B LEU* 1.3 71.2 - - - +
221B LYS* 1.3 59.6 + - - +
223B GLN* 3.7 21.5 + - - +
259B ILE* 4.8 5.2 - - + -
260B PRO* 3.7 37.5 + - - +
261B ASP* 5.3 8.0 - - - +
262B THR* 5.3 5.4 - - - -
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Residues in contact with LYS 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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130B PHE* 3.2 24.3 - - + -
217B GLN 2.9 9.7 + - - +
218B LYS* 2.9 17.3 + - - +
220B GLN* 1.3 81.0 - - - +
222B TYR* 1.3 66.6 + - + +
223B GLN* 3.3 6.9 + - - +
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Residues in contact with TYR 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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128B LEU* 3.6 57.3 + - + +
129B THR* 3.1 32.2 - - - +
130B PHE* 3.8 29.9 - + - -
131B ASN 3.7 18.4 + - - -
132B LEU* 6.0 0.9 - - + -
218B LYS* 2.9 29.9 + - + +
219B LEU* 5.1 0.7 - - - -
221B LYS* 1.3 80.1 - - + +
223B GLN* 1.3 70.4 + - - +
224B PRO* 3.3 8.7 - - + +
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Residues in contact with GLN 223 (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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130B PHE* 6.1 0.3 - - - -
131B ASN* 4.7 7.4 + - - -
132B LEU 4.8 0.2 + - - -
219B LEU 2.7 14.5 + - - +
220B GLN* 3.7 24.3 + - - +
221B LYS 4.4 5.1 - - - +
222B TYR* 1.3 79.5 - - - +
224B PRO* 1.3 69.7 - - - +
261B ASP 4.7 11.5 + - - -
262B THR* 4.8 12.2 - - - +
263B GLU 6.2 0.7 - - - +
264B THR* 4.0 7.4 - - - +
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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
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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