Contacts of the helix formed by residues 218 - 231 (chain K) in PDB entry 5FWP
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 218 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217K ASN* 1.3 83.0 - - - +
219K GLU* 1.3 54.9 + - - +
220K ALA* 3.4 8.7 + - - +
221K ASP* 2.7 30.9 + - - -
222K GLN* 2.7 32.8 + - - +
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Residues in contact with GLU 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174K VAL* 5.3 4.5 - - + +
178K LEU* 4.9 10.8 - - + +
185K VAL* 3.6 7.1 - - - +
186K LEU* 3.2 50.9 - - + +
188K GLN* 2.8 35.4 + - - +
218K SER* 1.3 75.0 - - - +
220K ALA* 1.3 57.3 + - - +
222K GLN* 3.4 2.6 + - - +
223K LEU* 3.0 32.1 + - - +
243K SER* 4.5 1.2 + - - -
244K LEU* 3.9 14.3 - - + +
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Residues in contact with ALA 220 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218K SER* 3.2 7.7 + - - +
219K GLU* 1.3 76.7 - - - +
221K ASP* 1.3 61.0 + - - +
223K LEU 3.4 0.9 + - - +
224K GLY* 2.9 22.5 + - - -
244K LEU* 3.9 17.2 - - + +
245K PRO* 4.9 6.3 - - + -
249K PHE* 3.6 36.1 - - + -
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Residues in contact with ASP 221 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216K GLY* 4.1 1.8 - - - -
217K ASN* 3.5 29.4 + - - +
218K SER* 2.7 28.6 + - - +
220K ALA* 1.3 74.9 - - - +
222K GLN* 1.3 66.8 + - - +
224K GLY* 3.1 11.4 + - - +
225K LYS* 3.2 22.0 + - - +
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Residues in contact with GLN 222 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177K THR* 3.1 17.8 - - - +
178K LEU* 3.5 20.8 + - + +
179K TRP* 3.5 17.5 + - - +
186K LEU* 3.6 20.4 - - + -
214K PHE* 3.3 32.7 - - - +
216K GLY* 2.8 29.5 + - - +
217K ASN 5.5 0.6 - - - +
218K SER 2.7 17.4 + - - +
219K GLU 3.5 6.5 - - - +
221K ASP* 1.3 76.9 - - - +
223K LEU* 1.3 62.1 + - - +
225K LYS* 3.0 3.7 + - - +
226K ILE* 3.0 28.9 + - + +
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Residues in contact with LEU 223 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183K PRO* 3.7 34.1 - - + -
186K LEU* 3.7 15.0 - - + -
187K LEU* 4.2 3.1 - - + -
219K GLU 3.0 13.7 + - - +
220K ALA 3.6 6.7 - - - +
221K ASP 3.2 0.2 - - - -
222K GLN* 1.3 77.2 - - - +
224K GLY* 1.3 54.9 + - - +
226K ILE* 3.0 6.9 + - + -
227K PHE* 2.8 53.2 + - + -
238K TRP* 4.0 27.8 - - + -
244K LEU* 3.4 29.4 - - + -
249K PHE* 4.1 4.9 - - + -
278K PHE* 3.9 9.4 - - + -
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Residues in contact with GLY 224 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220K ALA 2.9 14.5 + - - -
221K ASP* 3.1 9.7 + - - -
223K LEU* 1.3 77.4 - - - +
225K LYS* 1.3 59.3 + - - +
227K PHE* 4.1 5.1 - - - -
228K ASP* 3.4 10.2 + - - +
249K PHE* 5.4 2.9 - - - -
252K ARG* 2.9 33.7 + - - -
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Residues in contact with LYS 225 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214K PHE* 3.2 20.4 - - + -
215K CYS 3.5 45.8 - - - +
216K GLY* 3.8 4.5 - - - -
221K ASP* 3.4 15.9 - - - +
222K GLN* 3.0 7.5 + - - +
224K GLY* 1.3 77.8 - - - +
226K ILE* 1.3 66.0 + - - +
227K PHE 3.3 1.6 - - - -
228K ASP* 3.3 26.0 + - - +
255K ARG* 4.8 0.7 + - - -
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Residues in contact with ILE 226 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183K PRO* 4.5 6.3 - - + -
186K LEU* 3.6 28.3 - - + -
198K TRP* 3.4 37.5 - - + +
214K PHE* 3.6 35.4 - - + -
222K GLN* 3.0 21.7 + - + +
223K LEU* 3.0 14.3 + - + +
225K LYS* 1.3 77.0 - - - +
227K PHE* 1.3 63.9 - - + +
229K LEU 3.1 12.6 + - - -
230K ILE* 3.3 32.9 + - + +
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Residues in contact with PHE 227 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223K LEU* 2.8 41.7 + - + +
224K GLY* 4.1 3.4 - - - -
226K ILE* 1.3 73.7 - - + +
228K ASP* 1.3 61.3 + - - +
230K ILE* 3.9 9.4 - - + -
231K GLY* 2.8 43.7 + - - -
232K LEU* 3.5 48.5 - - + -
233K PRO* 5.5 0.2 - - + -
238K TRP* 3.7 13.7 - + - -
249K PHE* 3.7 17.3 - + - -
252K ARG* 3.7 16.3 - - - +
278K PHE* 3.5 44.4 - + + -
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Residues in contact with ASP 228 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224K GLY 3.4 15.2 - - - +
225K LYS* 3.3 21.4 + - - +
226K ILE 3.1 1.0 - - - -
227K PHE* 1.3 77.9 - - - +
229K LEU* 1.3 53.4 + - - +
252K ARG* 2.7 35.1 + - - +
253K GLY 3.8 7.4 - - - +
255K ARG* 2.7 49.7 + - - +
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Residues in contact with LEU 229 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213K LEU* 3.9 19.3 - - + -
214K PHE* 3.6 35.7 - - + -
225K LYS 4.1 0.4 + - - -
226K ILE 3.1 2.4 + - - -
228K ASP* 1.3 81.2 - - - +
230K ILE* 1.3 60.9 + - - +
231K GLY 3.4 0.7 - - - -
254K PRO* 3.2 5.0 - - - +
255K ARG* 2.9 57.3 + - + +
257K VAL* 3.9 20.8 - - + +
260K VAL* 3.7 23.8 - - + -
261K VAL* 5.1 0.2 - - + -
273K LEU* 4.3 4.9 - - - +
276K LEU* 3.7 20.6 - - + -
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Residues in contact with ILE 230 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214K PHE* 4.7 0.7 - - + -
226K ILE* 3.4 33.2 - - + +
227K PHE* 3.9 8.1 - - + -
229K LEU* 1.3 79.3 - - + +
231K GLY* 1.3 68.6 + - - +
254K PRO* 3.7 10.8 - - - +
273K LEU* 3.9 19.0 - - + +
276K LEU* 3.4 57.0 - - + +
277K THR* 4.5 4.0 - - - +
278K PHE* 3.4 30.3 - - + +
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Residues in contact with GLY 231 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227K PHE* 2.8 21.6 + - - -
229K LEU 3.4 1.8 - - - -
230K ILE* 1.3 95.7 - - - +
232K LEU* 1.3 62.6 + - - +
233K PRO* 4.1 4.8 - - - +
252K ARG 3.4 11.2 - - - -
253K GLY 3.7 12.1 - - - -
254K PRO* 3.7 5.2 - - - +
278K PHE* 5.3 1.0 - - - +
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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