Contacts of the helix formed by residues 224 - 241 (chain F) in PDB entry 5NSS
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 GLY 224 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F ARG 4.3 5.6 - - - -
39F GLY 3.0 30.7 - - - +
40F THR* 3.3 5.8 - - - -
222F TRP 3.2 2.0 - - - -
223F PRO* 1.3 76.2 - - - +
225F ASN* 1.3 70.3 + - - +
227F ARG 3.1 11.8 + - - -
228F GLU* 3.3 16.4 + - - +
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Residues in contact with ASN 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F SER* 5.4 5.6 - - - -
40F THR* 3.7 18.2 - - - +
176F LEU* 4.3 14.4 - - + +
177F PRO 3.3 27.1 - - - +
178F PRO* 4.4 0.4 - - + +
179F LEU* 4.4 10.3 - - - +
222F TRP* 3.5 14.5 + - - +
223F PRO 3.2 7.0 + - - +
224F GLY* 1.3 79.0 - - - +
226F ILE* 1.3 63.1 + - - +
228F GLU* 3.6 10.4 + - - +
229F LEU* 3.9 5.4 + - - +
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Residues in contact with ILE 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ALA* 5.0 12.6 - - + -
14F SER* 5.7 2.7 - - - -
15F PHE* 3.9 28.9 - - + +
40F THR 4.4 2.6 + - - +
41F GLY* 6.3 0.7 - - - -
225F ASN* 1.3 77.7 - - - +
227F ARG* 1.3 59.5 + - - +
228F GLU 3.2 0.2 - - - -
229F LEU* 3.3 8.6 + - - +
230F LYS* 2.9 28.9 + - - +
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Residues in contact with ARG 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F GLY* 3.2 25.4 - - - +
40F THR 4.4 2.0 + - - -
41F GLY* 3.5 24.5 - - - +
224F GLY 3.1 2.5 + - - +
226F ILE* 1.3 76.3 - - - +
228F GLU* 1.3 59.3 + - - +
230F LYS* 3.7 7.7 - - - +
231F ASN* 2.9 32.2 + - - +
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Residues in contact with GLU 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F GLY 4.4 0.6 + - - -
222F TRP* 4.2 17.0 - - + -
223F PRO 4.7 0.2 - - - -
224F GLY* 3.3 31.3 + - - +
225F ASN 3.9 6.1 - - - +
226F ILE 3.2 0.6 - - - -
227F ARG* 1.3 79.2 - - - +
229F LEU* 1.3 56.6 + - - +
231F ASN* 4.4 2.1 - - - +
232F VAL* 2.8 31.8 + - - +
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Residues in contact with LEU 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F ILE* 5.7 7.9 - - + +
189F MET* 4.6 22.6 - - + +
190F ALA* 5.3 1.9 - - + +
193F PHE* 4.2 3.4 - - + +
222F TRP* 5.6 3.7 - - + +
225F ASN 3.9 5.8 + - - +
226F ILE* 3.3 12.5 + - - +
228F GLU* 1.3 76.6 - - - +
230F LYS* 1.3 60.9 + - - +
232F VAL* 4.1 5.2 - - - -
233F VAL* 2.9 32.7 + - - +
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Residues in contact with LYS 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F PHE* 4.4 15.5 - - + +
197F MET* 5.3 0.3 - - - +
226F ILE 2.9 16.8 + - - +
227F ARG* 3.3 9.2 + - - +
229F LEU* 1.3 78.1 - - - +
231F ASN* 1.3 57.4 + - - +
233F VAL* 3.9 1.0 - - - +
234F GLU* 2.9 30.7 + - - +
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Residues in contact with ASN 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227F ARG 2.9 16.6 + - - +
228F GLU* 4.4 2.9 - - - +
230F LYS* 1.3 73.9 - - - +
232F VAL* 1.3 60.8 + - - +
234F GLU* 3.8 5.5 - - - +
235F ARG* 2.9 29.8 + - - +
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Residues in contact with VAL 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F LEU* 6.4 2.5 - - + -
228F GLU 2.8 24.0 + - - +
229F LEU* 4.0 5.4 - - - +
231F ASN* 1.3 75.5 - - - +
233F VAL* 1.3 60.5 + - - +
235F ARG* 3.2 1.9 + - - -
236F SER* 2.9 27.4 + - - -
250F ILE* 5.9 3.4 - - + -
251F ILE 3.3 27.1 - - - +
252F ILE* 4.2 15.0 - - + +
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Residues in contact with VAL 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F ALA* 3.8 27.4 - - + +
193F PHE* 3.7 23.6 - - + -
194F ALA* 4.0 6.2 - - + +
229F LEU 2.9 19.7 + - - +
232F VAL* 1.3 77.1 - - - +
234F GLU* 1.3 57.5 + - - +
236F SER* 4.1 4.7 - - - +
237F VAL* 2.9 34.0 + - - +
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Residues in contact with GLU 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F PHE 5.0 0.2 + - - -
197F MET* 3.7 27.1 - - + +
230F LYS 2.9 21.3 + - - +
231F ASN* 3.9 7.0 - - - +
233F VAL* 1.3 78.1 - - - +
235F ARG* 1.3 50.7 + - - +
238F TYR* 2.6 41.3 + - + +
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Residues in contact with ARG 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231F ASN 2.9 20.2 + - - +
232F VAL* 3.2 5.6 + - - +
234F GLU* 1.3 76.6 - - - +
236F SER* 1.3 52.7 + - - +
238F TYR* 4.6 1.8 - - - -
239F ARG* 2.7 39.0 + - - +
251F ILE* 4.3 17.7 - - + +
171G PHE 6.1 0.9 - - - +
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Residues in contact with SER 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F VAL 2.9 16.2 + - - -
233F VAL* 4.1 4.9 - - - -
235F ARG* 1.3 76.3 - - - +
237F VAL* 1.3 60.2 + - - +
239F ARG* 3.4 3.5 + - - +
240F HIS* 2.9 29.8 + - - +
247F LEU* 4.8 12.8 - - - +
249F ASP 4.7 3.6 - - - -
250F ILE* 3.7 33.4 - - - -
251F ILE* 3.8 6.2 - - - +
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Residues in contact with VAL 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F ALA* 3.9 31.2 - - + +
197F MET* 5.2 4.3 - - + -
198F CYS* 5.5 4.7 - - + +
201F ILE* 4.9 3.7 - - - +
206F PHE* 6.5 0.7 - - - -
233F VAL 2.9 18.6 + - - +
234F GLU* 4.7 2.0 - - - +
236F SER* 1.3 76.9 - - - +
238F TYR* 1.3 58.3 + - - +
240F HIS* 3.3 5.1 + - - +
241F GLY* 3.0 27.2 + - - -
247F LEU* 5.7 2.9 - - - -
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Residues in contact with TYR 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197F MET* 5.6 2.9 + - + +
201F ILE* 4.2 24.1 - - + +
234F GLU* 2.6 24.1 + - + +
235F ARG* 4.5 2.2 - - - +
237F VAL* 1.3 77.7 - - - +
239F ARG* 1.3 61.3 + - - +
240F HIS 4.3 0.3 - - - -
241F GLY* 4.1 6.9 + - - -
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Residues in contact with ARG 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235F ARG 2.7 24.0 + - - +
236F SER* 3.8 5.2 - - - +
238F TYR* 1.3 76.9 - - - +
240F HIS* 1.3 63.2 + - - +
251F ILE* 6.1 2.0 - - + -
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Residues in contact with HIS 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236F SER 2.9 18.4 + - - +
237F VAL* 3.7 5.6 - - - +
238F TYR 4.3 0.2 - - - -
239F ARG* 1.3 80.9 - - - +
241F GLY* 1.3 65.5 + - - +
242F THR* 3.2 17.5 + - - +
245F TYR 5.9 1.1 - - - +
247F LEU* 4.8 15.3 - - + -
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Residues in contact with GLY 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F ILE* 5.5 8.1 - - - -
203F LEU* 5.4 15.6 - - - +
237F VAL 3.0 13.0 + - - -
238F TYR* 4.1 6.3 + - - -
239F ARG 3.8 0.2 - - - -
240F HIS* 1.3 78.2 - - - +
242F THR* 1.3 56.6 + - - +
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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