Contacts of the helix formed by residues 225 - 241 (chain J) 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 ASN 225 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38J ARG 5.9 0.2 - - - +
39J GLY 4.7 0.2 - - - -
40J THR* 4.2 24.5 - - - +
179J LEU* 5.1 8.5 - - + -
222J TRP* 3.4 19.5 + - - +
223J PRO 3.3 6.4 - - - +
224J GLY* 1.3 75.8 - - - +
226J ILE* 1.3 65.5 + - - +
228J GLU* 3.3 2.9 + - - +
229J LEU* 3.2 19.9 + - - +
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Residues in contact with ILE 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39J GLY 3.4 13.4 + - - +
40J THR* 4.7 8.9 - - - +
41J GLY* 5.2 1.3 - - - +
224J GLY 3.1 0.2 + - - -
225J ASN* 1.3 78.9 - - - +
227J ARG* 1.3 57.0 + - - +
229J LEU* 3.3 7.4 + - - +
230J LYS* 2.9 30.8 + - - +
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Residues in contact with ARG 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39J GLY* 3.5 15.4 + - - +
224J GLY* 2.9 16.1 + - - +
226J ILE* 1.3 80.8 - - - +
228J GLU* 1.3 56.3 + - - +
230J LYS* 4.1 3.8 - - - +
231J ASN* 2.9 33.4 + - - +
167K ASP* 4.8 15.7 - - + +
171K PHE* 5.4 10.6 - - + +
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Residues in contact with GLU 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222J TRP* 4.5 8.7 - - + -
223J PRO 4.5 7.0 - - - -
224J GLY* 3.5 27.9 + - - +
225J ASN 3.3 8.1 + - - +
227J ARG* 1.3 78.0 - - - +
229J LEU* 1.3 53.2 + - - +
231J ASN* 4.8 2.2 - - - -
232J VAL* 2.7 41.5 + - + +
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Residues in contact with LEU 229 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189J MET* 5.3 19.3 - - + +
190J ALA* 6.3 0.7 - - - -
193J PHE* 4.3 4.6 - - + +
225J ASN 3.2 12.8 + - - +
226J ILE* 3.8 9.9 - - - +
227J ARG 3.3 0.2 - - - -
228J GLU* 1.3 75.7 - - - +
230J LYS* 1.3 60.7 + - - +
232J VAL* 4.5 2.0 - - - -
233J VAL* 2.9 33.1 + - - +
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Residues in contact with LYS 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193J PHE* 4.7 8.7 - - + +
196J GLN* 6.4 1.6 - - + -
226J ILE 2.9 17.4 + - - +
227J ARG* 4.1 4.9 - - - +
229J LEU* 1.3 75.0 - - - +
231J ASN* 1.3 60.3 + - - +
233J VAL* 4.1 2.6 - - - +
234J GLU* 2.9 33.1 + - - +
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Residues in contact with ASN 231 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227J ARG 2.9 19.3 + - - +
228J GLU* 4.6 2.2 - - - +
230J LYS* 1.3 78.1 - - - +
232J VAL* 1.3 56.5 + - - +
234J GLU* 4.8 2.5 - - - -
235J ARG* 2.9 34.1 + - - +
251J ILE* 4.8 0.6 - - - +
171K PHE* 4.3 22.9 - - + +
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Residues in contact with VAL 232 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228J GLU* 2.7 23.8 + - + +
229J LEU* 4.4 3.1 - - - +
231J ASN* 1.3 76.7 - - - +
233J VAL* 1.3 58.7 + - - +
236J SER* 2.8 32.2 + - - -
250J ILE* 4.8 4.0 - - + +
251J ILE* 4.0 29.9 + - + +
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Residues in contact with VAL 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190J ALA* 5.4 5.2 - - - +
193J PHE* 4.0 26.0 - - + +
194J ALA* 5.2 2.2 - - - +
197J MET* 4.4 3.5 - - + +
229J LEU 2.9 21.5 + - - +
230J LYS 4.1 1.1 - - - +
232J VAL* 1.3 76.1 - - - +
234J GLU* 1.3 59.8 + - - +
236J SER* 3.8 3.8 - - - -
237J VAL* 2.9 32.6 + - - +
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Residues in contact with GLU 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197J MET* 4.0 23.4 - - + +
230J LYS 2.9 18.8 + - - +
231J ASN* 4.4 2.9 - - - +
233J VAL* 1.3 76.5 - - - +
235J ARG* 1.3 58.8 + - - +
237J VAL* 4.4 0.5 - - - +
238J TYR* 2.9 34.1 + - - +
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Residues in contact with ARG 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231J ASN 2.9 22.4 + - - +
234J GLU* 1.3 76.1 - - - +
236J SER* 1.3 58.8 + - - +
238J TYR* 4.4 4.3 - - - -
239J ARG* 2.9 33.1 + - - +
251J ILE* 3.9 19.6 - - + +
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Residues in contact with SER 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232J VAL 2.8 23.9 + - - -
233J VAL* 3.8 4.7 - - - -
234J GLU 3.3 0.2 - - - -
235J ARG* 1.3 74.8 - - - +
237J VAL* 1.3 59.4 + - - +
239J ARG* 4.2 1.9 - - - +
240J HIS* 2.9 32.9 + - - +
247J LEU* 5.6 2.0 - - - -
249J ASP 4.1 6.3 - - - +
250J ILE* 3.7 30.1 - - - +
251J ILE* 4.0 5.3 - - - +
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Residues in contact with VAL 237 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197J MET* 4.7 13.0 - - + -
207J PRO* 4.1 26.7 - - + -
233J VAL 2.9 16.8 + - - +
234J GLU 4.4 1.3 - - - +
236J SER* 1.3 77.0 - - - +
238J TYR* 1.3 60.8 + - - +
240J HIS* 4.6 4.3 - - - -
241J GLY* 3.2 20.1 + - - -
242J THR 4.2 10.1 + - - +
243J SER* 6.4 0.2 - - - -
247J LEU* 5.7 2.5 - - - -
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Residues in contact with TYR 238 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234J GLU 2.9 22.6 + - - +
235J ARG* 4.2 3.8 - - - +
237J VAL* 1.3 79.4 - - - +
239J ARG* 1.3 60.4 + - - +
241J GLY* 3.9 7.1 + - - -
24K HIS* 5.1 20.6 - - + +
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Residues in contact with ARG 239 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235J ARG 2.9 21.9 + - - +
236J SER* 4.2 2.2 - - - +
238J TYR* 1.3 74.9 - - - +
240J HIS* 1.3 65.8 + - - +
241J GLY* 4.8 0.2 - - - -
24K HIS* 5.9 3.8 - - - -
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Residues in contact with HIS 240 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236J SER 2.9 19.5 + - - +
237J VAL* 4.3 3.1 - - - +
239J ARG* 1.3 80.0 - - - +
241J GLY* 1.3 60.6 + - - +
242J THR* 3.5 8.5 - - - +
247J LEU* 3.7 27.6 - - + -
249J ASP* 5.4 5.4 - - + +
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Residues in contact with GLY 241 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237J VAL 3.2 12.3 + - - -
238J TYR 3.9 6.3 + - - -
239J ARG 3.5 1.4 - - - -
240J HIS* 1.3 79.0 - - - +
242J THR* 1.3 58.4 + - - +
243J SER 4.2 1.2 + - - -
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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