Contacts of the helix formed by residues 225 - 241 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37G GLU* 5.9 1.3 - - + -
38G ARG 5.1 0.4 - - - +
39G GLY 3.6 10.3 - - - +
40G THR* 3.7 21.5 - - - -
177G PRO 5.2 2.9 - - - +
178G PRO* 5.8 0.7 - - + -
179G LEU* 3.8 28.9 - - + +
222G TRP* 3.1 10.3 + - - +
223G PRO 3.2 4.6 - - - +
224G GLY* 1.3 78.0 - - - +
226G ILE* 1.3 59.7 + - - +
227G ARG 3.3 0.2 + - - -
229G LEU* 3.1 29.0 + - - +
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Residues in contact with ILE 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G GLY* 3.2 17.3 + - - +
225G ASN* 1.3 77.6 - - - +
227G ARG* 1.3 57.2 + - - +
229G LEU* 4.4 6.3 - - - -
230G LYS* 2.8 37.0 + - + +
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Residues in contact with ARG 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G ARG* 3.9 15.7 - - + +
39G GLY* 4.1 4.6 + - - -
224G GLY* 3.0 15.5 + - - +
226G ILE* 1.3 78.7 - - - +
228G GLU* 1.3 57.9 + - - +
230G LYS* 4.3 1.3 - - - +
231G ASN* 2.9 32.6 + - - +
125J GLU* 5.6 11.0 - - + -
164J ASP* 6.5 0.4 - - + -
167J ASP 4.8 2.4 - - - +
168J ARG* 5.8 5.6 - - + +
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Residues in contact with GLU 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222G TRP* 3.8 19.7 - - + -
223G PRO 4.2 1.1 - - - -
224G GLY* 3.4 28.0 + - - +
225G ASN 3.5 1.8 + - - -
226G ILE 3.5 0.2 - - - -
227G ARG* 1.3 77.1 - - - +
229G LEU* 1.3 60.4 + - - +
231G ASN* 3.8 3.9 - - - +
232G VAL* 2.9 31.5 + - - +
252G ILE* 4.5 5.4 - - - +
167J ASP* 4.9 12.6 - - + +
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Residues in contact with LEU 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G ILE* 6.5 1.3 - - + -
189G MET* 5.6 10.5 - - + -
193G PHE* 5.8 0.4 - - - -
222G TRP* 4.0 13.0 - - + +
225G ASN 3.1 17.8 + - - +
226G ILE* 4.4 4.7 - - - +
228G GLU* 1.3 76.8 - - - +
230G LYS* 1.3 61.0 + - - +
232G VAL* 3.9 3.2 - - - +
233G VAL* 2.9 32.7 + - - +
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Residues in contact with LYS 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193G PHE* 4.9 11.3 - - + +
226G ILE* 2.8 24.2 + - + +
227G ARG* 4.3 1.8 - - - +
229G LEU* 1.3 76.9 - - - +
231G ASN* 1.3 57.0 + - - +
233G VAL* 4.6 3.4 - - - +
234G GLU* 2.8 34.8 + - + +
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Residues in contact with ASN 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227G ARG 2.9 22.2 + - - +
228G GLU* 4.0 3.4 - - - +
230G LYS* 1.3 76.8 - - - +
232G VAL* 1.3 52.5 + - - +
234G GLU* 4.7 2.5 - - - -
235G ARG* 2.7 39.5 + - - +
167J ASP 4.2 17.0 - - - +
168J ARG* 4.7 14.8 - - + +
171J PHE* 4.4 7.7 - - + +
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Residues in contact with VAL 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228G GLU 2.9 19.5 + - - +
229G LEU* 3.9 4.5 - - - +
231G ASN* 1.3 75.7 - - - +
233G VAL* 1.3 60.2 + - - +
235G ARG* 3.9 3.0 - - - +
236G SER* 2.9 32.6 + - - -
251G ILE 3.8 14.7 - - - +
252G ILE* 3.4 26.5 - - - +
254G PRO* 5.1 7.4 - - + +
171J PHE* 6.0 0.2 - - - -
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Residues in contact with VAL 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G ALA* 4.4 20.2 - - + +
193G PHE* 3.8 26.0 - - + -
194G ALA* 4.8 3.1 - - + +
229G LEU 2.9 17.5 + - - +
232G VAL* 1.3 77.1 - - - +
234G GLU* 1.3 58.7 + - - +
236G SER* 4.9 2.2 - - - -
237G VAL* 2.9 35.3 + - - +
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Residues in contact with GLU 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193G PHE* 5.1 4.6 - - + +
197G MET* 4.4 17.5 - - + -
230G LYS 2.8 22.0 + - - +
231G ASN* 4.5 2.5 - - - +
233G VAL* 1.3 78.0 - - - +
235G ARG* 1.3 54.2 + - - +
238G TYR* 2.6 38.9 + - + +
29J ASP 6.4 0.7 - - - -
30J LYS* 4.0 7.8 - - + +
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Residues in contact with ARG 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231G ASN 2.7 23.8 + - - +
232G VAL 3.9 2.7 - - - +
234G GLU* 1.3 76.3 - - - +
236G SER* 1.3 54.2 + - - +
239G ARG* 2.6 39.5 + - - +
254G PRO* 4.0 22.4 - - + -
30J LYS* 4.0 16.8 - - + +
171J PHE* 4.3 11.2 - - + -
172J ASP* 5.0 6.5 - - + -
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Residues in contact with SER 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232G VAL 2.9 17.3 + - - -
233G VAL* 4.3 2.5 - - - -
235G ARG* 1.3 76.2 - - - +
237G VAL* 1.3 60.8 + - - +
239G ARG* 3.9 1.3 - - - -
240G HIS* 2.9 32.2 + - - +
247G LEU* 5.8 7.6 - - - -
250G ILE* 5.8 10.1 - - - -
251G ILE 6.1 0.9 - - - -
254G PRO* 5.2 4.4 - - - +
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Residues in contact with VAL 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194G ALA* 4.3 21.5 - - + +
197G MET* 4.1 17.9 - - + -
198G CYS* 5.6 1.1 - - + +
207G PRO* 6.1 6.7 - - + -
233G VAL 2.9 19.2 + - - +
236G SER* 1.3 76.2 - - - +
238G TYR* 1.3 63.2 + - - +
240G HIS* 3.5 4.5 + - - +
241G GLY* 3.4 18.7 + - - -
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Residues in contact with TYR 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197G MET* 4.6 13.8 - - + +
201G ILE* 6.0 4.7 - - + -
234G GLU* 2.6 25.3 + - + +
237G VAL* 1.3 80.5 - - - +
239G ARG* 1.3 59.2 + - - +
240G HIS 3.4 0.7 + - - -
241G GLY* 3.9 7.6 + - - -
28J LEU* 3.3 17.7 - - - +
29J ASP* 3.8 28.0 - - + +
30J LYS* 4.0 9.9 - - + +
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Residues in contact with ARG 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235G ARG* 2.6 23.9 + - - +
236G SER* 4.4 1.6 - - - +
238G TYR* 1.3 75.2 - - - +
240G HIS* 1.3 64.9 + - - +
25J LEU* 6.5 0.7 - - - -
28J LEU* 4.2 10.3 - - + +
30J LYS* 5.3 2.2 - - + +
172J ASP* 5.3 11.9 - - + -
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Residues in contact with HIS 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207G PRO* 6.2 2.7 - - + -
236G SER 2.9 21.2 + - - +
237G VAL* 3.7 7.0 - - - +
238G TYR 3.2 0.6 - - - -
239G ARG* 1.3 80.3 - - - +
241G GLY* 1.3 64.0 + - - +
242G THR* 3.4 13.2 + - - +
247G LEU* 6.0 5.8 - - + -
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Residues in contact with GLY 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237G VAL 3.4 10.6 + - - -
238G TYR 3.9 6.0 + - - -
239G ARG 3.8 0.4 - - - -
240G HIS* 1.3 78.9 - - - +
242G THR* 1.3 57.5 + - - +
243G SER 4.2 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