Contacts of the helix formed by residues 225 - 241 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37L GLU* 5.9 1.1 - - + -
39L GLY 3.6 10.5 - - - +
40L THR* 3.7 22.7 - - - +
177L PRO 5.2 2.5 - - - +
178L PRO* 5.8 0.4 - - + -
179L LEU* 3.8 29.1 - - + +
222L TRP* 3.1 9.6 + - - +
223L PRO 3.2 3.9 - - - +
224L GLY* 1.3 77.5 - - - +
226L ILE* 1.3 60.0 + - - +
229L LEU* 3.1 29.4 + - - +
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Residues in contact with ILE 226 (chain L).
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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39L GLY* 3.2 16.7 + - - +
225L ASN* 1.3 78.0 - - - +
227L ARG* 1.3 57.5 + - - +
229L LEU* 4.4 6.3 - - - -
230L LYS* 2.8 35.5 + - + +
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Residues in contact with ARG 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L ARG 3.9 12.8 - - - +
39L GLY* 4.2 4.1 + - - -
224L GLY* 3.0 15.9 + - - +
226L ILE* 1.3 77.8 - - - +
228L GLU* 1.3 58.7 + - - +
230L LYS* 4.3 1.2 - - - +
231L ASN* 2.9 32.7 + - - +
163N ALA* 4.4 4.9 - - + +
164N ASP* 4.2 26.5 - - + +
167N ASP* 4.1 12.5 - - + +
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Residues in contact with GLU 228 (chain L).
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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222L TRP* 3.8 19.5 - - + -
223L PRO 4.2 0.7 - - - -
224L GLY* 3.4 29.1 + - - +
225L ASN 3.5 1.4 + - - -
227L ARG* 1.3 76.7 - - - +
229L LEU* 1.3 60.8 + - - +
231L ASN* 3.8 4.3 - - - +
232L VAL* 2.9 31.0 + - - +
252L ILE* 4.5 5.6 - - + +
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Residues in contact with LEU 229 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186L ILE* 6.5 0.9 - - + -
189L MET* 5.6 10.8 - - + -
193L PHE* 5.8 0.4 - - - -
222L TRP* 4.0 14.0 - - + +
225L ASN 3.1 18.0 + - - +
226L ILE* 4.4 4.5 - - - +
228L GLU* 1.3 75.4 - - - +
230L LYS* 1.3 60.0 + - - +
232L VAL* 3.4 4.0 + - - +
233L VAL* 2.9 32.8 + - - +
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Residues in contact with LYS 230 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193L PHE* 4.9 11.0 - - + +
226L ILE* 2.8 23.3 + - + +
227L ARG* 4.3 1.8 - - - +
229L LEU* 1.3 76.9 - - - +
231L ASN* 1.3 57.9 + - - +
233L VAL* 4.8 2.7 - - - -
234L GLU* 2.8 35.1 + - + +
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Residues in contact with ASN 231 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227L ARG 2.9 22.2 + - - +
228L GLU* 4.0 4.7 - - - +
230L LYS* 1.3 76.7 - - - +
232L VAL* 1.3 51.7 + - - +
234L GLU* 4.7 2.0 - - - -
235L ARG* 2.7 39.3 + - - +
167N ASP* 4.4 18.6 - - + +
171N PHE 4.0 11.7 - - - +
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Residues in contact with VAL 232 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228L GLU 2.9 19.5 + - - +
229L LEU* 3.9 4.5 - - - +
231L ASN* 1.3 75.4 - - - +
233L VAL* 1.3 59.1 + - - +
235L ARG* 3.9 3.4 - - - +
236L SER* 2.9 32.2 + - - -
251L ILE 3.8 15.2 - - - +
252L ILE* 3.4 25.8 - - - +
254L PRO* 5.1 7.3 - - + +
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Residues in contact with VAL 233 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L ALA* 4.4 20.2 - - + +
193L PHE* 3.8 25.8 - - + -
194L ALA* 4.8 3.5 - - + +
229L LEU 2.9 17.3 + - - +
230L LYS 4.5 0.2 - - - +
232L VAL* 1.3 76.5 - - - +
234L GLU* 1.3 58.5 - - - +
236L SER* 4.3 2.4 - - - -
237L VAL* 2.9 34.5 + - - +
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Residues in contact with GLU 234 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193L PHE* 5.1 4.9 - - + +
197L MET* 4.4 17.7 - - + -
230L LYS* 2.8 22.2 + - + +
231L ASN* 4.5 2.5 - - - +
233L VAL* 1.3 78.0 - - - +
235L ARG* 1.3 54.2 + - - +
238L TYR* 2.6 39.6 + - + +
171N PHE* 5.3 4.0 - - + +
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Residues in contact with ARG 235 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231L ASN 2.7 24.4 + - - +
232L VAL 3.9 2.5 - - - +
234L GLU* 1.3 76.5 - - - +
236L SER* 1.3 56.0 + - - +
238L TYR* 4.8 0.7 - - - -
239L ARG* 2.6 39.1 + - - +
254L PRO* 4.0 20.2 - - + -
171N PHE* 3.9 5.1 + - - +
172N ASP* 3.8 27.8 - - + -
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Residues in contact with SER 236 (chain L).
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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232L VAL 2.9 17.5 + - - -
233L VAL* 4.3 2.2 - - - -
235L ARG* 1.3 76.3 - - - +
237L VAL* 1.3 58.9 + - - +
239L ARG* 4.4 1.3 - - - +
240L HIS* 2.9 31.9 + - - +
250L ILE* 5.8 10.1 - - - -
251L ILE 6.1 1.1 - - - -
254L PRO* 5.2 4.9 - - - +
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Residues in contact with VAL 237 (chain L).
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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194L ALA* 4.3 21.5 - - + +
197L MET* 4.1 17.3 - - + -
198L CYS* 5.6 1.1 - - + +
207L PRO* 6.1 4.3 - - + -
233L VAL 2.9 20.6 + - - +
236L SER* 1.3 75.0 - - - +
238L TYR* 1.3 62.8 + - - +
240L HIS* 3.7 3.9 - - - +
241L GLY* 3.4 18.5 + - - -
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Residues in contact with TYR 238 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197L MET* 4.6 14.0 - - + +
201L ILE* 6.0 4.5 - - + -
234L GLU* 2.6 25.3 + - + +
235L ARG* 4.6 0.7 - - - +
237L VAL* 1.3 80.7 - - - +
239L ARG* 1.3 59.9 + - - +
240L HIS 3.4 0.9 + - - -
241L GLY* 3.9 7.6 + - - -
171N PHE* 6.6 0.2 - - + -
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Residues in contact with ARG 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235L ARG* 2.6 25.8 + - + +
236L SER* 4.4 1.8 - - - +
238L TYR* 1.3 75.0 - - - +
240L HIS* 1.3 64.6 + - - +
172N ASP* 5.4 7.2 - - + -
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Residues in contact with HIS 240 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236L SER 2.9 22.1 + - - +
237L VAL* 3.7 6.1 - - - +
238L TYR 3.2 0.4 - - - -
239L ARG* 1.3 81.4 - - - +
241L GLY* 1.3 64.7 + - - +
242L THR* 3.4 13.7 + - - +
247L LEU* 6.0 5.8 - - + -
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Residues in contact with GLY 241 (chain L).
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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237L VAL 3.4 11.2 + - - -
238L TYR 3.9 5.3 + - - -
239L ARG 3.8 0.6 - - - -
240L HIS* 1.3 79.1 - - - +
242L THR* 1.3 58.2 + - - +
243L 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