Contacts of the helix formed by residues 225 - 241 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37K GLU* 6.2 3.1 - - + -
38K ARG 5.0 4.7 - - - +
39K GLY 5.4 3.1 - - - +
177K PRO 5.9 2.2 - - - +
179K LEU* 5.5 5.8 - - + +
182K ARG* 6.2 3.6 - - - -
222K TRP* 3.4 14.9 + - - +
223K PRO 3.2 7.0 - - - +
224K GLY* 1.3 78.6 - - - +
226K ILE* 1.3 63.7 + - - +
227K ARG 3.4 0.2 + - - -
228K GLU* 4.3 1.6 - - - +
229K LEU* 3.4 18.2 + - - +
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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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39K GLY 4.7 11.7 + - - +
224K GLY 3.2 0.2 + - - -
225K ASN* 1.3 77.1 - - - +
227K ARG* 1.3 59.7 + - - +
229K LEU* 3.8 7.6 - - - +
230K LYS* 2.9 32.4 + - - +
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Residues in contact with ARG 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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38K ARG* 4.1 12.0 + - + +
39K GLY* 4.5 9.1 - - - -
224K GLY* 3.0 16.3 + - - +
226K ILE* 1.3 79.3 - - - +
228K GLU* 1.3 56.1 + - - +
230K LYS* 3.9 2.2 - - - +
231K ASN* 2.9 31.8 + - - +
167L ASP* 3.7 38.6 - - + +
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Residues in contact with GLU 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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222K TRP* 4.8 13.2 - - + -
224K GLY* 3.7 27.1 + - - +
225K ASN 3.7 2.0 + - - +
227K ARG* 1.3 75.9 - - - +
229K LEU* 1.3 60.4 + - - +
231K ASN* 4.0 5.1 - - - +
232K VAL* 2.9 32.4 + - - +
252K ILE 4.3 7.6 - - - +
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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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189K MET* 5.4 13.7 - - + +
193K PHE* 4.7 7.8 - - + +
222K TRP* 6.0 2.6 - - + +
225K ASN 3.4 16.1 + - - +
226K ILE* 3.9 7.6 - - - +
227K ARG 3.3 0.6 - - - -
228K GLU* 1.3 78.9 - - - +
230K LYS* 1.3 57.8 + - - +
232K VAL* 4.4 1.9 - - - +
233K VAL* 2.9 33.4 + - - +
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Residues in contact with LYS 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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193K PHE* 5.4 4.3 - - - -
226K ILE* 2.9 19.2 + - + +
227K ARG* 4.2 2.2 - - - +
229K LEU* 1.3 76.7 - - - +
231K ASN* 1.3 58.4 + - - +
233K VAL* 4.2 4.0 - - - +
234K GLU* 2.9 32.1 + - - +
171L PHE* 4.4 2.3 - - - +
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Residues in contact with ASN 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 ARG 2.9 21.1 + - - +
228K GLU* 4.0 6.1 - - - +
230K LYS* 1.3 76.5 - - - +
232K VAL* 1.3 60.0 + - - +
235K ARG* 2.9 33.0 + - - +
252K ILE 5.8 1.1 - - - +
253K ASP* 6.3 1.1 - - - -
254K PRO* 6.0 4.7 - - + -
167L ASP 4.5 5.4 - - - +
170L ALA 4.7 3.8 - - - +
171L PHE* 3.4 33.2 - - + +
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Residues in contact with VAL 232 (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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217K LEU* 6.1 4.3 - - + -
228K GLU 2.9 19.2 + - - +
229K LEU* 4.4 2.2 - - - +
231K ASN* 1.3 76.6 - - - +
233K VAL* 1.3 57.2 + - - +
235K ARG* 4.6 2.9 - - - -
236K SER* 2.9 33.3 + - - -
251K ILE 3.5 16.7 - - - +
252K ILE* 3.4 26.4 + - - +
253K ASP* 5.6 1.6 - - - +
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Residues in contact with VAL 233 (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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190K ALA* 5.5 2.7 - - - +
193K PHE* 3.8 32.5 - - + +
194K ALA* 4.8 4.2 - - + +
197K MET* 4.6 3.0 - - + +
229K LEU 2.9 21.6 + - - +
230K LYS* 4.2 3.6 - - - +
232K VAL* 1.3 77.9 - - - +
234K GLU* 1.3 57.2 + - - +
236K SER* 4.6 2.7 - - - -
237K VAL* 2.9 34.1 + - - +
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Residues in contact with GLU 234 (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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197K MET* 4.8 12.1 - - + -
230K LYS 2.9 20.7 + - - +
231K ASN 4.1 1.6 - - - +
233K VAL* 1.3 76.0 - - - +
235K ARG* 1.3 59.6 + - - +
238K TYR* 2.9 34.4 + - - +
30L LYS* 5.3 12.1 - - + -
171L PHE* 4.5 15.0 - - + +
172L ASP* 6.1 2.5 - - + -
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Residues in contact with ARG 235 (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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231K ASN 2.9 19.7 + - - +
232K VAL* 4.3 4.3 - - - +
234K GLU* 1.3 78.4 - - - +
236K SER* 1.3 57.9 + - - +
238K TYR* 4.3 2.4 - - - +
239K ARG* 2.9 32.4 + - - +
251K ILE 5.7 1.8 - - - +
253K ASP 5.6 0.9 - - - -
254K PRO* 4.7 17.5 - - + -
171L PHE 3.4 15.6 + - - +
172L ASP* 5.2 4.9 - - - +
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Residues in contact with SER 236 (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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232K VAL 2.9 21.1 + - - -
233K VAL* 4.2 2.9 - - - -
235K ARG* 1.3 75.9 - - - +
237K VAL* 1.3 59.3 + - - +
239K ARG* 3.8 2.9 - - - +
240K HIS* 2.9 31.2 + - - +
247K LEU* 4.8 6.7 - - - +
249K ASP 5.1 2.5 - - - -
250K ILE* 4.1 30.5 - - - +
251K ILE 4.9 5.4 + - - +
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Residues in contact with VAL 237 (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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194K ALA* 5.3 10.8 - - + +
197K MET* 4.2 21.5 - - + -
198K CYS* 5.4 2.7 - - + +
233K VAL 2.9 20.4 + - - +
234K GLU 4.5 0.4 - - - +
236K SER* 1.3 77.4 - - - +
238K TYR* 1.3 62.5 + - - +
240K HIS* 4.0 3.9 - - - +
241K GLY* 3.5 18.5 + - - -
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Residues in contact with TYR 238 (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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234K GLU 2.9 22.3 + - - +
235K ARG* 4.3 2.7 - - - +
237K VAL* 1.3 79.9 - - - +
239K ARG* 1.3 59.2 + - - +
240K HIS 3.6 0.3 + - - -
241K GLY* 4.3 4.3 + - - -
21L GLN* 3.7 17.6 - - - +
24L HIS* 4.3 11.2 - - - +
25L LEU* 3.7 26.2 - - + -
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Residues in contact with ARG 239 (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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235K ARG 2.9 21.8 + - - +
236K SER* 4.1 3.8 - - - +
238K TYR* 1.3 76.4 - - - +
240K HIS* 1.3 64.6 + - - +
21L GLN* 4.1 22.1 - - + +
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Residues in contact with HIS 240 (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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207K PRO* 6.5 0.9 - - + -
236K SER 2.9 18.9 + - - +
237K VAL* 4.0 5.6 - - - +
238K TYR 3.3 0.4 - - - -
239K ARG* 1.3 80.3 - - - +
241K GLY* 1.3 61.2 + - - +
242K THR* 3.3 18.8 + - - +
247K LEU* 4.1 22.9 - - + -
249K ASP 5.9 1.1 - - - +
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Residues in contact with GLY 241 (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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237K VAL 3.5 11.3 + - - -
238K TYR 4.3 4.5 + - - -
239K ARG 3.8 0.6 - - - -
240K HIS* 1.3 77.1 - - - +
242K THR* 1.3 58.9 + - - +
243K SER 4.0 1.7 + - - -
24L HIS* 5.0 13.5 - - - -
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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