Contacts of the helix formed by residues 259 - 269 (chain K) in PDB entry 5ANC
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 LYS 259 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210K ASP* 3.3 20.1 + - + +
211K TRP 3.8 23.8 - - - +
212K SER* 5.1 4.3 - - - +
258K ILE* 1.3 79.6 - - - +
260K LYS* 1.3 77.5 + - + +
261K GLU* 3.4 34.7 - - + +
262K VAL* 3.5 16.5 + - + +
263K LEU* 3.2 22.2 + - - +
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Residues in contact with LYS 260 (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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246K GLU 5.8 1.8 - - - +
249K ALA* 3.8 5.7 - - + +
250K ARG* 3.7 32.7 - - + +
253K SER* 3.7 27.0 + - - +
254K GLN* 5.9 2.2 - - - +
258K ILE 5.2 0.2 - - - +
259K LYS* 1.3 84.0 - - + +
261K GLU* 1.3 61.5 + - + +
263K LEU* 3.2 5.6 + - - +
264K MET* 2.9 45.8 + - + +
358K MET* 5.6 9.6 - - + -
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Residues in contact with GLU 261 (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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212K SER* 3.5 19.9 + - - -
213K THR 3.7 18.0 - - - +
214K GLY* 5.4 0.5 - - - -
215K LEU* 3.8 28.9 + - + +
259K LYS* 3.4 24.0 + - + +
260K LYS* 1.3 79.5 - - + +
262K VAL* 1.3 61.7 - - + +
264K MET* 3.3 15.3 + - + +
265K LYS* 3.3 18.9 + - - +
361K GLN* 4.2 17.4 + - - +
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Residues in contact with VAL 262 (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 GLN* 3.9 11.5 + - - +
206K GLU* 3.3 26.2 - - - +
207K GLN* 5.1 1.8 - - - +
210K ASP 4.2 8.3 - - - +
212K SER* 3.9 10.1 - - - +
213K THR* 3.4 40.6 - - - +
258K ILE* 4.1 16.4 - - + -
259K LYS* 3.5 21.1 + - + +
260K LYS 3.2 0.4 - - - -
261K GLU* 1.3 76.5 - - - +
263K LEU* 1.3 62.9 + - + +
265K LYS* 3.4 6.9 + - - +
266K THR* 3.2 22.9 + - + +
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Residues in contact with LEU 263 (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 GLN* 5.7 2.0 - - - +
249K ALA* 3.2 23.8 - - + +
252K TYR* 3.6 26.0 - - + -
253K SER* 3.2 37.0 - - - +
258K ILE* 3.7 33.7 - - + +
259K LYS 3.2 14.1 + - - +
260K LYS* 3.2 7.3 + - - +
262K VAL* 1.3 78.2 - - + +
264K MET* 1.3 60.0 + - - +
266K THR* 2.4 28.9 + - + +
267K LEU* 2.9 21.5 + - + +
273K ILE* 5.8 3.1 - - + -
292K LEU* 6.3 0.2 - - + -
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Residues in contact with MET 264 (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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215K LEU* 3.6 25.8 - - + -
230K GLY* 3.6 28.7 - - - +
245K ILE* 3.1 34.5 - - + +
246K GLU* 4.0 17.0 - - + -
249K ALA* 3.7 13.7 - - + -
260K LYS* 2.9 37.7 + - + +
261K GLU* 3.7 11.4 - - + +
262K VAL 3.3 0.2 - - - -
263K LEU* 1.3 76.7 - - - +
265K LYS* 1.3 58.1 + - - +
267K LEU* 3.2 2.3 + - - -
268K TRP* 2.9 25.6 + - - +
358K MET* 4.0 22.2 - - + -
361K GLN* 6.2 0.2 - - - +
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Residues in contact with LYS 265 (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 THR* 3.0 24.1 + - + +
196K SER* 3.1 35.9 + - - +
197K GLN* 4.8 2.0 - - - +
213K THR* 3.6 29.5 - - + +
214K GLY 3.8 13.6 + - - +
215K LEU* 3.7 13.8 - - + +
261K GLU 3.3 9.1 + - - +
262K VAL* 3.5 10.1 - - - +
264K MET* 1.3 77.3 - - - +
266K THR* 1.3 64.9 + - + +
268K TRP* 3.2 18.9 + - + +
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Residues in contact with THR 266 (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 THR* 3.5 12.3 + - - -
197K GLN* 3.3 35.7 - - - +
207K GLN* 4.5 3.4 - - - +
262K VAL* 3.2 11.6 + - + +
263K LEU* 2.4 37.4 + - + +
265K LYS* 1.3 82.0 - - - +
267K LEU* 1.3 55.9 + - - +
269K GLY 2.9 19.9 - - - +
271K TYR* 3.8 34.6 - - + +
273K ILE* 6.3 0.9 - - + -
292K LEU* 3.7 14.4 - - - +
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Residues in contact with LEU 267 (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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166K LEU* 5.3 0.9 - - - +
234K PHE* 5.6 1.6 - - - -
245K ILE* 3.8 17.0 - - + +
248K PHE* 3.7 15.7 - - + +
249K ALA* 3.6 35.7 - - + +
252K TYR* 4.5 14.8 - - + -
263K LEU* 2.9 24.1 + - + +
264K MET* 3.2 4.9 + - - +
266K THR* 1.3 78.5 + - - +
268K TRP* 1.3 63.6 + - - +
269K GLY 3.6 4.0 - - - +
292K LEU* 3.4 26.9 - - + -
293K PHE* 3.4 45.8 - - + -
297K ILE* 5.1 2.9 - - + -
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Residues in contact with TRP 268 (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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143K LEU* 4.8 5.8 - - + -
163K TYR* 5.5 1.4 - - - -
166K LEU* 3.6 29.6 - - + +
170K LEU* 3.6 30.3 - - + -
189K ARG 4.4 5.2 - - - -
191K GLU 3.6 22.0 - - - -
192K ARG* 4.9 2.2 - - + +
193K GLU* 5.1 7.9 - - - +
225K PHE* 3.9 12.8 - - - -
226K SER* 3.6 25.0 + - - -
227K PRO* 3.6 41.5 - - + +
232K VAL* 4.0 20.5 - - + +
245K ILE* 3.8 7.4 - - + -
264K MET 2.9 10.7 + - - +
265K LYS* 3.2 14.5 + - + +
267K LEU* 1.3 78.5 - - - +
269K GLY* 1.3 63.4 + - - +
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Residues in contact with GLY 269 (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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163K TYR* 3.5 16.2 + - - -
192K ARG* 3.9 8.3 - - - -
193K GLU 3.5 26.6 + - - -
194K THR* 3.8 6.6 + - - -
266K THR 2.9 14.4 - - - +
267K LEU* 3.6 4.2 - - - -
268K TRP* 1.3 83.5 - - - +
270K ASP* 1.3 63.4 + - - -
271K TYR 4.0 0.3 + - - -
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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