Contacts of the helix formed by residues 244 - 256 (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 GLY 244 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233K VAL* 3.9 4.7 - - - -
234K PHE* 3.8 18.6 - - - -
243K PHE* 1.3 78.1 - - - +
245K ILE* 1.3 65.8 + - - -
246K GLU* 3.3 14.0 + - - -
247K HIS* 3.4 1.9 + - - +
248K PHE* 3.1 35.9 + - - -
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Residues in contact with ILE 245 (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 PRO* 6.1 0.9 - - + -
230K GLY* 4.5 8.1 - - - +
232K VAL* 3.4 44.7 + - + +
234K PHE* 4.4 10.9 - - + -
244K GLY* 1.3 69.4 - - - -
246K GLU* 1.3 66.4 + - - +
248K PHE* 3.2 12.2 + - + +
249K ALA* 2.9 27.9 + - - +
264K MET* 3.1 49.4 - - + +
267K LEU* 3.8 17.2 - - + +
268K TRP* 3.6 26.0 - - + +
293K PHE* 6.2 0.2 - - + -
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Residues in contact with GLU 246 (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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230K GLY 4.1 15.0 - - - +
231K ASN* 5.1 1.3 - - - -
232K VAL 3.9 9.4 - - - +
233K VAL* 4.0 10.2 - - - +
242K GLY 5.1 0.9 - - - +
243K PHE* 4.2 7.4 - - - -
244K GLY* 3.7 16.1 + - - -
245K ILE* 1.3 87.5 + - - +
247K HIS* 1.3 62.7 + - + +
249K ALA* 3.2 4.6 + - - +
250K ARG* 2.9 32.0 + - - +
260K LYS* 5.8 2.1 - - - +
264K MET* 4.0 12.6 - - - -
351K ILE* 5.5 4.3 - - - +
354K ALA* 4.3 25.6 - - + +
355K VAL* 5.4 10.5 - - - +
358K MET* 4.1 28.7 - - + -
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Residues in contact with HIS 247 (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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242K GLY 4.6 6.1 - - - -
243K PHE* 3.6 38.8 - + + +
244K GLY 3.5 12.3 - - - +
246K GLU* 1.3 82.7 - - - +
248K PHE* 1.3 68.6 + - + +
250K ARG* 3.1 48.0 + - - +
251K ILE* 3.2 37.8 + - + +
301K ILE* 6.5 0.7 - - + -
323K LEU* 5.9 1.1 - - + -
325K LEU* 4.2 22.9 - - + +
348K TRP* 4.6 24.2 + + - +
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Residues in contact with PHE 248 (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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148K ILE* 3.9 25.4 - - + -
234K PHE* 3.5 30.1 - + + -
243K PHE* 4.2 21.5 - + - -
244K GLY* 3.1 17.9 - - - -
245K ILE* 3.2 13.6 + - + +
247K HIS* 1.3 82.6 - - + +
249K ALA* 1.3 61.8 + - - +
251K ILE 3.4 2.3 + - - -
252K TYR* 3.3 18.2 + - - +
267K LEU* 3.7 14.6 - - + -
293K PHE* 4.2 24.2 - + - -
297K ILE* 3.4 41.3 - - + +
298K LEU* 4.0 20.0 - - + -
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Residues in contact with ALA 249 (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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245K ILE 2.9 13.8 + - - +
246K GLU* 3.4 9.0 - - - +
248K PHE* 1.3 76.0 - - - +
250K ARG* 1.3 53.9 + - - +
252K TYR* 3.2 2.2 + - - -
253K SER* 2.7 35.9 + - - -
260K LYS* 3.8 20.2 - - + +
263K LEU* 3.2 15.7 - - + +
264K MET* 3.7 22.2 - - + -
267K LEU* 3.6 9.6 - - + +
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Residues in contact with ARG 250 (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* 2.9 13.4 + - - +
247K HIS* 3.1 51.4 + - - +
249K ALA* 1.3 76.9 - - - +
251K ILE* 1.3 63.5 + - + +
253K SER* 3.2 10.1 + - - -
254K GLN* 3.1 35.8 + - + +
260K LYS* 3.7 25.1 - - + +
325K LEU* 4.5 22.3 - - - +
348K TRP 5.6 3.0 + - - -
353K HIS* 3.4 34.7 + - - -
354K ALA* 4.5 11.3 - - - +
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Residues in contact with ILE 251 (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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247K HIS* 3.2 41.4 + - + +
248K PHE 3.7 0.7 - - - +
249K ALA 3.2 0.2 - - - -
250K ARG* 1.3 77.5 - - + +
252K TYR* 1.3 62.6 + - - +
254K GLN* 3.2 21.2 + - - +
255K LYS* 3.5 24.6 + - - +
297K ILE* 3.4 37.5 - - + -
323K LEU* 3.2 49.4 - - + +
324K GLY* 4.7 7.3 - - - +
325K LEU* 5.3 5.6 - - + -
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Residues in contact with TYR 252 (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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248K PHE 3.3 6.4 + - - +
249K ALA* 3.2 10.2 + - - +
251K ILE* 1.3 80.3 - - - +
253K SER* 1.3 62.0 + - - +
255K LYS* 3.2 28.2 + - + +
256K ILE* 4.2 2.9 + - - +
257K GLY 4.9 1.2 + - - -
258K ILE* 4.9 10.7 - - + +
263K LEU* 3.6 28.9 - - + -
267K LEU* 4.5 11.9 - - + -
273K ILE* 4.2 15.0 - - + +
275K MET* 5.1 2.9 - - - -
278K LYS* 3.9 26.3 - - + -
292K LEU* 3.9 40.0 + - + +
295K GLN* 4.8 6.1 + - - +
296K LEU* 3.7 27.7 - - + +
297K ILE* 3.9 27.8 - - + +
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Residues in contact with SER 253 (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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249K ALA 2.7 22.3 + - - -
250K ARG* 3.2 8.6 + - - -
252K TYR* 1.3 76.0 - - - +
254K GLN* 1.3 63.1 - - - +
255K LYS 3.2 1.2 + - - -
256K ILE 4.0 0.3 - - - -
257K GLY* 3.3 26.2 + - - -
258K ILE 3.3 23.2 + - - +
260K LYS* 3.7 24.5 - - - +
263K LEU* 3.2 12.2 - - - +
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Residues in contact with GLN 254 (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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250K ARG* 3.1 27.4 + - + +
251K ILE* 3.2 11.6 + - - +
253K SER* 1.3 79.1 - - - +
255K LYS* 1.3 61.4 + - + +
256K ILE* 4.8 0.8 - - - -
260K LYS* 5.9 2.0 - - - +
324K GLY* 4.5 21.7 + - - +
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Residues in contact with LYS 255 (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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251K ILE* 3.6 36.6 - - - +
252K TYR* 3.2 27.0 + - + +
253K SER 3.2 0.6 + - - -
254K GLN* 1.3 79.6 - - + +
256K ILE* 1.3 64.0 + - + +
278K LYS* 4.9 10.8 - - - +
296K LEU* 3.8 39.7 - - + +
297K ILE* 4.0 10.6 - - - +
300K ASN* 5.2 4.8 + - - +
322K SER 4.3 13.9 + - - -
324K GLY* 6.0 0.2 - - - -
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Residues in contact with ILE 256 (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 4.1 17.7 - - - +
208K VAL* 4.1 29.8 - - + +
252K TYR 4.2 1.7 + - - +
253K SER 3.8 2.4 + - - -
254K GLN 5.1 0.7 - - - -
255K LYS* 1.3 81.4 - - + +
257K GLY* 1.3 61.2 + - - +
258K ILE* 4.2 10.1 - - + -
277K ALA 4.2 16.8 - - - +
278K LYS* 4.1 22.7 - - + -
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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