Contacts of the helix formed by residues 244 - 256 (chain C) in PDB entry 4AY1
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 244 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214C PHE* 3.5 16.6 - - - -
229C PRO* 3.4 16.2 - - + +
230C LEU 3.6 1.8 + - - +
231C SER 3.6 15.3 - - - +
232C LYS* 3.5 24.6 - - - +
236C ASP* 5.4 0.5 - - - +
240C SER 5.0 0.3 - - - +
241C SER* 3.1 24.3 - - - +
242C TYR 3.1 2.8 + - - +
243C TYR* 1.3 77.5 + - - +
245C VAL* 1.3 67.3 + - - +
246C GLU* 3.4 12.9 - - - +
247C TYR* 2.9 36.0 - - - +
248C ALA* 3.1 17.7 + - - +
322C GLN* 5.2 0.2 - - - +
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Residues in contact with VAL 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C SER* 3.8 17.7 - - - +
214C PHE* 4.0 9.0 - - + -
228C SER* 3.7 22.7 - - - +
229C PRO 2.9 20.4 + - - +
230C LEU* 3.8 21.1 - - + +
244C ASN* 1.3 71.5 - - - +
246C GLU* 1.3 64.5 + - - +
248C ALA* 3.3 2.2 + - - +
249C VAL* 2.9 26.7 + - + +
264C MET* 3.6 40.8 - - + -
265C GLY 5.1 1.6 - - - +
345C LYS* 4.3 8.3 - - + -
348C PHE* 4.5 0.7 - - + -
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Residues in contact with GLU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C LEU* 2.9 23.1 + - + +
231C SER* 2.5 32.8 + - - +
232C LYS 4.8 0.3 + - - -
244C ASN* 3.5 6.3 - - - +
245C VAL* 1.3 76.9 - - - +
247C TYR* 1.3 58.6 + - - +
249C VAL* 3.5 1.9 + - - +
250C GLY* 3.0 26.3 + - - -
348C PHE* 3.5 38.0 - - + -
352C LEU* 5.5 1.2 - - - +
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Residues in contact with TYR 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C ARG* 2.7 42.4 + - + -
241C SER* 4.0 15.3 - - - +
242C TYR* 3.3 50.9 - + + +
244C ASN* 2.9 19.7 - - - +
246C GLU* 1.3 73.1 - - - +
248C ALA* 1.3 64.9 + - - +
250C GLY* 3.3 1.2 + - - +
251C TYR* 2.8 53.5 + + + +
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C ALA* 3.2 46.7 - - + +
191C ILE* 5.3 1.1 - - - -
209C LEU* 4.2 9.2 - - + -
211C SER* 5.1 0.2 - - - -
214C PHE* 4.1 2.2 - - + -
242C TYR 4.5 0.6 + - - +
244C ASN 3.1 14.6 + - - +
245C VAL* 3.7 3.8 - - - +
247C TYR* 1.3 84.9 - - - +
249C VAL* 1.3 62.4 + - - +
251C TYR* 3.4 4.4 + - - +
252C TRP* 3.1 29.8 + - + -
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Residues in contact with VAL 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C LEU* 3.7 23.3 - - + -
245C VAL* 2.9 20.5 + - + +
246C GLU 3.8 3.4 - - - +
248C ALA* 1.3 75.7 - - - +
250C GLY* 1.3 62.6 + - - +
252C TRP* 3.4 4.3 + - - +
253C ILE* 3.2 27.4 + - + +
262C VAL* 4.7 5.5 - - + +
264C MET* 4.1 11.4 - - + -
348C PHE* 4.0 12.8 - - + -
352C LEU* 3.9 18.8 - - + -
354C LEU* 3.8 44.2 - - + -
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Residues in contact with GLY 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C GLU 3.0 15.7 + - - -
247C TYR* 3.7 2.7 - - - -
249C VAL* 1.3 79.2 - - - +
251C TYR* 1.3 57.6 + - - +
253C ILE* 3.5 7.4 + - - +
254C HIS* 2.8 30.7 + - - +
352C LEU* 5.5 4.7 - - - -
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Residues in contact with TYR 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C ARG* 3.4 41.9 + - + -
191C ILE* 4.0 32.1 - - + -
192C ASP* 2.6 37.1 + - - -
247C TYR* 2.8 41.9 + + + +
248C ALA* 3.7 5.6 - - - +
249C VAL 3.2 0.2 - - - -
250C GLY* 1.3 74.3 - - - +
252C TRP* 1.3 60.0 + - - +
254C HIS* 3.3 23.9 + + + +
255C LYS* 2.9 53.5 + - + +
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Residues in contact with TRP 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C VAL* 3.3 32.5 - - + -
185C SER 3.0 19.7 + - - -
191C ILE* 3.3 20.9 - - + +
195C TYR* 3.4 42.8 - + + -
197C VAL* 3.8 34.9 - - + +
200C LEU* 4.5 7.0 - - + -
207C ILE* 3.8 22.7 - - + -
209C LEU* 3.5 18.7 - - + +
248C ALA 3.1 26.5 + - - +
249C VAL* 3.9 4.9 - - - +
251C TYR* 1.3 75.7 - - - +
253C ILE* 1.3 62.2 + - - +
255C LYS* 3.3 6.4 + - - +
256C GLY 3.1 6.2 + - - -
257C MET* 3.0 43.1 + - + +
262C VAL* 4.7 5.8 - - + -
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Residues in contact with ILE 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C VAL* 3.2 23.2 + - + +
250C GLY* 3.7 5.6 - - - +
252C TRP* 1.3 75.0 - - - +
254C HIS* 1.3 66.6 + - - +
256C GLY* 2.9 16.3 + - - -
257C MET 3.3 20.0 + - - +
258C PRO* 5.9 0.4 - - + -
259C SER* 3.6 32.3 - - - +
262C VAL* 4.3 7.4 - - + -
352C LEU* 4.6 9.0 - - + +
354C LEU* 3.9 17.5 - - + -
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Residues in contact with HIS 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C GLY 2.8 22.8 + - - +
251C TYR* 3.3 29.4 + + + +
253C ILE* 1.3 74.8 - - - +
255C LYS* 1.3 68.1 + - + +
256C GLY* 3.4 1.6 + - - -
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Residues in contact with LYS 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C ILE* 4.6 5.6 + - + -
192C ASP* 3.1 31.9 + - - +
195C TYR 5.1 4.9 + - - -
197C VAL* 3.4 44.3 - - + +
198C GLU* 3.9 14.2 - - - +
251C TYR* 2.9 51.2 + - + +
252C TRP* 3.3 2.7 + - - +
253C ILE 3.2 0.2 - - - -
254C HIS* 1.3 84.2 - - + +
256C GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C VAL* 4.0 5.4 - - - -
198C GLU* 4.7 9.5 - - - +
201C ALA* 3.7 11.0 - - - +
252C TRP 3.1 0.2 + - - -
253C ILE 2.9 11.2 + - - -
254C HIS 3.2 1.5 - - - -
255C LYS* 1.3 81.1 - - - +
257C MET* 1.3 65.2 + - - +
258C PRO* 3.3 9.7 - - - +
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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