Contacts of the helix formed by residues 243 - 257 (chain P) in PDB entry 5G04
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 LEU 243 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216P LYS* 4.0 39.0 - - + +
238P TYR* 3.7 32.7 - - + +
242P GLN* 1.3 81.3 - - - +
244P ILE* 1.3 58.5 + - - +
245P GLU* 3.3 24.0 + - + +
246P GLU* 3.4 21.1 + - + +
247P ALA 3.1 19.2 + - - -
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Residues in contact with ILE 244 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238P TYR 3.9 15.3 - - - +
239P THR* 4.7 5.4 - - - +
241P LEU 4.2 6.5 - - - +
242P GLN* 4.2 10.3 - - - +
243P LEU* 1.3 73.1 - - - +
245P GLU* 1.3 60.0 + - - +
247P ALA* 3.4 8.5 - - + +
248P LEU* 2.6 55.5 + - + +
272P ALA* 3.7 34.3 - - + +
273P TYR* 4.8 6.3 - - + -
275P ASN* 4.6 11.7 - - + -
276P ILE* 3.4 42.4 - - + -
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Residues in contact with GLU 245 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243P LEU* 4.1 25.7 - - + +
244P ILE* 1.3 84.7 + - - +
246P GLU* 1.3 69.9 + - + +
248P LEU* 3.6 9.5 + - - +
249P GLN* 3.2 21.7 + - - +
276P ILE* 4.9 11.5 - - + +
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Residues in contact with GLU 246 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238P TYR* 3.8 26.7 - - + +
243P LEU* 3.6 26.5 - - + +
244P ILE 3.2 0.2 - - - -
245P GLU* 1.3 80.2 - - + +
247P ALA* 1.3 58.7 + - - +
249P GLN* 3.4 20.1 + - - +
250P LYS* 2.9 34.5 + - + +
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Residues in contact with ALA 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235P ALA 3.8 11.9 - - - +
238P TYR* 3.3 35.1 - - + -
239P THR* 4.3 6.7 - - - +
243P LEU 3.1 7.0 + - - +
244P ILE* 3.1 15.6 + - + +
246P GLU* 1.3 72.4 - - - +
248P LEU* 1.3 55.4 + - - +
250P LYS* 3.0 7.0 + - - +
251P TYR* 2.7 45.0 + - + -
272P ALA* 5.7 4.0 - - + -
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Residues in contact with LEU 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244P ILE* 2.6 30.9 + - + +
245P GLU* 3.6 9.9 - - - +
247P ALA* 1.3 72.0 - - - +
249P GLN* 1.3 52.7 + - - +
251P TYR* 3.3 5.5 + - - +
252P GLN* 2.8 50.6 + - + +
269P ILE* 4.0 34.3 - - + +
272P ALA* 5.4 8.0 - - + +
273P TYR* 3.7 37.9 - - + +
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Residues in contact with GLN 249 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245P GLU 3.2 10.8 + - - +
246P GLU* 3.6 24.2 - - - +
248P LEU* 1.3 74.4 - - - +
250P LYS* 1.3 67.4 + - + +
252P GLN* 3.1 23.2 + - - +
253P ASN* 3.2 14.9 + - - +
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Residues in contact with LYS 250 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231P GLU* 4.2 33.0 + - + +
234P LEU* 3.6 34.3 - - - +
235P ALA* 3.9 14.4 - - + -
238P TYR* 3.5 31.2 + - + -
246P GLU* 2.9 24.6 + - - +
247P ALA* 3.0 9.2 + - - +
249P GLN* 1.3 77.3 - - + +
251P TYR* 1.3 61.1 + - - +
253P ASN* 3.5 19.8 + - - +
254P LEU* 3.6 12.9 - - - +
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Residues in contact with TYR 251 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232P PHE* 4.1 5.5 + + - -
235P ALA* 3.4 33.9 - - + -
236P HIS* 3.6 13.9 + - - +
239P THR* 5.3 3.8 - - - -
247P ALA* 2.7 33.2 + - + +
248P LEU* 3.7 4.0 - - - +
250P LYS* 1.3 70.9 - - - +
252P GLN* 1.3 66.2 + - - +
254P LEU* 3.1 34.5 + - + +
255P ILE* 3.2 13.5 + - - +
264P TYR* 3.6 21.6 + + - -
265P ILE* 4.4 17.1 - - + +
268P GLN* 3.2 38.8 - - + +
269P ILE* 3.3 32.8 - - + +
272P ALA* 6.0 3.8 - - + -
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Residues in contact with GLN 252 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248P LEU* 2.8 39.4 + - + +
249P GLN* 3.1 21.5 + - - +
251P TYR* 1.3 75.4 + - - +
253P ASN* 1.3 59.1 + - - +
255P ILE* 2.9 43.6 - - - +
256P ASP* 3.2 10.0 + - - +
269P ILE* 5.2 8.9 - - - +
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Residues in contact with ASN 253 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P PHE* 3.9 15.5 - - - -
231P GLU* 2.7 30.1 + - - +
249P GLN* 3.2 13.0 + - - +
250P LYS* 3.5 12.3 - - - +
251P TYR 3.3 0.2 - - - -
252P GLN* 1.3 76.8 - - - +
254P LEU* 1.3 56.2 + - - +
256P ASP* 3.3 8.9 + - - +
257P VAL* 3.0 27.4 + - - +
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Residues in contact with LEU 254 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P PHE* 4.5 12.3 - - + -
231P GLU* 3.9 25.4 - - + +
232P PHE* 3.8 50.3 - - + +
235P ALA* 5.1 2.5 - - + -
250P LYS 3.6 9.9 - - - +
251P TYR* 3.1 44.2 + - + +
253P ASN* 1.3 72.1 - - - +
255P ILE* 1.3 66.0 + - - +
257P VAL* 3.3 13.2 - - + +
259P PHE* 3.2 34.8 + - + +
265P ILE* 4.6 5.4 - - + -
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Residues in contact with ILE 255 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251P TYR 3.2 9.6 + - - +
252P GLN* 2.9 52.3 - - - +
254P LEU* 1.3 77.3 - - - +
256P ASP* 1.3 61.5 + - + +
258P GLY* 3.4 9.0 + - - -
260P SER* 3.6 40.2 - - - +
265P ILE* 4.0 21.6 - - + +
266P VAL* 5.7 4.9 - - + -
269P ILE* 6.0 5.2 - - + -
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Residues in contact with ASP 256 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252P GLN 3.2 15.1 + - - +
253P ASN* 3.5 9.8 - - - +
254P LEU 3.3 0.2 - - - -
255P ILE* 1.3 82.5 - - + +
257P VAL* 1.3 58.0 + - - +
258P GLY 3.3 0.8 + - - -
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Residues in contact with VAL 257 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P PHE* 3.7 46.0 - - + +
27P SER* 6.0 0.4 - - - -
29P LEU* 3.2 37.5 - - + +
253P ASN* 3.0 12.5 + - - +
254P LEU* 3.3 23.8 - - + +
255P ILE 3.3 0.2 - - - -
256P ASP* 1.3 75.7 - - - +
258P GLY* 1.3 56.4 + - - +
259P PHE* 3.7 17.0 - - + -
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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