Contacts of the helix formed by residues 240 - 252 (chain P) in PDB entry 5GJQ
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 TYR 240 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235P GLN* 6.6 0.2 - - - -
238P GLY* 3.2 34.3 - - - -
239P SER* 1.3 78.2 - - - +
241P LEU* 1.3 61.8 + - - +
242P SER 3.0 1.8 - - - -
243P ILE* 2.5 31.8 + - - +
244P CYS* 2.8 11.6 + - - +
273P TYR* 3.6 31.5 - + + +
276P LEU* 3.9 37.9 - - + -
277P ALA* 4.0 20.0 - - + +
278P PRO* 5.5 4.3 - - + -
349P LYS* 5.6 1.6 - - - +
350P ARG* 4.2 14.5 - - + +
353P ASP* 2.8 28.9 + - - -
357P ARG* 5.6 3.4 - - - -
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Residues in contact with LEU 241 (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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240P TYR* 1.3 78.1 - - - +
242P SER* 1.3 62.3 + - - +
244P CYS* 3.3 10.4 + - + +
245P LYS* 3.0 25.3 + - + +
274P VAL* 5.9 3.4 - - + -
277P ALA* 3.9 22.6 - - + +
278P PRO* 5.7 3.6 - - + +
280P ASP* 5.6 7.6 - - + -
282P GLU* 4.3 17.9 - - + +
283P GLN* 4.7 16.2 - - + +
286P LEU* 3.7 30.1 - - + -
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Residues in contact with SER 242 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234P ASP* 4.2 8.2 - - - -
239P SER* 4.3 18.3 - - - -
240P TYR 2.8 1.8 + - - +
241P LEU* 1.3 77.2 - - - +
243P ILE* 1.3 65.6 + - - -
245P LYS* 2.9 20.4 + - - +
246P HIS* 3.0 33.7 + - - -
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Residues in contact with ILE 243 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231P ILE* 4.1 7.6 - - + -
234P ASP* 4.6 12.2 - - + +
235P GLN* 5.2 3.8 - - + +
239P SER 4.5 5.4 - - - +
240P TYR* 2.5 22.0 + - - +
242P SER* 1.3 73.0 - - - +
244P CYS* 1.3 61.5 + - - +
246P HIS* 2.8 22.1 + - - +
247P TYR* 2.3 65.0 + - + +
273P TYR* 3.8 24.5 - - + -
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Residues in contact with CYS 244 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240P TYR 2.8 7.4 + - - +
241P LEU* 3.5 16.4 - - + +
243P ILE* 1.3 77.0 - - - +
245P LYS* 1.3 58.4 + - - +
247P TYR* 4.1 8.1 - - - +
248P ARG* 2.9 29.5 + - - +
270P VAL* 4.4 7.7 - - - +
273P TYR* 4.0 18.1 - - + +
274P VAL* 3.9 29.6 - - + +
286P LEU* 5.9 2.2 - - + -
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Residues in contact with LYS 245 (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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241P LEU* 3.0 23.1 + - + +
242P SER* 2.9 12.6 + - - +
244P CYS* 1.3 76.7 - - - +
246P HIS* 1.3 61.2 + - + +
248P ARG* 3.0 10.5 - - - +
249P ALA* 3.0 25.3 + - - +
286P LEU* 4.4 22.7 - - + -
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Residues in contact with HIS 246 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226P TYR* 6.3 0.7 - + - -
227P TYR* 3.9 33.8 - + + +
230P MET* 3.9 28.8 - - + +
231P ILE* 4.7 3.4 - - + +
234P ASP* 4.1 13.9 - - - -
242P SER* 3.0 44.8 + - - -
243P ILE* 2.8 11.1 + - - +
245P LYS* 1.3 74.7 - - + +
247P TYR* 1.3 61.7 + - + +
249P ALA* 2.4 30.3 + - - +
250P ILE* 2.9 14.5 + - - +
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Residues in contact with TYR 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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228P ASN* 6.1 0.9 - - - -
231P ILE* 1.9 45.1 - - + +
235P GLN* 4.7 0.2 - - - +
243P ILE* 2.3 65.2 + - + +
244P CYS* 4.1 4.7 - - - +
246P HIS* 1.3 73.5 - - + +
248P ARG* 1.3 62.5 + - - +
250P ILE* 3.1 15.0 - - + +
251P TYR* 2.9 27.0 + - - +
266P ALA* 4.6 12.5 - - + +
269P SER* 4.2 20.6 - - - -
270P VAL* 3.7 21.2 - - + +
273P TYR* 3.8 20.3 + + - -
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Residues in contact with ARG 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 CYS 2.9 16.5 + - - +
245P LYS* 3.0 15.9 - - - +
247P TYR* 1.3 75.8 - - - +
249P ALA* 1.3 64.8 + - - +
251P TYR* 3.0 14.1 + - + +
252P ASP* 3.0 30.6 + - - -
270P VAL* 4.0 7.5 - - + +
286P LEU* 5.5 11.0 - - + -
290P ILE* 5.9 7.6 - - + -
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Residues in contact with ALA 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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223P LYS* 4.4 7.2 + - - -
227P TYR* 3.9 27.4 - - + +
245P LYS 3.0 12.6 + - - +
246P HIS* 2.4 20.3 + - - +
248P ARG* 1.3 69.6 - - - +
250P ILE* 1.3 67.0 + - - +
252P ASP* 2.8 27.4 + - - +
253P THR* 3.9 1.6 + - - -
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Residues in contact with ILE 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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223P LYS* 4.6 5.2 - - - +
224P LEU* 3.6 37.2 - - + +
227P TYR* 4.4 18.2 - - + -
228P ASN* 3.8 22.2 - - - +
246P HIS 2.9 7.0 + - - +
247P TYR* 3.1 33.9 - - + +
249P ALA* 1.3 76.3 - - - +
251P TYR* 1.3 61.0 + - - +
253P THR* 2.7 37.3 + - - -
256P ILE* 3.0 18.9 - - + +
266P ALA* 5.2 8.5 - - + -
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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
----------------------------------------------------------
247P TYR 2.9 22.5 + - - +
248P ARG* 3.0 12.3 + - + +
250P ILE* 1.3 75.8 - - - +
252P ASP* 1.3 63.7 + - - +
253P THR 3.2 2.0 + - - -
256P ILE* 3.6 13.1 - - - +
257P GLN* 3.9 15.6 + - + +
263P TRP* 3.8 38.5 - + + -
266P ALA* 5.0 5.4 - - + -
267P LEU* 3.8 29.1 - - + +
270P VAL* 5.0 6.3 - - + -
290P ILE* 6.4 2.7 - - + -
293P ASP* 2.7 32.3 + - - -
295P LYS* 3.8 17.5 - - - +
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Residues in contact with ASP 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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223P LYS* 5.9 0.2 - - - -
248P ARG* 3.2 25.6 - - - -
249P ALA* 2.8 16.5 + - - +
251P TYR* 1.3 81.8 - - - +
253P THR* 1.3 61.3 + - - +
254P PRO* 3.5 3.8 - - - +
257P GLN* 4.1 8.1 - - - +
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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