Contacts of the helix formed by residues 243 - 261 (chain S) 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 ASP 243 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201S ARG* 4.0 19.3 - - - +
204S ASP* 2.9 36.9 - - + +
205S LEU* 3.2 26.8 + - - +
238S ALA* 3.7 6.6 + - + +
241S ARG* 3.3 3.6 - - + -
242S HIS* 1.3 75.0 - - - +
244S ALA* 1.3 67.7 + - - +
245S ASP* 3.4 8.1 + - - +
246S GLY* 4.1 7.3 + - - -
247S GLN* 3.0 25.8 + - - +
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Residues in contact with ALA 244 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242S HIS* 3.7 5.4 + - - +
243S ASP* 1.3 74.1 + - - +
245S ASP* 1.3 64.7 + - - +
247S GLN* 3.2 6.4 - - - +
248S ALA* 3.0 24.6 + - - +
277S PRO* 3.7 25.1 - - + +
278S GLU 3.7 10.5 - - - +
279S GLN* 3.0 33.0 - - + +
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Residues in contact with ASP 245 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205S LEU* 3.5 31.2 - - + -
208S ALA* 5.1 8.1 - - - -
243S ASP* 3.4 2.8 + - - +
244S ALA* 1.3 80.3 - - - +
246S GLY* 1.3 64.3 + - - +
248S ALA* 3.2 5.1 + - - +
249S THR* 3.0 24.9 + - - -
279S GLN 4.2 5.8 + - - +
280S ALA* 5.6 3.8 - - - +
281S ASN* 5.2 18.8 - - - +
284S GLU* 5.4 6.5 - - - +
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Residues in contact with GLY 246 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204S ASP* 4.4 12.1 - - - -
205S LEU* 5.0 0.8 - - - +
208S ALA* 4.1 20.8 - - - +
238S ALA* 5.4 4.3 - - - -
243S ASP* 3.7 12.5 + - - -
244S ALA 3.5 0.4 - - - -
245S ASP* 1.3 78.2 - - - +
247S GLN* 1.3 65.7 + - - +
249S THR* 3.5 1.6 + - - -
250S LEU* 3.0 23.6 + - - +
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Residues in contact with GLN 247 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235S LEU* 3.7 14.1 - - + +
238S ALA* 3.9 28.0 - - + +
239S THR* 4.0 16.4 - - - +
242S HIS* 5.3 1.6 - - - -
243S ASP 3.0 24.1 + - - +
244S ALA* 3.2 10.1 - - - +
245S ASP 3.2 0.4 - - - -
246S GLY* 1.3 74.3 - - - +
248S ALA* 1.3 67.2 + - - +
250S LEU* 2.9 15.1 + - - +
251S LEU* 2.9 20.0 + - + +
277S PRO* 4.6 9.9 - - + -
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Residues in contact with ALA 248 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244S ALA 3.0 14.5 + - - +
245S ASP* 3.7 5.4 - - - +
247S GLN* 1.3 78.1 - - - +
249S THR* 1.3 63.9 + - - +
251S LEU* 3.3 7.4 + - - +
252S ASN* 2.9 36.1 + - - +
276S PHE* 5.3 6.1 - - + -
277S PRO* 4.7 16.5 - - + +
280S ALA* 6.2 4.0 - - + -
284S GLU* 4.8 11.0 - - + -
288S TYR* 6.5 0.4 - - + -
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Residues in contact with THR 249 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208S ALA* 4.0 29.1 + - - +
211S TYR* 5.0 1.6 - - - +
212S TYR* 4.9 3.8 + - - +
245S ASP* 3.0 17.9 + - - -
246S GLY 3.6 5.4 - - - -
248S ALA* 1.3 75.4 - - - +
250S LEU* 1.3 65.0 + - - +
252S ASN* 3.0 15.2 + - - +
253S LEU* 2.9 33.5 + - - +
284S GLU* 4.8 12.9 - - - +
287S ARG* 5.3 6.5 + - - +
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Residues in contact with LEU 250 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211S TYR* 4.8 13.9 - - + -
231S LEU* 2.5 68.4 - - + +
234S ARG* 4.0 11.4 - - + +
235S LEU* 3.1 32.5 - - + +
238S ALA* 5.8 2.0 - - + -
246S GLY 3.0 17.0 + - - +
247S GLN* 2.9 8.2 + - - +
249S THR* 1.3 73.5 - - - +
251S LEU* 1.3 64.0 + - - +
253S LEU* 2.9 24.8 + - + +
254S LEU* 3.0 14.4 + - + +
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Residues in contact with LEU 251 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235S LEU* 3.4 24.5 - - + -
247S GLN* 2.9 22.9 + - + +
248S ALA* 3.4 10.3 - - - +
250S LEU* 1.3 76.4 - - - +
252S ASN* 1.3 67.4 + - - +
254S LEU* 3.0 14.7 - - - +
255S LEU* 2.9 31.7 + - + +
274S SER* 5.8 4.0 - - - +
288S TYR* 6.1 2.5 - - + -
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Residues in contact with ASN 252 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248S ALA* 2.9 22.9 + - - +
249S THR* 3.3 8.6 - - - +
251S LEU* 1.3 77.0 - - - +
253S LEU* 1.3 59.3 + - + +
255S LEU* 3.2 9.0 + - - +
256S ARG* 2.9 31.6 + - - +
284S GLU* 3.3 41.0 + - - +
287S ARG* 4.0 13.9 - - + +
288S TYR* 3.8 30.0 - - - +
291S TYR* 4.1 14.1 - - + -
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Residues in contact with LEU 253 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211S TYR* 3.5 44.4 - - + +
212S TYR* 4.1 11.7 - - + +
215S ALA* 4.2 24.0 - - + -
231S LEU* 5.2 8.5 - - + -
249S THR* 2.9 24.8 + - - +
250S LEU* 2.9 18.8 + - + +
252S ASN* 1.3 78.7 - - + +
254S LEU* 1.3 56.5 + - - +
256S ARG* 3.3 15.6 + - - +
257S ASN* 2.9 25.1 + - - +
287S ARG* 6.1 2.5 - - - +
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Residues in contact with LEU 254 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228S ARG* 4.3 21.3 + - + -
231S LEU* 5.1 7.9 - - + -
232S HIS* 5.0 10.3 - - + -
235S LEU* 4.6 12.8 - - + -
250S LEU 3.0 11.8 + - - +
251S LEU* 3.0 24.7 - - - +
253S LEU* 1.3 74.9 - - - +
255S LEU* 1.3 68.6 + - + +
257S ASN* 3.0 10.7 + - - +
258S TYR* 2.9 27.1 + - + -
270S LEU* 5.8 5.4 - - + -
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Residues in contact with LEU 255 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251S LEU* 2.9 25.7 + - + +
252S ASN* 3.5 10.3 - - - +
254S LEU* 1.3 78.1 - - + +
256S ARG* 1.3 64.4 + - - +
258S TYR* 2.8 19.1 + - + +
259S LEU* 3.0 17.3 + - + +
267S ALA* 4.0 26.9 - - + +
270S LEU* 4.1 23.3 - - + -
271S VAL* 4.9 8.1 - - + -
288S TYR* 4.1 30.1 - - + -
291S TYR* 4.5 24.9 - - + -
292S THR* 5.6 1.6 - - - +
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Residues in contact with ARG 256 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252S ASN 2.9 14.0 + - - +
253S LEU* 3.5 20.2 - - - +
255S LEU* 1.3 75.8 - - - +
257S ASN* 1.3 57.7 + - - +
259S LEU* 3.4 3.7 + - - +
260S HIS* 2.8 45.9 + - + -
291S TYR* 2.5 56.6 + - + +
13Y LEU 5.3 4.9 + - - -
14Y GLU* 4.3 20.1 + - - +
15Y GLU* 5.9 0.8 - - - +
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Residues in contact with ASN 257 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224S LEU* 3.8 22.4 - - - -
228S ARG* 2.0 61.4 + - + +
253S LEU 2.9 13.6 + - - +
254S LEU* 3.1 14.8 - - - +
255S LEU 3.0 0.2 - - - -
256S ARG* 1.3 75.4 - - - +
258S TYR* 1.3 63.9 + - - +
260S HIS* 3.1 9.7 + - - +
261S TYR* 2.8 20.1 + - - -
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Residues in contact with TYR 258 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228S ARG* 3.4 18.4 - - - +
254S LEU 2.9 16.9 + - - -
255S LEU* 2.8 14.3 + - + +
257S ASN* 1.3 72.7 - - - +
259S LEU* 1.3 60.3 + - + +
261S TYR* 2.9 27.8 - - - +
263S LEU* 3.2 27.1 + - + +
266S GLN* 4.1 21.8 - - + -
267S ALA* 3.8 22.0 - - + -
270S LEU* 6.5 0.2 - - + -
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Residues in contact with LEU 259 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255S LEU* 3.0 18.6 + - + +
256S ARG* 3.7 6.3 - - - +
258S TYR* 1.3 86.2 - - + +
260S HIS* 1.3 55.2 + - - +
261S TYR 2.8 16.8 - - - +
262S SER* 5.4 0.9 - - - +
263S LEU 4.1 9.9 - - - +
264S TYR* 4.7 3.1 - - + -
267S ALA* 4.3 4.7 - - + -
290S TYR* 6.3 0.2 - - + -
291S TYR* 4.8 17.0 - - + -
294S ARG* 4.1 22.7 - - + -
295S ILE* 3.5 36.6 - - + -
298S ILE* 4.9 8.1 - - + -
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Residues in contact with HIS 260 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256S ARG* 2.8 42.2 + - + +
257S ASN* 3.6 9.2 - - - +
259S LEU* 1.3 71.6 - - - +
261S TYR* 1.3 64.0 + - + +
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Residues in contact with TYR 261 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224S LEU* 5.4 6.7 - - + -
228S ARG* 3.3 20.2 - - - -
257S ASN* 2.8 18.1 + - - -
258S TYR* 2.9 18.0 - - - +
259S LEU* 2.8 20.3 - - - +
260S HIS* 1.3 77.0 - - + +
262S SER* 1.3 60.0 + - - +
263S LEU* 4.1 10.5 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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