Contacts of the helix formed by residues 259 - 277 (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 GLU 259 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255P CYS 3.7 6.5 + - - +
256P ILE 4.0 0.6 + - - -
257P GLN 3.6 0.4 - - - -
258P ALA* 1.3 80.1 - - + +
260P SER* 1.3 60.4 + - - +
261P GLU* 3.2 3.1 - - + +
262P LYS* 2.9 64.0 + - + +
263P TRP* 3.0 18.2 + - - -
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Residues in contact with SER 260 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258P ALA 3.2 5.7 + - - -
259P GLU* 1.3 71.0 - - - +
261P GLU* 1.3 59.6 + - - +
262P LYS 3.5 0.3 + - - -
263P TRP* 3.3 28.8 + - - +
264P GLN* 3.2 34.5 + - - +
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Residues in contact with GLU 261 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259P GLU* 3.2 2.8 - - + +
260P SER* 1.3 77.3 - - - +
262P LYS* 1.3 65.5 + - - +
264P GLN* 4.6 4.4 - - - +
265P GLN* 4.1 11.4 + - - +
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Residues in contact with LYS 262 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224P LEU* 6.5 0.4 - - - -
255P CYS* 3.5 13.2 + - - +
256P ILE* 3.5 44.4 - - + -
259P GLU* 2.9 41.0 + - + +
261P GLU* 1.3 77.8 - - - +
263P TRP* 1.3 64.5 + - - +
264P GLN 3.1 2.1 + - - -
265P GLN* 3.3 20.7 - - - +
266P ALA* 4.1 4.5 + - - +
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Residues in contact with TRP 263 (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* 3.8 25.9 - + + -
256P ILE* 3.2 17.0 - - + +
257P GLN* 3.1 27.8 + - - -
258P ALA 3.9 2.2 + - - -
259P GLU 3.0 19.5 + - - -
260P SER* 3.3 32.3 - - - +
261P GLU 3.8 0.2 - - - -
262P LYS* 1.3 76.8 - - - +
264P GLN* 1.3 80.8 + - + +
266P ALA* 3.6 6.3 + - - +
267P LEU* 2.9 59.1 + - + +
295P LYS* 4.3 23.6 - - + -
298P GLU* 4.4 23.6 - - + -
299P ILE* 5.1 3.4 - - + -
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Residues in contact with GLN 264 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260P SER* 3.2 22.8 + - - +
261P GLU* 5.1 3.8 - - - +
262P LYS 3.1 1.8 + - - -
263P TRP* 1.3 103.8 - - + +
265P GLN* 1.3 59.6 + - + +
267P LEU* 2.9 20.5 + - - +
268P LYS* 2.9 21.0 + - + +
299P ILE* 5.5 8.3 - - + -
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Residues in contact with GLN 265 (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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261P GLU 4.1 10.8 - - - +
262P LYS 3.3 19.3 - - - +
264P GLN* 1.3 74.6 - - + +
266P ALA* 1.3 56.1 + - - +
268P LYS* 3.9 11.0 - - - +
269P SER* 3.0 24.8 + - - -
332P SER* 5.7 4.9 - - - +
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Residues in contact with ALA 266 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247P TYR* 4.6 14.8 - - + +
250P ILE* 5.2 9.4 - - + -
251P TYR* 5.0 14.6 - - + -
256P ILE* 5.3 6.3 - - + -
262P LYS 4.6 3.8 - - - +
263P TRP* 3.6 11.2 + - - +
264P GLN 3.1 0.8 - - - -
265P GLN* 1.3 80.7 - - + +
267P LEU* 1.3 66.4 + - - +
268P LYS 3.2 0.2 - - - -
269P SER* 3.1 7.9 + - - -
270P VAL* 2.9 26.8 + - - +
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Residues in contact with LEU 267 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251P TYR* 3.8 34.2 - - + +
263P TRP* 2.9 44.4 + - + +
264P GLN 2.9 5.1 + - - +
266P ALA* 1.3 77.5 - - - +
268P LYS* 1.3 66.2 + - + +
270P VAL* 3.0 25.2 + - + +
271P VAL* 3.1 13.0 + - + +
290P ILE* 5.3 16.8 - - + -
293P ASP* 4.1 6.3 - - - +
295P LYS 4.3 1.6 - - - -
296P LEU* 4.2 34.3 - - + +
299P ILE* 4.4 12.6 - - + -
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Residues in contact with LYS 268 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264P GLN* 2.9 25.5 + - + +
265P GLN* 3.9 9.9 - - - +
267P LEU* 1.3 75.0 - - - +
269P SER* 1.3 55.6 + - - +
271P VAL* 2.7 34.4 + - - +
272P LEU* 2.9 18.0 + - + +
299P ILE* 5.2 11.8 - - + +
302P TYR* 4.9 19.3 - - + -
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Residues in contact with SER 269 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247P TYR* 4.2 19.7 - - - -
265P GLN 3.0 14.4 + - - -
266P ALA* 3.1 9.3 + - - -
268P LYS* 1.3 77.1 - - - +
270P VAL* 1.3 63.2 + - - +
272P LEU* 3.1 7.4 + - - +
273P TYR* 2.7 53.1 + - - -
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Residues in contact with VAL 270 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244P CYS* 4.4 7.1 - - + +
247P TYR* 3.7 35.6 - - + +
248P ARG* 4.0 8.1 - - + +
251P TYR* 5.0 4.7 - - + -
266P ALA 2.9 22.7 + - - +
267P LEU* 3.0 20.8 + - + +
269P SER* 1.3 74.5 - - - +
271P VAL* 1.3 66.8 + - + +
273P TYR* 4.1 2.9 - - - +
274P VAL* 3.0 29.1 + - + +
290P ILE* 5.0 16.8 - - + -
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Residues in contact with VAL 271 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267P LEU* 3.1 16.6 + - + +
268P LYS* 2.7 17.2 + - - +
270P VAL* 1.3 71.0 - - - +
272P LEU* 1.3 68.7 + - + +
274P VAL* 2.8 20.0 + - - +
275P ILE* 2.9 11.1 + - + +
290P ILE* 4.7 15.7 - - + +
296P LEU* 4.3 24.2 - - + -
302P TYR* 4.3 22.4 - - + +
305P LEU* 3.8 28.7 - - + -
306P LEU* 4.5 14.6 - - + -
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Residues in contact with LEU 272 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268P LYS* 2.9 24.7 + - + +
269P SER* 3.1 9.4 + - - +
271P VAL* 1.3 79.4 - - + +
273P TYR* 1.3 62.5 + - + +
275P ILE* 3.3 9.1 + - - +
276P LEU* 3.0 37.9 + - + +
302P TYR* 6.2 4.0 - - + -
305P LEU* 5.1 6.1 - - + -
328P LEU* 4.9 17.3 - - + -
341P PHE* 5.4 8.5 - - + -
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Residues in contact with TYR 273 (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 GLN* 4.3 16.0 - - + +
239P SER 5.4 0.7 - - - -
240P TYR* 3.6 34.4 - + + +
243P ILE* 3.8 28.9 - - + -
244P CYS* 4.0 20.6 - - + +
247P TYR* 3.8 19.7 + + - -
269P SER* 2.7 51.4 + - - +
270P VAL* 4.8 0.4 - - - -
272P LEU* 1.3 76.8 - - + +
274P VAL* 1.3 63.0 + - - +
275P ILE 3.0 1.8 - - - -
276P LEU* 2.9 8.6 + - + +
277P ALA* 2.8 32.2 + - - +
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Residues in contact with VAL 274 (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* 5.9 3.1 - - + -
244P CYS* 3.9 18.6 - - + -
270P VAL* 3.0 21.1 + - + +
271P VAL* 2.8 9.9 + - - +
273P TYR* 1.3 72.2 - - - +
275P ILE* 1.3 58.4 + - - +
277P ALA* 4.1 7.6 + - + +
283P GLN* 3.6 28.3 + - + +
286P LEU* 4.9 11.0 - - + -
287P VAL* 2.5 48.6 - - + +
290P ILE* 4.9 15.0 - - + -
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Residues in contact with ILE 275 (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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271P VAL* 2.9 10.4 + - + +
272P LEU* 3.3 14.6 - - - +
274P VAL* 1.3 79.3 - - - +
276P LEU* 1.3 65.4 + - + +
277P ALA 3.5 6.9 - - - +
283P GLN* 4.9 1.9 + - - -
305P LEU* 4.6 20.0 - - + -
309P PHE* 3.4 38.4 - - + -
354P LEU* 3.8 22.9 - - + -
357P ARG* 3.6 13.5 - - - +
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Residues in contact with LEU 276 (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* 3.9 40.4 - - + -
272P LEU* 3.0 23.9 + - + +
273P TYR* 2.9 10.8 + - + +
275P ILE* 1.3 75.4 - - + +
277P ALA* 1.3 58.6 + - - +
341P PHE* 4.9 14.6 - - + -
350P ARG* 4.4 19.5 - - + +
353P ASP* 4.2 11.6 - - + +
354P LEU* 3.9 45.1 - - + +
357P ARG* 2.5 34.8 + - + +
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Residues in contact with ALA 277 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240P TYR* 4.0 6.4 - - - +
241P LEU* 3.9 36.3 - - + +
273P TYR 2.8 20.8 + - - +
274P VAL* 4.3 8.3 - - - +
275P ILE 3.3 5.1 - - - +
276P LEU* 1.3 74.9 - - - +
278P PRO* 1.3 75.1 - - + +
279P PHE 3.7 0.2 + - - -
283P GLN* 3.1 21.1 + - + +
357P ARG* 3.2 8.0 + - - -
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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
------------------------------------------------------------
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