Contacts of the helix formed by residues 249 - 268 (chain G) in PDB entry 4PIW
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 ALA 249 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G VAL* 3.9 33.2 - - + -
245G ALA 3.9 0.9 + - - +
246G GLN 3.0 10.9 + - - +
248G GLU* 1.3 80.7 - - + +
250G ALA* 1.3 57.4 + - - +
251G ASP 3.3 2.2 - - - -
252G ARG* 3.2 23.9 + - + +
253G ILE* 2.9 31.4 + - + +
357G TYR* 5.6 0.2 - - - +
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Residues in contact with ALA 250 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G TRP* 3.9 17.9 - - + -
158G MSE 3.9 15.5 - - + -
183G TYR* 3.0 35.9 + - + +
246G GLN 3.2 1.8 + - - -
247G LEU* 3.4 20.4 + - + +
248G GLU 3.4 1.2 + - - -
249G ALA* 1.3 78.2 - - - +
251G ASP* 1.3 57.8 + - - +
253G ILE 3.4 0.3 + - - -
254G ASN* 2.9 28.4 + - - +
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Residues in contact with ASP 251 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G TRP* 5.8 0.2 - - - -
43G ARG* 2.9 41.4 + - - -
158G MSE 3.2 7.8 - - - +
248G GLU 5.4 0.4 + - - -
249G ALA* 3.3 0.6 - - - +
250G ALA* 1.3 77.2 - - - +
252G ARG* 1.3 57.9 + - - +
254G ASN* 4.1 2.0 + - - +
255G GLN* 3.1 30.5 + - - +
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Residues in contact with ARG 252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G VAL* 5.8 6.4 - - - +
249G ALA* 3.2 25.8 + - + +
251G ASP* 1.3 78.1 - - - +
253G ILE* 1.3 63.4 + - - +
255G GLN* 4.1 3.1 - - - +
256G GLN* 3.2 23.3 + - + +
357G TYR* 3.5 23.3 - - + +
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Residues in contact with ILE 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G PRO* 4.5 7.2 - - + -
10G VAL* 4.0 22.4 - - + -
182G ASN 4.0 16.4 - - - +
183G TYR* 3.9 22.7 - - + +
246G GLN* 4.1 17.5 - - - +
249G ALA* 2.9 22.8 + - + +
250G ALA 3.9 2.9 - - - +
252G ARG* 1.3 74.1 - - - +
254G ASN* 1.3 65.2 + - - +
256G GLN* 3.2 3.1 + - - +
257G ARG* 3.0 37.5 + - - +
357G TYR* 3.5 39.2 - - + -
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Residues in contact with ASN 254 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G MSE 3.4 35.8 + - + +
182G ASN* 5.2 1.5 + - - +
183G TYR* 4.0 8.3 + - - +
250G ALA 2.9 19.8 + - - +
251G ASP* 4.1 4.4 + - - +
253G ILE* 1.3 77.8 - - - +
255G GLN* 1.3 58.1 + - - +
257G ARG* 3.4 7.0 + - - +
258G LEU* 3.0 41.1 + - - +
288G GLN 5.1 1.6 + - - -
289G ASN* 3.4 28.6 - - - +
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Residues in contact with GLN 255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251G ASP 3.1 18.6 + - - +
252G ARG* 4.1 4.3 - - - +
254G ASN* 1.3 79.1 - - - +
256G GLN* 1.3 62.4 + - - +
258G LEU* 3.4 20.8 + - - +
259G ALA* 3.1 25.2 + - + +
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Residues in contact with GLN 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252G ARG* 3.2 20.3 + - + +
253G ILE 3.2 4.9 + - - +
255G GLN* 1.3 75.4 - - - +
257G ARG* 1.3 59.8 + - - +
259G ALA* 3.2 11.2 + - - +
260G LEU* 3.0 48.6 + - + +
357G TYR* 3.7 38.2 + - + +
359G LEU 4.6 5.7 + - - -
361G PRO* 5.7 6.7 - - - +
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Residues in contact with ARG 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G ASN* 5.3 2.8 - - - +
8G PRO* 5.3 3.2 - - - +
180G THR 5.2 4.2 + - - -
181G LLP 4.7 3.2 + - - -
182G ASN* 3.3 44.1 + - - +
253G ILE* 3.0 34.3 + - + +
254G ASN* 3.8 4.7 - - - +
255G GLN 3.4 0.2 - - - -
256G GLN* 1.3 76.4 - - - +
258G LEU* 1.3 57.4 + - - +
260G LEU* 3.3 9.3 + - - +
261G TRP* 2.8 29.6 + - - +
289G ASN 4.3 1.3 - - - +
290G ALA* 3.0 27.8 + - + +
291G HIS* 2.7 31.9 + - - -
355G LEU* 3.6 23.1 + - + +
356G PHE* 3.5 26.1 - - - +
357G TYR* 3.6 19.9 - - - +
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Residues in contact with LEU 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254G ASN* 3.0 41.6 + - - +
255G GLN* 3.6 24.9 - - - +
256G GLN 3.2 0.2 - - - -
257G ARG* 1.3 76.3 - - - +
259G ALA* 1.3 61.6 + - - +
261G TRP* 3.7 3.1 - - + +
262G GLN* 3.4 23.9 + - - +
287G VAL* 5.9 4.5 - - + -
288G GLN* 4.0 33.9 - - + +
290G ALA* 3.7 19.7 - - + +
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Residues in contact with ALA 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255G GLN* 3.1 16.8 + - - +
256G GLN* 3.5 15.9 - - - +
257G ARG 3.2 0.2 - - - -
258G LEU* 1.3 77.4 - - - +
260G LEU* 1.3 62.1 + - + +
262G GLN* 3.6 3.4 + - - +
263G ASN* 3.0 35.0 + - - +
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Residues in contact with LEU 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256G GLN* 3.0 43.1 + - + +
257G ARG* 3.3 2.0 + - - +
259G ALA* 1.3 77.0 - - + +
261G TRP* 1.3 62.7 + - - +
263G ASN* 3.9 4.0 - - - +
264G TYR* 3.6 12.8 + - - -
355G LEU* 3.6 22.4 - - + -
356G PHE 3.3 26.9 - - - +
357G TYR 4.4 0.7 - - - +
359G LEU* 3.9 27.4 - - + +
360G SER 5.5 1.3 - - - +
361G PRO* 5.6 3.6 - - + -
364G GLN* 2.7 50.1 + - + +
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Residues in contact with TRP 261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257G ARG 2.8 17.4 + - - +
258G LEU* 3.7 7.2 - - + +
259G ALA 3.2 0.4 - - - -
260G LEU* 1.3 78.9 - - - +
262G GLN* 1.3 73.0 + - + +
264G TYR* 3.4 3.6 + - - +
265G TYR* 3.4 37.9 + + + -
280G PRO* 4.0 23.7 - - + +
282G ILE* 3.8 16.8 - - + -
288G GLN* 3.2 37.2 + - - +
290G ALA* 3.8 20.6 - - + -
292G MSE 2.9 29.0 + - - -
293G PHE* 3.3 51.6 - + + +
355G LEU* 4.1 6.7 - - + -
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Residues in contact with GLN 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258G LEU 3.4 13.3 + - - +
259G ALA* 3.6 2.9 + - - +
261G TRP* 1.3 87.2 - - + +
263G ASN* 1.3 61.9 + - - +
264G TYR 3.2 1.8 - - - -
265G TYR* 3.5 9.8 - - + -
266G ASP* 2.8 56.1 + - - +
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Residues in contact with ASN 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259G ALA* 3.0 29.3 + - - +
260G LEU* 3.9 3.8 - - - +
261G TRP 3.3 0.4 - - - -
262G GLN* 1.3 78.6 - - - +
264G TYR* 1.3 60.2 + - - +
266G ASP* 4.4 7.9 - - - +
267G ALA* 3.6 19.4 + - - +
364G GLN* 3.2 35.2 + - - +
368G ILE* 3.8 10.5 - - + +
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Residues in contact with TYR 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260G LEU 3.6 14.0 + - - -
261G TRP* 3.4 7.3 + - - +
263G ASN* 1.3 77.8 - - - +
265G TYR* 1.3 58.4 + - - +
267G ALA* 3.2 2.6 + - - +
268G LEU* 2.9 37.3 + - + +
293G PHE* 3.6 41.7 - + + -
353G LEU* 4.1 24.9 - - + -
354G PRO* 2.8 32.1 + - - +
355G LEU* 4.7 7.4 - - + -
359G LEU* 4.3 3.1 - - + +
364G GLN* 4.2 22.4 - - + +
367G VAL* 3.9 25.2 - - + +
368G ILE* 3.7 31.0 - - + -
371G LEU* 5.0 2.2 - - + -
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Residues in contact with TYR 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261G TRP* 3.4 25.8 + + + -
262G GLN* 3.1 20.7 + - + +
264G TYR* 1.3 80.0 - - - +
266G ASP* 1.3 65.2 + - - +
268G LEU 3.4 0.9 + - - +
269G ALA* 3.0 40.5 + - + +
273G LYS* 5.4 8.3 + - - -
279G LEU* 3.6 37.6 - - + +
280G PRO* 4.3 11.6 + - + -
293G PHE* 3.6 16.3 - + + -
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Residues in contact with ASP 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262G GLN* 2.8 51.3 + - - +
263G ASN* 4.4 8.7 + - - +
265G TYR* 1.3 80.3 - - - +
267G ALA* 1.3 58.1 + - - +
269G ALA* 4.0 6.1 - - - +
270G PRO* 4.0 12.8 - - - +
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Residues in contact with ALA 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263G ASN 3.6 14.7 + - - +
264G TYR* 3.2 4.1 + - - +
265G TYR 3.2 0.6 - - - -
266G ASP* 1.3 78.7 - - - +
268G LEU* 1.3 62.9 + - + +
269G ALA 3.3 2.7 - - - -
270G PRO* 3.7 10.9 - - - +
271G LEU* 4.9 1.4 - - - +
368G ILE* 3.6 32.3 - - + -
372G LEU* 3.8 22.0 - - + +
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Residues in contact with LEU 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264G TYR* 2.9 21.0 + - + +
265G TYR 3.7 2.0 - - - +
267G ALA* 1.3 80.4 - - + +
269G ALA* 1.3 62.9 + - - +
270G PRO 3.6 1.3 - - - -
271G LEU* 3.7 29.3 + - + +
272G ALA* 3.2 16.5 + - - +
277G ILE* 4.2 8.7 - - + +
279G LEU* 3.5 22.4 - - + +
293G PHE* 3.8 27.1 - - + -
295G ILE* 3.8 20.2 - - + -
353G LEU* 3.9 12.1 - - + -
368G ILE* 5.4 2.9 - - + -
371G LEU* 4.5 21.3 - - + -
372G LEU* 4.2 9.6 - - + -
375G PHE* 5.2 1.8 - - + -
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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