Contacts of the helix formed by residues 255 - 278 (chain F) in PDB entry 4Q44
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 HIS 255 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254F HIS* 1.3 94.9 + - + +
256F TRP* 1.3 64.2 + - - +
257F SER* 3.8 15.7 - - - +
258F GLU* 2.8 41.8 + - - +
259F CYS 3.4 3.6 + - - -
320F TRP* 3.5 7.8 - - - -
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Residues in contact with TRP 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255F HIS* 1.3 69.8 - - - +
257F SER* 1.3 70.2 + - - +
259F CYS* 3.0 32.0 + - + -
260F GLU* 2.9 44.3 + - + +
263F ILE* 4.1 13.2 - - + -
313F ILE* 3.3 34.5 - - + -
316F ALA* 3.7 5.2 - - + -
317F ARG* 3.4 67.7 - - + +
320F TRP* 3.7 31.3 - + + +
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Residues in contact with SER 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F HIS* 3.8 13.7 - - - +
256F TRP* 1.3 83.8 - - - +
258F GLU* 1.3 62.8 + - - +
260F GLU* 3.8 7.3 - - - +
261F ALA* 2.9 29.0 + - - +
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Residues in contact with GLU 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F ASP 5.1 1.2 - - - +
253F ILE* 3.4 26.0 - - + +
254F HIS 3.1 11.5 + - - -
255F HIS* 2.8 52.4 + - + +
256F TRP 3.1 0.4 - - - -
257F SER* 1.3 77.3 + - - +
259F CYS* 1.3 67.4 + - - +
261F ALA* 3.0 8.0 + - - +
262F ILE* 2.9 30.5 + - + +
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Residues in contact with CYS 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253F ILE* 3.7 11.6 - - + +
255F HIS 3.4 1.8 + - - -
256F TRP* 3.0 35.1 + - + +
258F GLU* 1.3 76.6 - - - +
260F GLU* 1.3 57.9 + - - +
262F ILE* 3.1 7.0 + - - +
263F ILE* 2.9 42.2 + - - +
290F LEU* 4.3 8.5 - - - -
316F ALA* 4.9 2.5 - - - -
320F TRP* 3.7 31.0 - - + -
332F VAL* 4.0 18.8 - - - +
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Residues in contact with GLU 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F TRP* 2.9 42.0 + - + +
257F SER* 3.8 7.0 - - - +
259F CYS* 1.3 76.8 - - - +
261F ALA* 1.3 65.7 + - - +
263F ILE* 3.2 9.0 + - - +
264F GLU* 2.8 64.2 + - + +
313F ILE* 3.3 27.7 - - - +
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Residues in contact with ALA 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257F SER 2.9 20.5 + - - +
258F GLU* 3.0 9.6 + - - +
260F GLU* 1.3 79.1 - - - +
262F ILE* 1.3 62.1 + - + +
264F GLU* 3.6 15.2 - - - +
265F ARG* 3.2 28.9 - - - +
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Residues in contact with ILE 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247F ARG* 4.8 9.6 - - + +
249F MET* 3.6 46.4 - - + -
253F ILE* 3.9 17.7 - - + -
258F GLU* 2.9 21.3 + - + +
259F CYS 3.5 5.2 - - - +
261F ALA* 1.3 76.5 - - + +
263F ILE* 1.3 59.1 + - - +
264F GLU 3.1 1.8 - - - -
265F ARG* 2.8 38.8 + - + +
266F LEU* 2.9 25.4 + - + +
332F VAL* 3.6 21.1 - - + -
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Residues in contact with ILE 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F TRP* 4.1 11.0 - - + -
259F CYS* 2.9 31.5 + - - +
260F GLU* 3.2 7.2 + - - +
262F ILE* 1.3 75.4 - - - +
264F GLU* 1.3 56.7 + - - +
266F LEU* 3.0 7.8 + - + -
267F TYR* 2.9 33.9 + - + +
309F LYS* 5.4 1.1 - - + +
312F LEU* 4.7 2.2 - - + +
313F ILE* 4.0 26.9 - - + +
316F ALA* 3.5 32.8 - - + -
332F VAL* 4.1 17.5 - - + -
334F LEU* 3.9 28.3 - - + -
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Residues in contact with GLU 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260F GLU* 2.8 44.6 + - + +
261F ALA* 3.6 11.2 - - - +
263F ILE* 1.3 76.2 - - - +
265F ARG* 1.3 59.0 + - + +
267F TYR* 4.7 0.9 - - - +
268F PRO* 3.3 21.5 - - - +
309F LYS* 2.6 47.0 + - - +
313F ILE* 3.4 6.6 - - + +
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Residues in contact with ARG 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247F ARG* 4.4 20.8 - - - +
261F ALA* 3.2 29.4 + - - +
262F ILE* 2.8 22.4 + - + +
264F GLU* 1.3 78.3 - - + +
266F LEU* 1.3 67.4 + - + +
268F PRO* 3.6 9.9 - - - +
269F GLU* 3.8 13.9 - - - +
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Residues in contact with LEU 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245F VAL* 3.6 36.4 - - + +
246F GLU* 4.4 0.9 - - - -
247F ARG* 4.0 24.0 - - + +
262F ILE* 2.9 18.6 + - + +
263F ILE* 3.0 10.5 + - - +
265F ARG* 1.3 81.6 - - + +
267F TYR* 1.3 64.0 + - - +
269F GLU* 3.1 17.4 + - + +
270F LEU* 3.2 12.3 + - - +
332F VAL* 3.3 36.1 - - + +
333F GLY* 3.8 7.0 - - - -
334F LEU* 3.8 16.6 - - + +
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Residues in contact with TYR 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F ILE* 2.9 16.1 + - + +
264F GLU 4.7 1.3 - - - +
266F LEU* 1.3 76.7 - - - +
268F PRO* 1.3 72.6 - - + +
269F GLU 3.2 0.2 + - - -
270F LEU* 3.2 4.8 + - + +
271F GLU* 2.9 42.6 + - + +
281F LEU* 5.1 1.9 - - - +
307F LEU* 2.8 55.3 + - + +
308F ASN* 3.9 4.8 - - - -
309F LYS* 3.7 57.7 + - + +
312F LEU* 4.4 13.7 - - + -
334F LEU* 3.6 10.3 - - + +
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Residues in contact with PRO 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264F GLU 3.3 22.2 - - - +
265F ARG* 3.6 11.0 - - - +
267F TYR* 1.3 96.4 - - + +
269F GLU* 1.3 63.4 - - - +
271F GLU* 3.4 15.8 + - + +
272F ARG* 2.9 29.3 + - - +
309F LYS* 6.1 1.8 - - - +
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Residues in contact with GLU 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245F VAL* 4.1 18.8 - - + -
265F ARG 3.8 16.2 - - - +
266F LEU* 3.1 10.2 + - + +
268F PRO* 1.3 81.8 - - - +
270F LEU* 1.3 64.0 - - - +
272F ARG* 3.2 23.9 + - - +
273F ARG* 3.0 31.9 + - - +
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Residues in contact with LEU 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F VAL* 3.6 40.4 - - + +
244F GLY* 4.5 2.2 - - - -
245F VAL* 3.6 21.9 - - + +
266F LEU 3.2 8.1 + - - +
267F TYR* 3.7 9.0 - - + +
269F GLU* 1.3 78.6 - - - +
271F GLU* 1.3 56.9 + - - +
273F ARG* 3.6 1.4 + - - +
274F LEU* 3.0 29.8 + - + +
307F LEU* 3.7 29.4 - - + -
312F LEU* 4.3 4.7 - - + -
334F LEU* 3.6 35.0 - - + -
335F HIS 4.4 0.2 - - - +
336F VAL* 4.1 12.3 - - + -
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Residues in contact with GLU 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267F TYR* 2.9 36.2 + - + +
268F PRO* 3.6 13.7 - - + +
270F LEU* 1.3 76.2 - - - +
272F ARG* 1.3 63.4 + - - +
275F ALA* 3.1 25.6 + - + +
281F LEU* 4.1 22.2 - - + +
307F LEU* 3.5 23.1 - - + +
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Residues in contact with ARG 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268F PRO 2.9 17.9 + - - +
269F GLU* 3.2 25.7 + - - +
271F GLU* 1.3 78.9 + - - +
273F ARG* 1.3 80.2 + - - +
275F ALA* 3.7 5.2 + - - +
276F LYS* 3.2 53.5 + - - +
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Residues in contact with ARG 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240F ARG* 4.1 17.2 + - - +
243F VAL* 4.0 12.7 - - + +
244F GLY 2.5 27.7 + - - -
245F VAL* 3.2 15.4 - - - +
269F GLU* 3.0 19.8 + - - +
270F LEU 4.0 3.1 - - - +
272F ARG* 1.3 93.1 - - - +
274F LEU* 1.3 64.2 + - - +
276F LYS* 3.3 26.1 + - + +
277F VAL* 3.9 2.4 + - - +
842G G 3.0 37.2 + - - -
843G G 2.5 31.2 + - - -
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Residues in contact with LEU 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F VAL* 4.3 14.8 - - + +
270F LEU* 3.0 19.1 + - + +
271F GLU 4.1 2.9 - - - +
273F ARG* 1.3 76.7 - - - +
275F ALA* 1.3 52.1 + - - +
276F LYS 3.1 0.4 - - - -
277F VAL* 3.1 5.2 + - + -
278F LYS* 2.6 47.6 + - + +
281F LEU* 3.8 16.4 - - + -
283F ILE* 3.6 28.0 - - + -
307F LEU* 3.6 32.8 - - + -
336F VAL* 4.1 7.9 - - + -
338F LEU* 3.7 29.6 - - + -
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Residues in contact with ALA 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271F GLU* 3.1 20.9 + - + +
272F ARG* 4.0 6.5 - - - +
273F ARG 3.2 0.4 - - - -
274F LEU* 1.3 76.1 - - - +
276F LYS* 1.3 61.3 + - - +
278F LYS 3.7 11.2 - - - -
279F PRO* 3.6 28.0 - - + +
281F LEU* 4.1 10.5 - - + +
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Residues in contact with LYS 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240F ARG* 5.7 0.4 - - - +
272F ARG* 3.2 58.4 - - - +
273F ARG* 3.4 14.7 - - + +
274F LEU 3.1 0.8 - - - -
275F ALA* 1.3 77.9 - - - +
277F VAL* 1.3 66.0 + - + +
279F PRO* 5.1 2.1 - - - +
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Residues in contact with VAL 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240F ARG* 3.3 39.0 - - + +
243F VAL* 5.5 1.1 - - + -
273F ARG 4.2 4.3 - - - +
274F LEU* 3.1 7.0 + - + +
276F LYS* 1.3 83.6 - - + +
278F LYS* 1.3 69.9 + - + +
279F PRO* 3.9 6.0 - - - +
338F LEU* 4.5 21.8 - - + -
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Residues in contact with LYS 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F LEU* 2.6 34.6 + - + +
275F ALA* 3.7 3.1 - - - -
277F VAL* 1.3 81.7 - - + +
279F PRO* 1.3 60.7 - - + +
280F ASP* 2.6 38.8 + - - +
281F LEU* 2.8 23.4 + - - +
282F LEU* 3.4 37.6 - - - +
338F LEU* 5.7 5.8 - - + -
339F LEU* 4.2 14.0 - - - +
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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
------------------------------------------------------------
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