Contacts of the helix formed by residues 253 - 271 (chain M) in PDB entry 5IIO
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 ASN 253 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251M ASN* 2.8 12.1 + - - +
252M HIS* 1.3 82.7 - - - +
254M LEU* 1.3 57.5 + - - +
255M HIS* 3.2 10.0 - - - -
256M ILE* 2.9 28.2 + - + +
257M THR* 2.8 25.3 + - - +
286M LEU* 3.3 32.0 + - + +
289M PHE* 4.3 2.8 + - - +
291M LYS 3.0 24.0 + - - -
292M PRO* 3.6 2.3 - - - +
293M VAL* 2.9 34.8 + - - +
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Residues in contact with LEU 254 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251M ASN* 3.4 33.0 + - + +
252M HIS 3.7 1.0 - - - -
253M ASN* 1.3 76.3 - - - +
255M HIS* 1.3 65.0 + - - +
256M ILE 3.1 0.9 + - - -
257M THR* 3.7 4.9 - - - +
258M GLU* 3.1 59.0 + - + +
261M GLU* 6.2 0.2 - - - +
287M LYS* 5.9 1.6 - - - -
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Residues in contact with HIS 255 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252M HIS 3.7 21.7 + - - -
253M ASN* 4.0 8.9 + - - -
254M LEU* 1.3 79.1 + - - +
256M ILE* 1.3 86.0 + - + +
258M GLU* 4.7 5.4 - - - -
259M LYS* 2.7 37.8 + - - +
292M PRO* 4.9 9.7 - - + +
293M VAL 5.4 0.6 + - - -
316M ILE* 3.7 11.1 - - + +
317M LEU* 3.8 20.5 - - + +
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Residues in contact with ILE 256 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253M ASN* 2.9 33.5 + - + +
255M HIS* 1.3 99.8 - - + +
257M THR* 1.3 64.6 + - - +
258M GLU 3.2 2.3 + - - -
259M LYS* 3.2 5.7 + - - +
260M LEU* 3.1 28.9 + - + +
286M LEU* 3.7 23.8 - - + -
293M VAL* 4.8 4.5 - - + +
313M ILE* 3.8 35.4 - - + +
316M ILE* 4.1 24.1 - - + +
317M LEU* 4.6 7.6 - - + -
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Residues in contact with THR 257 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251M ASN* 3.1 27.6 + - - +
253M ASN 2.8 18.8 + - - +
254M LEU* 3.4 7.3 + - - +
256M ILE* 1.3 72.8 - - - +
258M GLU* 1.3 58.8 + - - +
260M LEU* 3.8 7.5 - - - +
261M GLU* 2.9 35.8 + - - +
283M ILE* 3.9 27.0 - - + +
286M LEU* 3.6 35.0 - - + -
287M LYS* 4.1 8.5 - - + +
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Residues in contact with GLU 258 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254M LEU* 3.1 51.7 + - + +
255M HIS* 4.9 4.2 - - - +
257M THR* 1.3 79.1 + - - +
259M LYS* 1.3 69.9 + - + +
261M GLU* 3.5 12.2 + - - +
262M VAL* 3.4 23.3 + - - +
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Residues in contact with LYS 259 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255M HIS* 2.7 35.2 + - - +
256M ILE 3.2 5.5 + - - +
258M GLU* 1.3 80.2 + - + +
260M LEU* 1.3 66.0 + - - +
262M VAL* 3.3 19.8 + - - +
263M LEU* 3.5 4.7 + - - +
316M ILE* 4.0 30.4 - - + +
320M GLY* 3.2 29.4 + - - +
321M HIS* 4.3 4.7 - - - +
322M LEU* 4.4 14.0 - - + +
325M LEU* 3.7 30.0 - - + +
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Residues in contact with LEU 260 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256M ILE* 3.1 26.9 + - + +
257M THR* 3.9 4.5 - - - +
259M LYS* 1.3 74.2 - - - +
261M GLU* 1.3 61.2 + - - +
263M LEU* 3.1 6.1 + - - +
264M ALA* 2.8 27.7 + - - +
279M TYR* 3.9 25.5 - - + -
282M ALA* 5.3 1.3 - - + -
283M ILE* 3.8 21.0 - - + +
286M LEU* 3.7 30.3 - - + -
309M MET* 4.1 22.7 - - + +
312M LYS* 4.4 13.7 - - + -
313M ILE* 4.9 3.1 - - + +
316M ILE* 4.7 4.7 - - + -
322M LEU* 4.4 17.9 - - + -
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Residues in contact with GLU 261 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257M THR* 2.9 19.7 + - - +
258M GLU* 3.7 13.7 - - - +
259M LYS 3.2 0.2 - - - -
260M LEU* 1.3 77.4 - - - +
262M VAL* 1.3 63.5 + - - +
264M ALA* 3.2 3.5 + - + +
265M LYS* 2.9 26.5 + - - +
283M ILE* 3.6 26.8 - - + +
287M LYS* 2.9 32.5 + - - -
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Residues in contact with VAL 262 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258M GLU 3.4 16.6 - - - +
259M LYS* 3.4 12.1 - - - +
260M LEU 3.2 0.4 - - - -
261M GLU* 1.3 77.1 - - + +
263M LEU* 1.3 58.3 + - - +
265M LYS* 3.6 5.6 + - - +
266M ALA* 3.1 26.5 + - - +
325M LEU* 3.7 22.4 - - + -
328M ILE* 3.7 14.1 - - + -
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Residues in contact with LEU 263 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259M LYS 3.5 6.4 + - - +
260M LEU* 3.1 9.3 + - + +
262M VAL* 1.3 79.6 - - - +
264M ALA* 1.3 65.3 + - - +
266M ALA* 3.3 6.9 + - + +
267M TYR* 3.0 48.1 + - + -
279M TYR* 3.4 28.7 - - + +
312M LYS* 4.3 2.7 - - - -
322M LEU* 3.9 24.5 - - + -
324M LYS* 3.6 31.9 - - + -
325M LEU* 4.2 13.0 - - + -
328M ILE* 4.3 16.2 - - + -
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Residues in contact with ALA 264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260M LEU 2.8 13.3 + - - +
261M GLU* 3.5 9.4 - - + +
263M LEU* 1.3 76.5 - - - +
265M LYS* 1.3 57.1 + - - +
267M TYR* 3.3 5.9 + - - +
268M SER* 2.9 28.5 + - - -
276M ALA* 3.9 10.5 - - - +
279M TYR* 3.7 29.1 - - + -
280M ALA* 4.8 3.4 - - + +
283M ILE* 4.1 11.4 - - + -
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Residues in contact with LYS 265 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261M GLU 2.9 19.9 + - - +
262M VAL* 3.9 5.4 - - - +
264M ALA* 1.3 71.9 - - - +
266M ALA* 1.3 57.4 - - - +
268M SER* 3.2 13.5 + - - -
269M VAL* 2.9 49.8 + - + +
332M VAL* 6.0 1.6 - - + -
336M GLU* 3.6 42.1 - - - +
339M SER* 4.9 4.2 + - - -
340M ASN* 4.4 11.5 + - - -
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Residues in contact with ALA 266 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262M VAL 3.1 16.1 + - - +
263M LEU* 3.4 14.8 - - + +
264M ALA 3.2 0.2 - - - -
265M LYS* 1.3 76.8 - - - +
267M TYR* 1.3 63.6 + - + +
269M VAL* 3.5 1.4 + - - +
270M GLN* 3.2 34.6 + - - +
328M ILE* 4.3 29.8 - - + -
332M VAL* 4.1 19.0 - - + +
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Residues in contact with TYR 267 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263M LEU* 3.0 37.7 + - + -
264M ALA 3.8 4.3 - - - +
266M ALA* 1.3 76.5 - - + +
268M SER* 1.3 62.8 + - - +
270M GLN* 3.3 14.4 + - + -
271M GLY 3.1 4.3 + - - -
272M ASP* 3.0 48.7 + - + +
275M ARG* 3.4 28.2 + - + -
276M ALA* 4.2 7.6 - - - +
279M TYR* 3.6 38.1 - + - -
324M LYS* 3.5 20.7 + - - -
1P G 2.8 19.1 + - - -
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Residues in contact with SER 268 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264M ALA 2.9 14.1 + - - -
265M LYS* 3.2 22.2 + - - -
267M TYR* 1.3 77.3 - - - +
269M VAL* 1.3 60.5 + - - +
271M GLY* 2.9 20.3 + - - -
272M ASP 4.7 1.3 - - - -
273M LYS* 5.4 2.3 + - - +
276M ALA* 3.7 17.0 - - - +
346M THR* 4.5 4.2 - - - -
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Residues in contact with VAL 269 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265M LYS* 2.9 50.1 + - + +
266M ALA 3.6 10.8 - - - +
268M SER* 1.3 73.1 - - - +
270M GLN* 1.3 61.8 + - + +
271M GLY 3.2 0.7 - - - -
332M VAL* 3.9 31.6 - - + +
335M LEU* 4.0 23.5 - - + +
336M GLU* 3.8 22.9 - - + +
339M SER* 4.0 10.4 + - - +
346M THR* 3.2 21.2 + - - +
349M ALA* 5.2 0.5 - - - +
350M GLN* 4.9 0.3 + - - +
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Residues in contact with GLN 270 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266M ALA* 3.2 24.1 + - - +
267M TYR* 3.8 15.7 - - - +
268M SER 3.1 1.0 - - - -
269M VAL* 1.3 77.3 - - - +
271M GLY* 1.3 60.3 + - - +
272M ASP* 3.4 3.5 + - + +
328M ILE* 5.8 0.2 - - - +
329M SER* 3.8 28.3 + - - +
331M SER* 4.4 4.0 + - - -
332M VAL* 3.8 15.0 - - + +
335M LEU* 4.0 19.7 - - + -
346M THR* 3.5 2.2 - - - -
350M GLN* 3.4 16.6 + - - +
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Residues in contact with GLY 271 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267M TYR 3.9 0.2 - - - -
268M SER 2.9 13.7 + - - -
269M VAL 3.2 1.0 - - - -
270M GLN* 1.3 80.6 - - - +
272M ASP* 1.3 59.8 + - - +
273M LYS* 3.0 16.2 + - - +
346M THR* 3.3 25.3 - - - +
350M GLN* 4.4 1.6 - - - -
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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