Contacts of the helix formed by residues 247 - 262 (chain N) in PDB entry 2EIN
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 ILE 247 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74N MET* 5.1 0.2 - - - -
243N VAL 3.3 5.2 + - - +
244N TYR* 3.0 19.0 + - + +
246N LEU* 1.3 80.5 - - - +
248N LEU* 1.3 65.7 + - + +
249N PRO* 3.5 1.8 - - - -
250N GLY* 3.0 5.9 + - - +
251N PHE* 2.9 58.8 + - + -
344N PHE* 4.3 6.5 - - + -
348N PHE* 3.7 22.0 - - + -
380N VAL 3.6 24.5 - - - +
384N GLY 4.3 2.0 - - - -
385N ALA* 3.8 17.7 - - - +
516N HEA 3.9 25.8 - - + -
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Residues in contact with LEU 248 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187N SER* 3.4 12.1 - - - +
190N ILE* 3.7 29.8 - - + -
191N THR* 3.2 22.9 - - - +
194N LEU* 4.5 12.3 - - + -
244N TYR* 2.9 25.3 + - + +
247N ILE* 1.3 75.3 - - + +
249N PRO* 1.3 66.9 - - + +
251N PHE* 2.9 40.6 + - + +
252N GLY 2.9 9.7 + - - -
277N MET* 4.4 26.5 - - + +
280N ILE* 4.4 15.0 - - + -
281N GLY* 4.9 3.8 - - - -
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Residues in contact with PRO 249 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74N MET* 3.9 28.7 - - + +
75N ILE* 4.2 14.8 - - + -
184N PHE* 3.6 13.4 - - + -
187N SER* 3.7 12.8 - - - +
188N VAL* 5.2 6.1 - - + -
191N THR* 3.6 19.5 - - + +
245N ILE 3.5 20.6 - - - +
247N ILE 3.6 2.5 - - - +
248N LEU* 1.3 93.4 - - + +
250N GLY* 1.3 56.1 + - - +
252N GLY* 3.0 2.8 + - - -
253N MET* 2.9 33.4 + - + +
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Residues in contact with GLY 250 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74N MET* 3.2 26.6 - - - +
247N ILE* 3.0 10.0 + - - -
249N PRO* 1.3 75.1 - - - +
251N PHE* 1.3 61.3 + - - +
253N MET* 3.2 3.6 + - - +
254N ILE* 2.8 38.0 + - - +
344N PHE* 4.8 2.9 - - - -
388N ALA* 3.8 14.6 - - - -
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Residues in contact with PHE 251 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244N TYR* 6.1 0.4 - + - -
247N ILE* 2.9 41.4 + - + -
248N LEU* 3.1 31.4 - - + +
250N GLY* 1.3 75.0 - - - +
252N GLY* 1.3 63.6 + - - +
254N ILE* 3.3 0.6 + - - -
255N SER* 3.1 27.4 + - - -
277N MET* 4.5 5.6 - - - -
280N ILE* 4.4 14.4 - - + -
316N THR* 4.5 7.4 - - + -
319N LYS* 3.9 30.7 - - + -
323N TRP* 3.4 28.1 - + - -
344N PHE* 3.7 18.2 - + - -
348N PHE* 3.4 31.6 - + - -
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Residues in contact with GLY 252 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183N LEU* 4.5 2.9 - - - -
184N PHE* 3.8 18.8 - - - -
187N SER* 3.5 20.3 - - - -
248N LEU 2.9 10.1 + - - -
249N PRO 3.0 5.3 + - - -
251N PHE* 1.3 76.0 - - - +
253N MET* 1.3 61.2 + - - +
255N SER* 3.1 16.5 + - - -
256N HIS* 3.2 15.6 + - - -
277N MET* 4.9 1.5 - - - -
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Residues in contact with MET 253 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74N MET* 4.0 31.9 - - + -
78N PHE* 3.7 48.0 - - + -
184N PHE* 3.5 16.5 - - + -
249N PRO 2.9 14.6 + - - +
250N GLY* 3.8 4.7 - - - +
252N GLY* 1.3 70.1 - - - -
254N ILE* 1.3 64.2 + - - +
256N HIS* 3.1 3.1 + - - +
257N ILE* 2.9 36.0 + - + +
388N ALA* 3.9 19.5 - - + +
389N ILE* 4.1 4.9 - - - -
392N GLY* 4.1 6.7 - - - -
396N TRP* 3.9 26.9 - - + -
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Residues in contact with ILE 254 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250N GLY 2.8 24.5 + - - +
251N PHE 3.6 4.5 - - - +
253N MET* 1.3 73.3 - - - +
255N SER* 1.3 57.6 + - - +
257N ILE* 4.5 6.1 - - + -
258N VAL* 2.9 44.4 + - + +
323N TRP* 3.5 32.8 - - + +
340N TRP 5.1 0.2 - - - +
341N ALA* 3.8 24.0 - - + -
344N PHE* 3.8 44.9 - - + -
345N ILE* 4.7 3.4 - - + -
388N ALA* 4.3 12.6 - - + -
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Residues in contact with SER 255 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183N LEU* 3.8 30.6 - - - +
251N PHE 3.1 11.1 + - - -
252N GLY* 3.1 8.9 + - - -
254N ILE* 1.3 75.8 - - - +
256N HIS* 1.3 63.6 + - - +
258N VAL* 4.4 0.7 - - - +
259N THR* 2.9 30.5 + - - -
267N PRO* 4.6 3.8 - - - +
273N MET* 3.8 10.6 - - - +
319N LYS* 4.4 4.2 + - - -
323N TRP* 2.8 30.3 + - - +
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Residues in contact with HIS 256 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86N MET* 3.3 40.1 - - + +
182N PRO* 3.6 12.6 - - + +
183N LEU* 3.6 15.9 + - + -
184N PHE* 3.0 32.4 + - + +
252N GLY 3.2 13.7 + - - +
253N MET 3.1 7.9 + - - +
255N SER* 1.3 78.7 - - - +
257N ILE* 1.3 59.1 + - - +
259N THR* 3.2 6.5 + - - -
260N TYR* 2.8 32.8 + - - +
395N HIS* 5.7 2.2 - - - +
396N TRP* 4.1 17.6 - + + -
491N ASN* 5.2 8.8 + - - +
493N GLU* 4.8 1.6 + - - -
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Residues in contact with ILE 257 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253N MET* 2.9 27.8 + - + +
254N ILE* 3.8 10.8 - - + +
256N HIS* 1.3 74.7 - - - +
258N VAL* 1.3 62.4 + - - +
260N TYR* 4.3 4.5 - - - -
261N TYR* 3.0 45.8 + - + +
337N ALA* 3.6 24.7 - - + +
338N MET* 4.3 1.6 - - - +
341N ALA* 3.8 11.4 - - + -
388N ALA 4.8 1.3 - - - +
391N GLY* 3.5 12.8 - - - +
392N GLY* 3.5 34.1 - - - +
395N HIS* 4.5 18.2 - - + -
396N TRP* 4.8 3.8 - - + -
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Residues in contact with VAL 258 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254N ILE* 2.9 41.4 + - + +
255N SER 4.4 2.2 - - - +
257N ILE* 1.3 72.3 - - - +
259N THR* 1.3 54.5 + - - +
261N TYR 3.9 0.5 - - - -
262N SER* 2.5 41.2 + - - +
323N TRP* 3.5 26.2 - - + +
326N THR* 3.9 9.2 - - + -
327N LEU* 3.4 27.1 - - + -
338N MET* 4.2 8.0 - - - +
341N ALA* 3.9 16.6 - - + -
342N LEU* 5.8 0.4 - - + -
345N ILE* 4.3 13.7 - - + -
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Residues in contact with THR 259 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255N SER 2.9 19.6 + - - -
256N HIS* 3.2 5.5 + - - +
258N VAL* 1.3 75.4 - - - +
260N TYR* 1.3 67.0 - - - +
262N SER* 3.1 6.2 + - - -
264N LYS 3.0 42.4 + - - +
265N LYS 4.3 2.2 - - - +
266N GLU* 3.7 23.3 - - - +
267N PRO* 3.1 30.0 - - + +
326N THR* 3.5 12.3 - - - +
490N THR* 6.0 0.2 - - - +
491N ASN* 6.0 3.4 - - - +
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Residues in contact with TYR 260 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256N HIS 2.8 22.2 + - - +
257N ILE 3.6 4.5 - - - +
259N THR* 1.3 74.0 - - - +
261N TYR* 1.3 95.5 + + + +
263N GLY* 2.9 21.7 + - - -
264N LYS 4.8 1.1 - - - -
395N HIS* 3.6 23.3 - + + -
485N VAL* 3.7 14.4 - - + +
486N ASP* 3.0 35.4 + - + +
487N LEU* 3.8 20.8 - - + +
491N ASN* 3.7 34.5 - - + +
494N TRP* 4.7 8.7 - + - -
1Z ILE* 5.6 3.6 + - - +
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Residues in contact with TYR 261 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257N ILE* 3.0 40.1 + - + +
258N VAL 3.9 0.4 - - - -
260N TYR* 1.3 84.2 - + - +
262N SER* 1.3 58.2 + - - +
263N GLY 3.1 5.2 - - - -
331N ASN 3.5 0.9 - - - +
332N ILE* 3.5 2.4 - - - -
333N LYS* 2.9 58.5 + - + +
335N SER* 3.0 34.5 - - - -
337N ALA* 3.7 16.6 - - + +
338N MET* 3.9 20.1 - - + +
395N HIS* 2.4 53.8 + + - +
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Residues in contact with SER 262 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258N VAL 2.5 26.0 + - - -
259N THR 3.1 5.8 + - - -
261N TYR* 1.3 77.6 - - - +
263N GLY* 1.3 57.0 + - - +
264N LYS* 3.6 6.0 + - - -
326N THR* 3.3 19.6 + - - -
327N LEU* 3.2 34.4 + - - +
330N GLY* 2.9 9.8 - - - -
331N ASN 2.7 31.7 + - - -
332N ILE* 3.7 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
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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