Contacts of the helix formed by residues 269 - 281 (chain B) in PDB entry 4E2I
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 SER 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266B LYS* 6.1 1.6 - - - -
267B GLN 3.9 2.3 + - - -
268B VAL* 1.3 72.6 - - - +
270B TRP* 1.3 63.4 + - - +
271B LYS* 3.7 6.6 + - - +
272B LEU* 3.3 42.9 + - - +
273B VAL* 3.3 9.2 + - - +
323B ASN* 2.6 32.8 + - - -
336B ILE* 4.6 1.4 - - - +
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Residues in contact with TRP 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B VAL* 3.6 28.4 - - + +
269B SER* 1.3 71.8 + - - +
271B LYS* 1.3 57.1 + - - +
272B LEU 3.2 2.0 - - - -
273B VAL* 3.2 2.8 + - - +
274B THR* 2.8 37.7 + - - -
332B ASN* 5.1 8.1 - - + -
335B THR* 3.6 33.0 - - + -
336B ILE* 3.6 47.0 - - + +
339B GLN* 3.1 42.8 - - + +
328C ALA 5.7 3.1 - - - +
329C ASP* 6.2 3.4 - - - -
330C SER 5.1 4.0 - - - +
331C LYS* 3.3 58.2 - - + +
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B SER* 3.5 6.4 + - - +
270B TRP* 1.3 80.5 - - - +
272B LEU* 1.3 59.0 + - + +
274B THR* 3.7 7.4 - - - -
275B GLU* 2.9 38.9 + - - +
296C GLN* 4.2 23.1 - - - +
297C TYR* 6.0 2.6 - - - -
328C ALA* 4.5 21.6 + - + +
329C ASP* 4.2 26.6 - - - +
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B SER* 3.3 21.5 - - - +
270B TRP 3.2 0.6 - - - -
271B LYS* 1.3 78.1 - - + +
273B VAL* 1.3 64.7 + - - +
275B GLU* 3.1 19.3 + - - +
276B TYR* 3.0 19.4 + - - +
292B TYR* 4.1 0.7 - - - +
319B LYS* 4.9 8.5 - - + +
320B HIS* 3.2 29.1 - - + +
322B ALA* 5.8 2.9 - - + -
323B ASN* 3.5 36.3 - - + +
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B SER 3.3 9.9 - - - +
270B TRP 3.2 5.7 + - - +
272B LEU* 1.3 75.5 - - - +
274B THR* 1.3 58.9 + - - +
276B TYR* 3.3 4.3 + - - +
277B ALA* 3.0 26.0 + - - +
288B LEU* 5.1 4.6 - - + +
292B TYR* 3.5 29.6 - - + -
323B ASN* 3.2 25.6 - - - +
327B PHE* 4.8 3.1 - - + -
336B ILE* 3.6 33.0 - - + +
337B CYS* 4.2 24.0 - - - -
340B ALA* 4.4 4.0 - - + -
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Residues in contact with THR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B TRP* 2.8 22.8 + - - -
271B LYS* 3.7 9.0 - - - -
273B VAL* 1.3 73.1 - - - +
275B GLU* 1.3 60.5 + - - +
277B ALA* 3.2 2.3 + - - +
278B MET* 2.9 30.9 + - + +
336B ILE 5.3 1.7 + - - -
339B GLN* 4.2 12.5 + - - -
340B ALA* 3.9 17.6 + - - +
343B THR* 3.6 40.3 + - + +
333C GLN* 5.3 6.8 + - - +
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Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B LYS* 2.9 27.3 + - + +
272B LEU* 3.1 28.5 + - - +
274B THR* 1.3 77.2 - - - +
276B TYR* 1.3 61.9 + - - +
278B MET* 3.1 10.1 + - - +
279B GLU* 3.0 34.0 + - + +
319B LYS* 3.2 35.4 + - - -
320B HIS* 3.9 4.8 - - + -
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Residues in contact with TYR 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LEU 3.0 8.2 + - - +
273B VAL 3.3 7.8 + - - +
275B GLU* 1.3 76.6 - - - +
277B ALA* 1.3 62.2 + - - +
279B GLU* 3.2 6.1 + - - +
280B THR* 3.1 47.0 + - + +
288B LEU* 4.1 22.7 - - + -
291B MET* 3.9 23.2 - - + +
292B TYR* 3.6 21.3 - + + -
295B PHE* 3.8 19.4 - + - -
312B SER* 2.7 35.9 + - - -
316B TYR* 3.6 34.1 - + + -
320B HIS* 3.2 24.6 + + + +
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B VAL 3.0 14.5 + - - +
274B THR 3.3 9.4 - - - +
275B GLU 3.1 0.2 - - - -
276B TYR* 1.3 78.2 - - - +
278B MET* 1.3 53.9 + - - +
280B THR* 4.2 0.9 - - - -
281B LYS* 2.8 35.0 + - - -
282B CYS 3.3 4.0 + - - +
288B LEU* 3.8 20.2 - - + -
340B ALA* 3.5 23.6 - - + +
344B VAL* 3.7 19.6 - - + +
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Residues in contact with MET 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B THR* 2.9 21.8 + - + +
275B GLU* 3.1 10.1 + - + +
277B ALA* 1.3 76.7 - - + +
279B GLU* 1.3 66.7 + - - +
281B LYS* 3.7 16.5 - - - +
343B THR* 3.5 46.2 - - + +
344B VAL* 4.3 7.2 - - - -
347B LYS* 3.9 34.3 - - + +
293C LEU* 6.6 0.2 - - + -
297C TYR* 5.3 9.0 - - - +
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Residues in contact with GLU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B GLU* 3.0 31.4 + - + +
276B TYR* 3.3 9.6 - - - +
278B MET* 1.3 79.8 - - - +
280B THR* 1.3 63.4 + - - +
281B LYS* 3.0 15.7 + - - +
316B TYR* 3.5 44.7 + - + +
319B LYS* 5.5 6.5 - - - -
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Residues in contact with THR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B TYR* 3.1 41.6 + - + +
277B ALA* 3.8 1.0 + - - -
279B GLU* 1.3 76.5 - - - +
281B LYS* 1.3 69.4 + - - +
282B CYS* 3.0 20.4 + - - +
312B SER* 3.6 32.1 - - - -
316B TYR* 4.6 7.6 - - + -
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Residues in contact with LYS 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B ALA 2.8 13.0 + - - -
278B MET* 3.7 13.0 - - - +
279B GLU 3.0 13.9 - - - +
280B THR* 1.3 79.2 - - - +
282B CYS* 1.3 62.8 + - - +
283B ASP* 3.1 9.0 + - - +
344B VAL* 3.6 15.2 - - + +
348B LYS* 3.7 20.0 + - - +
363B ASN* 5.7 4.0 - - - +
367B ASP* 3.5 31.0 + - - -
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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
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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