Contacts of the helix formed by residues 269 - 281 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267K GLN 3.9 1.9 + - - -
268K VAL* 1.3 73.3 - - - +
270K TRP* 1.3 62.2 + - - +
271K LYS* 3.7 6.4 + - - +
272K LEU* 3.3 42.6 + - - +
273K VAL* 3.3 9.2 + - - +
323K ASN* 2.6 33.2 + - - -
336K ILE* 4.6 1.2 - - - +
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Residues in contact with TRP 270 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268K VAL* 3.6 22.4 - - + +
269K SER* 1.3 72.3 + - - +
271K LYS* 1.3 58.5 + - - +
272K LEU 3.2 2.5 - - - -
273K VAL* 3.3 2.9 + - - +
274K THR* 2.8 38.0 + - - +
332K ASN* 5.1 8.3 - - + -
335K THR* 3.6 33.7 - - + -
336K ILE* 3.6 47.0 - - + +
339K GLN* 3.2 37.7 - - + +
328L ALA 5.4 2.2 - - - +
329L ASP 5.8 3.1 - - - -
330L SER 4.7 6.5 - - - +
331L LYS* 2.9 72.2 - - + +
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Residues in contact with LYS 271 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269K SER* 3.5 6.8 + - - +
270K TRP* 1.3 80.4 - - - +
272K LEU* 1.3 57.6 + - + +
274K THR* 3.7 7.0 - - - -
275K GLU* 2.9 39.1 + - - +
296L GLN* 4.1 14.0 - - - +
297L TYR* 6.2 1.2 - - - -
328L ALA* 4.1 34.0 + - + +
329L ASP* 3.6 31.1 - - - +
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Residues in contact with LEU 272 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269K SER* 3.3 22.2 + - - +
270K TRP 3.2 0.6 - - - -
271K LYS* 1.3 77.5 - - + +
273K VAL* 1.3 60.7 + - - +
275K GLU* 3.1 20.1 + - - +
276K TYR* 2.9 24.4 + - - +
292K TYR* 4.1 0.4 - - - +
319K LYS* 4.9 8.7 - - + +
320K HIS* 3.2 28.5 - - - +
322K ALA* 5.8 2.9 - - + -
323K ASN* 3.5 35.7 - - + +
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Residues in contact with VAL 273 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269K SER 3.3 9.4 - - - +
270K TRP 3.3 5.1 + - - +
272K LEU* 1.3 74.8 - - - +
274K THR* 1.3 58.6 + - - +
276K TYR* 3.3 4.7 + - - +
277K ALA* 3.0 25.8 + - - +
288K LEU* 5.1 5.3 - - + +
292K TYR* 3.5 28.9 - - + -
323K ASN* 3.2 26.0 - - - +
327K PHE* 4.7 2.9 - - + -
336K ILE* 3.6 33.4 - - + +
337K CYS* 4.2 24.2 - - - -
340K ALA* 4.4 3.8 - - + -
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Residues in contact with THR 274 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270K TRP* 2.8 22.8 + - - +
271K LYS* 3.7 8.9 - - - -
273K VAL* 1.3 73.3 - - - +
275K GLU* 1.3 60.1 - - - +
277K ALA* 3.2 2.3 + - - +
278K MET* 2.9 31.2 + - + +
336K ILE 5.3 1.4 + - - -
339K GLN* 4.2 12.6 + - - -
340K ALA* 4.0 16.9 - - - +
343K THR* 3.6 40.5 + - + +
333L GLN* 4.8 10.0 + - - +
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Residues in contact with GLU 275 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271K LYS* 2.9 27.5 + - + +
272K LEU* 3.1 28.1 + - - +
274K THR* 1.3 77.1 - - - +
276K TYR* 1.3 63.0 + - - +
278K MET* 3.1 10.0 + - + +
279K GLU* 3.0 34.3 + - + +
319K LYS* 3.2 35.7 + - - -
320K HIS* 3.9 4.1 - - + -
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Residues in contact with TYR 276 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272K LEU 2.9 8.8 + - - +
273K VAL* 3.6 7.4 - - + +
275K GLU* 1.3 75.1 - - - +
277K ALA* 1.3 61.2 + - - +
279K GLU* 3.2 6.6 + - - +
280K THR* 3.1 46.2 + - + +
288K LEU* 4.1 23.6 - - + -
291K MET* 3.9 23.3 - - + +
292K TYR* 3.6 21.5 - + + -
295K PHE* 3.8 19.2 - + - -
312K SER* 2.7 36.6 + - - -
316K TYR* 3.6 34.1 - + + -
320K HIS* 3.2 24.8 + + + +
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Residues in contact with ALA 277 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273K VAL 3.0 14.1 + - - +
274K THR 3.3 9.0 - - - +
276K TYR* 1.3 78.2 - - - +
278K MET* 1.3 53.8 + - - +
280K THR* 4.2 1.1 - - - -
281K LYS* 2.8 35.2 + - - -
282K CYS 3.3 4.3 + - - +
288K LEU* 3.8 20.0 - - + -
340K ALA* 3.6 24.2 - - + +
344K VAL* 3.7 19.5 - - + +
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Residues in contact with MET 278 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274K THR* 2.9 22.4 + - + +
275K GLU* 3.1 10.3 + - + +
277K ALA* 1.3 76.9 - - + +
279K GLU* 1.3 65.9 + - - +
281K LYS* 3.6 17.3 - - - +
343K THR* 3.5 47.1 - - + +
344K VAL* 4.3 7.6 - - - -
347K LYS* 3.9 33.4 - - + +
293L LEU* 5.8 3.4 - - + -
297L TYR* 5.2 9.9 - - - +
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Residues in contact with GLU 279 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275K GLU* 3.0 30.9 + - + +
276K TYR* 3.3 9.6 - - - +
277K ALA 3.1 0.2 - - - -
278K MET* 1.3 81.1 - - - +
280K THR* 1.3 62.7 + - - +
281K LYS* 3.0 16.0 + - - +
316K TYR* 3.5 44.9 + - + +
319K LYS* 5.5 6.3 - - - -
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Residues in contact with THR 280 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276K TYR* 3.1 41.8 + - + +
277K ALA* 3.8 0.7 + - - -
279K GLU* 1.3 76.8 - - - +
281K LYS* 1.3 71.3 + - - +
282K CYS* 3.1 20.4 + - - +
312K SER* 3.6 32.1 - - - -
316K TYR* 4.6 7.9 - - + +
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Residues in contact with LYS 281 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277K ALA 2.8 12.7 + - - -
278K MET 3.6 11.4 - - - +
279K GLU 3.0 13.6 - - - +
280K THR* 1.3 79.1 - - - +
282K CYS* 1.3 63.3 + - - +
283K ASP* 3.1 11.6 + - - +
344K VAL* 3.6 13.9 - - + +
348K LYS* 3.7 18.5 + - - +
363K ASN* 5.7 4.0 - - - +
367K ASP* 3.5 30.8 + - - -
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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
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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