Contacts of the helix formed by residues 316 - 328 (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 TYR 316 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276K TYR* 3.6 32.1 - + + -
279K GLU* 3.5 50.1 + - + +
280K THR* 4.6 6.2 - - + +
295K PHE* 4.6 3.9 - - + -
311K PRO 3.3 23.8 - - - -
312K SER* 3.9 16.8 - - - +
313K HIS 3.1 4.6 + - - +
315K LYS* 1.3 101.6 + - + +
317K HIS* 1.3 64.9 + - - +
318K GLU 3.5 1.1 - - - -
319K LYS* 3.3 24.8 + - + -
320K HIS* 3.0 29.4 + - + +
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Residues in contact with HIS 317 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294K GLU 3.7 17.0 - - - -
295K PHE* 3.3 39.4 + + + -
298K SER 3.6 8.7 - - - -
299K PHE* 3.4 30.3 + + + +
302K CYS* 3.9 3.8 - - - -
305K CYS* 5.4 1.1 - - - -
313K HIS* 2.9 15.8 + - - +
314K TYR* 4.5 3.9 - - - -
315K LYS 3.9 0.4 - - - -
316K TYR* 1.3 77.0 - - - +
318K GLU* 1.3 55.2 + - + +
319K LYS 3.0 0.6 + - - -
320K HIS 3.1 0.5 + - - -
321K TYR* 2.6 63.4 + + + +
700K ZN 2.6 30.7 - - - -
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Residues in contact with GLU 318 (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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299K PHE* 3.6 50.6 - - + -
305K CYS* 5.1 7.5 - - - -
314K TYR 4.8 10.1 + - - +
315K LYS 5.6 0.4 - - - -
316K TYR 3.5 0.4 - - - +
317K HIS* 1.3 76.9 - - + +
319K LYS* 1.3 59.2 + - - +
321K TYR* 4.1 6.2 + - - +
322K ALA 5.3 0.7 + - - -
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Residues in contact with LYS 319 (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* 4.9 9.2 - - + +
275K GLU* 3.2 38.0 + - - -
279K GLU* 5.5 5.6 - - - -
315K LYS 4.8 4.5 - - - +
316K TYR* 3.3 31.1 + - + +
317K HIS 3.0 0.6 - - - -
318K GLU* 1.3 81.4 - - - +
320K HIS* 1.3 78.5 + - + +
321K TYR 3.6 0.2 - - - -
322K ALA* 5.3 2.6 + - - +
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Residues in contact with HIS 320 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272K LEU* 3.2 34.7 + - + +
275K GLU* 3.9 17.7 - - - +
276K TYR* 3.2 40.8 - + + +
279K GLU* 5.6 0.2 - - - +
292K TYR* 3.4 26.0 + + + +
295K PHE* 4.6 5.8 - + + -
316K TYR* 3.0 28.0 + - + +
317K HIS 3.4 1.6 - - - -
319K LYS* 1.3 101.9 + - + +
321K TYR* 1.3 59.2 + - - +
322K ALA 3.3 3.1 - - - +
323K ASN* 3.6 4.4 + - - +
324K ALA* 3.0 31.5 + - - +
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Residues in contact with TYR 321 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295K PHE 3.2 21.7 - - - +
296K GLN* 4.6 1.6 - - - -
297K TYR 2.9 37.9 + - - -
298K SER* 3.8 11.7 - - - -
299K PHE* 3.5 28.3 - + + -
300K GLU* 4.3 8.5 + - - +
317K HIS* 2.6 33.7 + - + +
318K GLU* 4.1 5.3 - - - +
319K LYS 3.6 1.2 - - - -
320K HIS* 1.3 75.0 - - - +
322K ALA* 1.3 64.8 + - - +
325K ALA* 3.2 29.6 + - + +
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Residues in contact with ALA 322 (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* 5.8 3.6 - - + -
318K GLU 5.3 0.8 + - - -
319K LYS 5.3 2.2 + - - +
320K HIS* 3.3 0.8 - - - -
321K TYR* 1.3 84.9 - - - +
323K ASN* 1.3 61.9 + - - +
325K ALA* 3.5 15.0 - - - +
326K ILE* 3.9 13.8 - - - +
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Residues in contact with ASN 323 (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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267K GLN 4.8 0.3 - - - +
268K VAL* 3.5 9.7 - - - +
269K SER* 2.6 50.5 + - - -
272K LEU* 3.5 23.6 - - + +
273K VAL* 3.2 12.9 - - - +
292K TYR* 2.8 28.7 + - - +
320K HIS* 3.6 4.0 + - - +
321K TYR 3.4 0.2 - - - -
322K ALA* 1.3 74.6 - - - +
324K ALA* 1.3 54.5 + - - +
325K ALA 3.0 2.2 - - - -
326K ILE* 3.0 9.7 + - - +
327K PHE* 2.8 33.9 + - - +
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Residues in contact with ALA 324 (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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292K TYR* 3.9 19.9 + - + +
295K PHE* 3.1 36.3 - - + +
296K GLN* 3.2 19.2 - - - +
320K HIS 3.0 20.4 + - - +
323K ASN* 1.3 77.0 - - - +
325K ALA* 1.3 60.4 + - - +
327K PHE* 3.2 19.6 + - - +
328K ALA 3.3 5.5 + - - -
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Residues in contact with ALA 325 (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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295K PHE 4.2 0.4 + - - -
296K GLN* 4.3 12.2 - - - +
321K TYR* 3.2 30.1 + - + +
322K ALA* 3.5 9.9 - - - +
323K ASN 3.0 0.2 - - - -
324K ALA* 1.3 79.3 - - - +
326K ILE* 1.3 62.0 + - + +
328K ALA* 4.1 6.4 - - - +
329K ASP* 4.0 12.3 - - - +
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Residues in contact with ILE 326 (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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266K LYS* 3.9 21.8 - - - +
267K GLN* 3.7 28.5 - - - +
268K VAL* 3.5 24.5 - - + +
322K ALA 3.9 15.3 - - - +
323K ASN* 3.0 8.3 + - - +
325K ALA* 1.3 77.7 - - + +
327K PHE* 1.3 66.1 + - - +
328K ALA 3.1 2.9 - - - -
329K ASP* 3.0 21.7 + - + +
330K SER 3.5 4.5 + - - -
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Residues in contact with PHE 327 (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* 3.9 8.3 - - + +
273K VAL* 4.7 2.0 - - + -
289K LEU* 3.7 10.5 - - + -
292K TYR* 3.7 30.5 - + + -
293K LEU* 3.5 33.2 - - + -
323K ASN* 2.8 16.4 + - - +
324K ALA* 3.2 16.1 + - - +
326K ILE* 1.3 78.0 - - - +
328K ALA* 1.3 62.3 + - - +
330K SER* 3.1 17.5 - - - -
333K GLN* 3.3 42.0 - - + +
336K ILE* 3.5 43.3 - - + -
337K CYS* 3.5 15.9 - - - -
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Residues in contact with ALA 328 (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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270J TRP* 5.3 0.7 - - - +
271J LYS* 3.9 28.2 + - + +
274J THR* 5.9 0.2 - - - -
296K GLN* 3.2 46.9 + - + +
324K ALA 3.3 3.0 + - - -
325K ALA 4.1 6.7 - - - +
326K ILE 3.1 0.2 - - - -
327K PHE* 1.3 79.8 - - - +
329K ASP* 1.3 67.5 + - - +
330K SER 3.3 3.5 + - - +
333K GLN* 3.0 18.6 - - - +
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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
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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