Contacts of the helix formed by residues 20 - 34 (chain 3) 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 GLU 20 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183 ASP* 5.4 1.8 + - - -
193 CYS* 1.3 77.1 - - - +
213 GLU* 1.3 67.6 + - - +
223 ALA* 3.8 19.9 + - - +
233 LEU* 3.0 36.8 + - + +
243 ILE* 3.0 11.1 + - - +
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Residues in contact with GLU 21 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203 GLU* 1.3 74.8 - - - +
223 ALA* 1.3 60.5 + - - +
243 ILE* 4.2 8.5 - - + +
253 GLU* 3.1 41.7 + - - +
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Residues in contact with ALA 22 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203 GLU* 3.1 21.2 + - + +
213 GLU* 1.3 78.5 - - - +
233 LEU* 1.3 63.9 + - + +
253 GLU* 3.8 9.7 + - - +
263 LYS* 3.4 19.6 + - - +
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Residues in contact with LEU 23 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183 ASP* 4.3 2.2 - - - +
193 CYS* 3.5 28.9 - - + -
203 GLU* 3.0 38.4 + - + +
223 ALA* 1.3 78.7 - - + +
243 ILE* 1.3 63.4 + - - +
263 LYS* 3.1 22.2 - - + +
273 LEU* 3.1 15.3 - - + +
573 LEU 3.9 17.0 - - - +
583 THR* 3.6 23.6 - - - +
593 SER* 3.4 27.1 - - - +
623 LEU* 5.4 3.3 - - + +
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Residues in contact with ILE 24 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53 ALA* 3.5 35.9 - - + +
83 LEU* 4.6 4.9 - - + +
93 ALA* 3.9 23.8 - - + +
123 LEU* 3.8 17.3 - - + -
193 CYS* 3.2 30.7 - - + +
203 GLU 3.0 14.7 + - - +
213 GLU* 4.2 6.7 - - + +
233 LEU* 1.3 75.9 - - - +
253 GLU* 1.3 62.0 + - - +
263 LYS 3.1 0.7 - - - -
273 LEU* 3.3 16.7 + - - +
283 VAL* 3.3 12.9 + - - +
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Residues in contact with GLU 25 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53 ALA* 4.4 13.9 - - + -
213 GLU* 3.1 31.9 + - - +
223 ALA* 4.1 8.5 - - - +
243 ILE* 1.3 74.6 - - - +
263 LYS* 1.3 62.2 + - - +
273 LEU 3.2 0.2 - - - -
283 VAL* 3.4 23.8 + - + +
293 GLU* 3.7 13.0 + - - +
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Residues in contact with LYS 26 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223 ALA 3.4 12.3 + - - +
233 LEU* 3.1 19.7 + - + +
243 ILE 3.1 0.2 - - - -
253 GLU* 1.3 80.6 - - - +
273 LEU* 1.3 61.5 + - + +
293 GLU* 3.6 31.5 + - - +
303 LEU* 4.0 7.4 + - + +
593 SER* 4.8 12.8 - - - +
623 LEU* 3.2 35.9 + - + +
633 ASN* 3.4 28.1 + - - +
663 GLU* 3.1 25.5 + - - +
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Residues in contact with LEU 27 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83 LEU* 3.5 31.0 - - + -
123 LEU* 5.8 5.2 - - + -
193 CYS* 5.7 5.2 - - - -
233 LEU* 3.1 20.2 - - + +
243 ILE* 3.3 7.6 + - - +
253 GLU 3.2 0.4 - - - -
263 LYS* 1.3 77.6 - - + +
283 VAL* 1.3 65.6 + - - +
293 GLU 3.0 2.2 - - - -
303 LEU* 3.0 45.2 + - + +
313 CYS* 3.3 11.6 - - - -
413 MET* 4.6 7.8 - - + +
423 VAL* 6.5 0.2 - - - -
453 LEU* 4.1 13.0 - - + -
623 LEU* 3.6 39.5 - - + -
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Residues in contact with VAL 28 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23 SER* 4.0 12.1 - - - -
33 ALA* 3.6 31.0 - - + +
43 SER 4.4 2.0 - - - +
53 ALA* 3.6 26.9 - - + +
83 LEU* 4.8 4.3 - - + -
243 ILE 3.3 17.3 - - - +
253 GLU* 3.4 20.4 - - + +
263 LYS 3.3 0.2 - - - -
273 LEU* 1.3 78.1 - - - +
293 GLU* 1.3 60.8 + - + +
313 CYS* 3.3 15.0 + - - +
323 VAL* 3.2 18.6 - - + +
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Residues in contact with GLU 29 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253 GLU 3.7 13.0 - - - +
263 LYS* 3.6 31.6 + - - +
273 LEU 3.0 0.4 - - - -
283 VAL* 1.3 76.5 - - + +
303 LEU* 1.3 54.3 + - - +
313 CYS 3.1 0.7 - - - -
323 VAL* 3.0 7.6 + - - +
333 GLN* 2.8 49.3 + - + +
663 GLU* 5.4 6.0 - - - +
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Residues in contact with LEU 30 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263 LYS* 4.0 4.2 + - + +
273 LEU* 3.0 41.7 + - + +
293 GLU* 1.3 78.1 - - - +
313 CYS* 1.3 58.5 + - - +
323 VAL 3.2 0.2 - - - -
333 GLN* 4.0 1.6 - - - -
343 TYR* 3.5 48.4 + - + +
353 GLY 4.0 0.9 + - - -
363 GLN* 4.0 6.6 + - - +
413 MET* 3.4 28.3 - - + -
453 LEU* 5.0 0.2 - - + -
623 LEU 4.7 7.6 - - - +
653 PHE* 3.7 20.4 - - + -
663 GLU* 3.5 38.6 - - + +
703 LEU* 4.5 2.7 - - + -
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Residues in contact with CYS 31 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33 ALA* 3.5 25.1 - - + +
83 LEU* 3.6 22.9 - - - -
273 LEU 3.3 16.8 - - - -
283 VAL 3.3 8.3 + - - +
293 GLU 3.1 0.8 - - - -
303 LEU* 1.3 76.9 - - - +
323 VAL* 1.3 61.1 + - - +
353 GLY* 3.3 22.7 - - - -
363 GLN 3.2 24.2 - - - +
373 ASN* 5.2 0.7 - - - -
383 GLU* 4.5 7.9 - - - +
413 MET* 3.9 9.2 - - - -
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Residues in contact with VAL 32 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13 MET 4.7 8.1 - - - +
23 SER* 4.5 26.5 - - - +
33 ALA* 4.9 0.2 - - + -
283 VAL* 3.2 19.5 - - + +
293 GLU* 3.0 8.7 + - - +
313 CYS* 1.3 82.2 - - + +
333 GLN* 1.3 70.3 + - - +
343 TYR 3.4 1.8 - - - -
353 GLY* 4.2 1.6 - - - -
763 LYS* 3.9 12.4 + - - +
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Residues in contact with GLN 33 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293 GLU* 2.8 28.2 + - + +
303 LEU* 4.6 0.2 - - - -
323 VAL* 1.3 90.1 + - - +
343 TYR* 1.3 83.4 + - + +
663 GLU* 4.6 10.1 - - - +
743 LEU* 4.5 4.0 - - - +
763 LYS* 3.6 18.4 - - - +
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Residues in contact with TYR 34 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303 LEU* 3.5 40.9 + - + +
333 GLN* 1.3 88.7 - - + +
353 GLY* 1.3 62.8 + - - +
363 GLN* 3.4 20.9 + - + +
663 GLU* 3.8 31.3 + - - +
703 LEU* 3.5 46.5 + - + +
713 SER* 4.7 1.0 - - - -
733 ARG 5.2 0.4 - - - -
743 LEU* 3.5 42.9 - - + +
753 SER* 4.2 14.2 + - - +
763 LYS* 3.2 22.6 - - - +
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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