Contacts of the helix formed by residues 20 - 34 (chain 5) 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 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185 ASP* 5.4 1.8 + - - -
195 CYS* 1.3 78.0 - - - +
215 GLU* 1.3 67.9 + - - +
225 ALA* 3.8 20.3 + - - +
235 LEU* 3.0 36.6 + - + +
245 ILE* 3.0 11.3 + - - +
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Residues in contact with GLU 21 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205 GLU* 1.3 75.4 + - - +
225 ALA* 1.3 58.6 + - - +
245 ILE* 3.7 8.9 + - + +
255 GLU* 3.1 41.4 + - + +
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Residues in contact with ALA 22 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205 GLU* 3.1 21.0 + - + +
215 GLU* 1.3 79.8 - - - +
235 LEU* 1.3 64.0 + - + +
255 GLU* 3.8 9.3 + - - +
265 LYS* 3.4 19.4 + - - +
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Residues in contact with LEU 23 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185 ASP* 4.3 1.8 - - - +
195 CYS* 3.5 27.8 - - + -
205 GLU* 3.0 38.8 + - + +
225 ALA* 1.3 78.8 - - + +
245 ILE* 1.3 64.6 + - - +
265 LYS* 3.1 22.4 + - + +
275 LEU* 3.1 15.2 - - + +
575 LEU 4.0 17.0 - - - +
585 THR* 3.6 23.6 - - - +
595 SER* 3.4 26.9 - - - +
625 LEU* 5.6 2.7 - - + -
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Residues in contact with ILE 24 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55 ALA* 3.5 35.0 - - + +
85 LEU* 4.6 4.7 - - + +
95 ALA* 3.9 24.2 - - + +
125 LEU* 3.8 17.3 - - + -
195 CYS* 3.2 30.1 - - + +
205 GLU 3.0 15.6 + - - +
215 GLU* 4.2 7.0 - - + +
235 LEU* 1.3 75.7 - - - +
255 GLU* 1.3 61.3 + - - +
265 LYS 3.1 0.2 - - - -
275 LEU* 3.3 16.3 + - - +
285 VAL* 3.2 13.7 + - - +
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Residues in contact with GLU 25 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55 ALA* 4.4 13.9 - - + -
215 GLU* 3.1 32.6 + - - +
225 ALA* 4.1 8.7 - - - +
245 ILE* 1.3 74.8 - - - +
265 LYS* 1.3 63.4 + - - +
275 LEU 3.2 0.4 - - - -
285 VAL* 3.4 24.7 + - + +
295 GLU* 3.7 12.6 + - - +
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Residues in contact with LYS 26 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225 ALA 3.4 13.1 + - - +
235 LEU* 3.1 19.5 + - + +
245 ILE 3.1 0.6 - - - -
255 GLU* 1.3 81.7 - - - +
275 LEU* 1.3 59.8 + - + +
295 GLU* 3.6 30.8 + - - +
305 LEU* 4.0 7.3 + - + +
595 SER* 4.8 12.8 - - - +
625 LEU* 3.2 36.9 + - + +
635 ASN* 3.4 27.1 + - - +
665 GLU* 3.1 25.1 + - - +
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Residues in contact with LEU 27 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85 LEU* 3.6 34.0 - - + +
125 LEU* 5.8 4.7 - - + -
195 CYS* 5.7 5.2 - - - -
235 LEU* 3.1 20.2 - - + +
245 ILE* 3.3 7.8 + - - +
255 GLU 3.2 0.4 - - - -
265 LYS* 1.3 76.7 - - + +
285 VAL* 1.3 65.1 - - - +
295 GLU 3.0 2.0 - - - -
305 LEU* 3.0 45.4 + - + +
315 CYS* 3.3 11.8 - - - -
415 MET* 4.6 7.4 - - + -
425 VAL* 6.5 0.2 - - - -
455 LEU* 4.1 13.2 - - + -
625 LEU* 3.6 38.8 - - + -
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Residues in contact with VAL 28 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25 SER* 4.0 12.8 - - - -
35 ALA* 3.6 29.8 - - + +
45 SER 4.4 2.2 - - - +
55 ALA* 3.6 28.5 - - + +
85 LEU* 4.8 3.6 - - + -
245 ILE 3.2 17.3 - - - +
255 GLU* 3.4 20.0 - - + +
265 LYS 3.3 0.2 - - - -
275 LEU* 1.3 78.1 - - - +
295 GLU* 1.3 59.8 + - + +
315 CYS* 3.3 16.1 + - - +
325 VAL* 3.2 18.4 - - + +
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Residues in contact with GLU 29 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255 GLU 3.7 13.2 - - - +
265 LYS* 3.6 31.6 - - - +
275 LEU 3.0 0.2 - - - -
285 VAL* 1.3 77.9 - - + +
305 LEU* 1.3 54.6 + - - +
315 CYS 3.1 0.4 - - - -
325 VAL* 3.0 7.2 + - - +
335 GLN* 2.8 49.2 + - + +
665 GLU* 5.4 5.5 - - - +
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Residues in contact with LEU 30 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265 LYS* 4.0 3.8 + - + +
275 LEU* 3.0 41.7 + - + +
295 GLU* 1.3 78.2 - - - +
315 CYS* 1.3 60.1 + - - +
325 VAL 3.2 0.2 - - - -
335 GLN* 4.0 1.3 - - - -
345 TYR* 3.5 47.6 + - + +
355 GLY 4.0 1.0 + - - -
365 GLN* 4.0 6.8 + - - +
415 MET* 3.4 29.6 - - + -
625 LEU 4.7 7.6 - - - +
655 PHE* 3.7 20.9 - - + -
665 GLU* 3.5 37.9 - - + +
705 LEU* 4.5 2.9 - - + -
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Residues in contact with CYS 31 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35 ALA* 3.5 24.6 - - + +
85 LEU* 3.6 23.1 - - - -
275 LEU 3.3 16.4 - - - -
285 VAL 3.5 7.9 - - - +
295 GLU 3.1 0.6 - - - -
305 LEU* 1.3 77.1 - - - +
325 VAL* 1.3 60.3 + - - +
355 GLY* 3.3 21.7 - - - -
365 GLN 3.2 25.3 - - - +
375 ASN* 5.1 1.3 - - - -
385 GLU* 4.5 8.5 - - - +
415 MET* 3.9 8.5 - - - -
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Residues in contact with VAL 32 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15 MET 4.7 8.5 - - - +
25 SER* 4.5 26.9 - - - +
35 ALA* 4.9 0.4 - - + -
285 VAL* 3.2 19.7 - - + +
295 GLU* 3.0 7.7 + - - +
315 CYS* 1.3 82.2 - - + +
335 GLN* 1.3 71.8 + - - +
345 TYR 3.4 1.3 - - - -
355 GLY* 4.2 1.6 - - - -
765 LYS* 3.9 12.0 + - - +
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Residues in contact with GLN 33 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295 GLU* 2.8 28.9 + - + +
305 LEU* 4.6 0.4 - - - -
325 VAL* 1.3 89.2 + - - +
345 TYR* 1.3 84.2 + - + +
665 GLU* 4.6 9.0 - - - +
745 LEU* 4.5 4.3 - - - +
765 LYS* 3.6 17.9 - - - +
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Residues in contact with TYR 34 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305 LEU* 3.5 40.9 + - + +
335 GLN* 1.3 90.4 - - + +
355 GLY* 1.3 63.5 + - - +
365 GLN* 3.4 20.8 + - + +
665 GLU* 3.8 31.3 + - - +
705 LEU* 3.5 50.1 + - + +
715 SER* 4.4 1.4 + - - -
735 ARG 5.2 0.2 - - - -
745 LEU* 3.5 37.5 - - + +
755 SER* 4.2 14.6 + - - +
765 LYS* 3.2 22.2 - - - +
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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