Contacts of the helix formed by residues 20 - 34 (chain 9) 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 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189 ASP* 5.4 1.8 + - - -
199 CYS* 1.3 78.4 - - - +
219 GLU* 1.3 69.6 + - - +
229 ALA* 3.8 21.4 + - - +
239 LEU* 3.0 35.4 + - + +
249 ILE* 3.0 10.4 + - - +
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Residues in contact with GLU 21 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209 GLU* 1.3 75.4 - - - +
229 ALA* 1.3 60.5 + - - +
249 ILE* 4.2 7.9 - - + +
259 GLU* 3.1 42.3 + - - +
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Residues in contact with ALA 22 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209 GLU* 3.1 21.0 + - + +
219 GLU* 1.3 79.5 - - - +
239 LEU* 1.3 63.6 + - + +
259 GLU* 3.8 10.1 + - - +
269 LYS* 3.4 19.6 + - - +
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Residues in contact with LEU 23 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189 ASP* 4.3 1.8 - - - +
199 CYS* 3.5 27.6 - - + -
209 GLU* 3.0 37.1 + - + +
229 ALA* 1.3 79.4 - - + +
249 ILE* 1.3 64.7 + - - +
269 LYS* 3.1 23.0 - - + +
279 LEU* 3.1 15.6 - - + +
579 LEU 3.9 17.7 - - - +
589 THR* 3.6 22.0 - - - +
599 SER* 3.4 27.1 - - - +
629 LEU* 5.4 4.2 - - + +
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Residues in contact with ILE 24 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59 ALA* 3.5 35.4 - - + +
89 LEU* 4.6 4.4 - - + +
99 ALA* 3.9 24.2 - - + +
129 LEU* 3.8 16.8 - - + -
199 CYS* 3.2 30.1 - - + +
209 GLU 3.0 14.9 + - - +
219 GLU* 4.2 6.5 - - + +
239 LEU* 1.3 75.0 - - - +
259 GLU* 1.3 61.6 + - + +
269 LYS 3.1 0.2 - - - -
279 LEU* 3.3 16.3 + - - +
289 VAL* 3.2 13.0 + - - +
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Residues in contact with GLU 25 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59 ALA* 4.4 13.9 - - + -
219 GLU* 3.1 32.2 + - - +
229 ALA* 4.1 8.0 - - - +
249 ILE* 1.3 74.4 - - - +
269 LYS* 1.3 62.9 + - - +
279 LEU 3.2 0.2 - - - -
289 VAL* 3.4 25.7 + - + +
299 GLU* 3.7 12.6 + - - +
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Residues in contact with LYS 26 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229 ALA 3.4 12.7 + - - +
239 LEU* 3.1 19.7 + - + +
259 GLU* 1.3 81.0 - - - +
279 LEU* 1.3 60.6 + - + +
299 GLU* 3.6 30.9 + - - +
309 LEU* 4.0 7.3 + - + +
599 SER* 4.8 13.2 - - - +
629 LEU* 3.2 35.3 + - + +
639 ASN* 3.4 28.3 + - - +
669 GLU* 3.1 26.4 + - - +
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Residues in contact with LEU 27 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89 LEU* 3.5 30.5 - - + -
129 LEU* 5.8 5.4 - - + -
199 CYS* 5.7 5.4 - - - -
239 LEU* 3.1 20.9 - - + +
249 ILE* 3.3 8.9 + - - +
259 GLU 3.2 0.2 - - - -
269 LYS* 1.3 78.2 - - + +
289 VAL* 1.3 65.2 + - - +
299 GLU 3.1 2.0 - - - -
309 LEU* 3.0 43.9 + - + +
319 CYS* 3.3 11.4 - - - -
419 MET* 4.6 8.0 - - + +
429 VAL* 6.5 0.2 - - - -
459 LEU* 4.1 13.0 - - + -
629 LEU* 3.6 38.4 - - + -
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Residues in contact with VAL 28 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29 SER* 4.0 12.3 - - - -
39 ALA* 3.6 29.6 - - + +
49 SER 4.4 2.7 - - - +
59 ALA* 3.6 26.9 - - + +
89 LEU* 4.8 3.6 - - + -
249 ILE 3.2 17.0 - - - +
259 GLU* 3.4 20.4 - - + +
269 LYS 3.3 0.4 - - - -
279 LEU* 1.3 79.1 - - - +
299 GLU* 1.3 61.9 + - + +
319 CYS* 3.3 15.0 + - - +
329 VAL* 3.2 18.4 - - + +
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Residues in contact with GLU 29 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259 GLU 3.7 13.0 - - - +
269 LYS* 3.6 32.0 - - - +
279 LEU 3.1 0.6 - - - -
289 VAL* 1.3 75.6 - - + +
309 LEU* 1.3 53.1 + - - +
319 CYS 3.1 0.4 - - - -
329 VAL* 3.0 7.5 + - - +
339 GLN* 2.8 49.1 + - + +
669 GLU* 5.4 6.3 - - - +
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Residues in contact with LEU 30 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269 LYS* 4.0 4.0 + - + +
279 LEU* 3.0 41.3 + - + +
299 GLU* 1.3 79.0 - - - +
319 CYS* 1.3 58.8 + - - +
329 VAL 3.2 0.2 - - - -
339 GLN* 4.0 1.6 - - - -
349 TYR* 3.5 50.1 + - + +
359 GLY 4.0 0.7 + - - -
369 GLN* 4.0 6.2 + - - +
419 MET* 3.4 27.6 - - + -
629 LEU 4.7 7.4 - - - +
659 PHE* 3.7 20.6 - - + -
669 GLU* 3.5 38.4 - - + +
709 LEU* 4.5 2.9 - - + -
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Residues in contact with CYS 31 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39 ALA* 3.6 24.2 - - + +
89 LEU* 3.6 23.3 - - - -
279 LEU 3.3 16.4 - - - -
289 VAL 3.3 7.8 + - - +
299 GLU 3.1 0.6 - - - -
309 LEU* 1.3 77.1 - - - +
329 VAL* 1.3 61.0 + - - +
359 GLY* 3.3 21.6 - - - -
369 GLN 3.2 25.1 - - - +
379 ASN* 5.2 0.7 - - - -
389 GLU* 4.4 8.7 - - - +
419 MET* 3.9 8.7 - - - -
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Residues in contact with VAL 32 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19 MET 4.7 8.7 - - - +
29 SER* 4.5 26.7 - - - +
39 ALA* 4.9 0.4 - - + -
289 VAL* 3.2 20.0 - - + +
299 GLU* 3.0 8.4 + - - +
319 CYS* 1.3 82.6 - - + +
339 GLN* 1.3 70.2 + - - +
349 TYR 3.4 1.6 - - - -
359 GLY* 4.2 2.0 - - - -
769 LYS* 3.9 12.0 + - - +
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Residues in contact with GLN 33 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299 GLU* 2.8 28.4 + - + +
309 LEU* 4.6 0.4 - - - -
329 VAL* 1.3 88.2 + - - +
349 TYR* 1.3 82.4 + - + +
669 GLU* 4.6 9.2 - - - +
749 LEU* 4.5 3.6 - - - +
769 LYS* 3.6 19.1 - - - +
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Residues in contact with TYR 34 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309 LEU* 3.5 40.2 + - + +
339 GLN* 1.3 88.9 - - + +
359 GLY* 1.3 62.5 + - - +
369 GLN* 3.4 20.8 + - + +
669 GLU* 3.8 31.6 + - - +
709 LEU* 3.5 51.1 + - + +
719 SER* 4.7 1.4 - - - -
739 ARG 5.2 0.4 - - - -
749 LEU* 3.5 37.4 - - + +
759 SER* 4.2 14.1 + - - +
769 LYS* 3.2 22.5 - - - +
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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