Contacts of the helix formed by residues 228 - 244 (chain I) in PDB entry 5DSV
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 PRO 228 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215I TRP* 3.4 20.0 - - + +
226I ILE* 3.5 11.4 - - + +
227I VAL* 1.4 90.6 - - + +
229I LYS* 1.3 59.7 + - - +
230I ASP* 3.4 18.4 - - - +
231I ILE* 3.1 24.3 + - + +
232I ARG* 3.3 7.8 + - - +
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Residues in contact with LYS 229 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60I GLU* 6.1 0.4 - - - -
228I PRO* 1.3 69.6 - - - +
230I ASP* 1.3 70.3 + - - +
231I ILE 3.1 1.3 - - - -
232I ARG* 3.9 27.9 - - - +
233I GLU* 3.0 54.8 + - + +
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Residues in contact with ASP 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228I PRO* 3.8 19.8 - - - +
229I LYS* 1.3 74.1 + - - +
231I ILE* 1.3 74.5 + - + +
233I GLU* 3.9 3.8 - - - +
234I GLU* 2.9 29.5 + - - +
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Residues in contact with ILE 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I ARG* 3.4 47.1 - - - +
190I VAL* 4.6 13.5 - - + -
215I TRP* 4.7 8.7 - - + -
227I VAL* 3.7 16.6 - - + -
228I PRO* 3.1 21.0 + - + +
230I ASP* 1.3 96.7 - - + +
232I ARG* 1.3 57.2 + - - +
234I GLU* 3.3 8.5 - - - +
235I ALA* 2.8 37.5 + - + +
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Residues in contact with ARG 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211I LEU 3.4 25.8 + - - -
212I GLU* 5.6 0.4 - - - +
213I LEU* 4.1 30.6 - - + +
226I ILE* 4.4 16.0 - - - +
227I VAL* 2.7 36.8 + - + +
228I PRO 3.3 4.6 + - - +
229I LYS* 3.9 36.4 - - - +
231I ILE* 1.3 74.8 - - - +
233I GLU* 1.3 61.3 + - + +
235I ALA 2.9 2.6 + - - -
236I GLU* 2.5 60.5 + - + +
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Residues in contact with GLU 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229I LYS* 3.0 47.5 + - + +
230I ASP* 3.9 3.0 + - - +
232I ARG* 1.3 81.1 - - + +
234I GLU* 1.3 57.4 + - - +
236I GLU* 3.5 14.8 - - - +
237I LYS* 2.9 30.1 + - - +
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Residues in contact with GLU 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I ARG* 3.9 22.3 + - - -
191I LYS* 3.6 28.8 + - - +
230I ASP 2.9 19.4 + - - +
231I ILE* 3.3 10.7 - - - +
233I GLU* 1.3 77.8 - - - +
235I ALA* 1.3 70.9 + - - +
237I LYS* 3.5 9.3 + - - +
238I TYR* 3.0 26.0 + - - +
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Residues in contact with ALA 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190I VAL* 4.1 14.1 - - + +
191I LYS* 3.9 28.7 - - + +
194I ALA* 4.1 8.9 - - + +
213I LEU* 5.2 0.9 - - + -
231I ILE* 2.8 23.8 + - + +
232I ARG* 2.9 3.3 + - - +
234I GLU* 1.3 77.3 + - - +
236I GLU* 1.3 59.7 + - - +
238I TYR* 3.3 10.9 + - - +
239I ALA* 3.0 28.6 + - - +
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Residues in contact with GLU 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194I ALA* 4.6 2.6 - - - +
198I TYR* 3.1 23.9 + - - +
209I PHE 5.7 0.3 - - - +
210I GLU* 5.8 1.2 - - - +
211I LEU* 3.9 33.9 + - + +
232I ARG* 2.5 47.0 + - + +
233I GLU* 3.5 13.4 - - - +
235I ALA* 1.3 69.3 - - - +
237I LYS* 1.3 66.1 + - - +
239I ALA* 3.2 9.0 + - - +
240I LYS* 3.0 40.9 + - - +
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Residues in contact with LYS 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233I GLU 2.9 18.5 + - - +
234I GLU* 3.5 9.6 - - - +
236I GLU* 1.3 76.8 - - - +
238I TYR* 1.3 61.9 + - - +
240I LYS* 3.1 16.0 + - + +
241I GLU* 3.0 47.6 + - + +
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Residues in contact with TYR 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191I LYS* 3.5 63.3 - - + -
192I GLU* 2.9 26.0 + - - -
195I LYS* 3.9 21.7 + - + +
234I GLU 3.0 14.6 + - - +
235I ALA 3.5 9.2 - - - +
237I LYS* 1.3 75.3 - - - +
239I ALA* 1.3 55.5 + - - +
241I GLU* 3.9 11.4 - - + +
242I SER* 2.6 51.2 + - - -
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Residues in contact with ALA 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194I ALA* 3.4 27.1 - - + +
195I LYS* 3.5 17.3 - - - +
198I TYR* 3.7 17.0 - - + +
235I ALA 3.0 10.9 + - - +
236I GLU 3.4 8.5 - - - +
237I LYS 3.2 0.2 - - - -
238I TYR* 1.3 78.5 - - - +
240I LYS* 1.3 66.1 + - - +
241I GLU 3.1 0.2 + - - -
242I SER* 3.4 5.3 + - - -
243I LEU* 2.9 26.1 + - - +
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Residues in contact with LYS 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198I TYR* 3.2 37.2 + - + -
236I GLU* 3.0 31.1 + - - +
237I LYS* 3.5 15.4 - - + +
239I ALA* 1.3 75.1 - - - +
241I GLU* 1.3 58.5 + - + +
243I LEU* 3.2 29.4 - - + +
244I LYS* 3.6 24.9 + - - +
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Residues in contact with GLU 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237I LYS* 3.0 51.5 + - + +
238I TYR* 3.9 9.5 - - + +
239I ALA 3.1 0.2 - - - -
240I LYS* 1.3 75.8 - - + +
242I SER* 1.3 60.2 + - - +
243I LEU 3.1 1.6 - - - -
244I LYS* 3.1 40.1 + - - +
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Residues in contact with SER 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195I LYS* 4.0 30.4 + - - +
238I TYR* 2.6 43.5 + - - -
239I ALA* 3.5 7.3 + - - -
241I GLU* 1.3 75.3 - - - +
243I LEU* 1.3 64.5 + - - +
244I LYS 4.2 4.0 - - - +
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Residues in contact with LEU 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195I LYS* 6.1 0.8 - - - +
198I TYR* 4.2 39.7 - - + +
199I ILE* 4.6 12.1 - - + +
203I GLU* 4.2 21.3 - - - +
239I ALA 2.9 13.8 + - - +
240I LYS* 3.2 24.0 - - + +
242I SER* 1.3 76.2 - - - +
244I LYS* 1.3 68.8 + - + +
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Residues in contact with LYS 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240I LYS* 3.6 24.2 + - - +
241I GLU* 3.1 27.1 + - - +
242I SER 4.2 4.4 - - - +
243I LEU* 1.3 87.9 - - + +
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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