Contacts of the helix formed by residues 201 - 215 (chain D) in PDB entry 5JLH
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 THR 201 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268B MET* 6.2 0.2 - - - +
269B GLU* 3.5 40.7 + - + +
270B SER* 4.7 4.7 + - - -
38D ARG* 4.8 5.2 - - - +
189D MET* 5.9 0.6 - - - +
199D PHE 3.6 1.1 + - - +
200D THR* 1.3 92.0 + - - +
202D THR* 1.3 71.4 + - - +
203D ALA* 3.2 10.5 - - + +
204D GLU* 3.0 20.4 + - - +
205D ARG* 2.8 30.1 + - - +
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Residues in contact with THR 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B GLU* 3.2 19.3 + - - -
65D THR* 4.1 2.3 + - - -
66D LEU* 3.5 50.2 + - + +
68D TYR* 5.8 5.2 - - + -
201D THR* 1.3 75.3 - - - +
203D ALA* 1.3 67.2 + - - +
205D ARG* 3.1 35.6 + - + +
206D GLU* 3.2 10.8 + - + +
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Residues in contact with ALA 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B GLU* 6.0 0.2 - - - +
61D ARG* 3.4 55.6 - - + +
62D GLY* 4.7 8.1 - - - +
64D LEU 5.2 3.6 + - - +
66D LEU* 4.6 3.7 - - - +
201D THR* 4.0 7.4 - - + +
202D THR* 1.3 82.3 - - - +
204D GLU* 1.3 65.6 + - - +
206D GLU* 3.1 14.2 + - - +
207D ILE* 3.5 3.6 + - - +
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Residues in contact with GLU 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D SER 4.6 2.1 - - - +
199D PHE* 3.4 38.0 - - + +
200D THR* 2.9 25.3 + - - -
201D THR* 3.0 33.8 + - - +
203D ALA* 1.3 74.6 - - + +
205D ARG* 1.3 61.8 + - - +
206D GLU 3.1 1.3 - - - -
207D ILE* 2.9 33.3 + - + +
208D VAL* 2.9 16.1 + - - +
241D LEU* 6.1 1.8 - - + -
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Residues in contact with ARG 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D TYR* 3.8 19.2 - - - -
182D ARG* 3.3 55.4 + - - +
185D THR* 3.9 14.8 - - + +
186D ASP* 3.3 34.5 + - - -
189D MET* 3.8 24.0 - - - -
199D PHE* 5.5 1.3 - - - -
201D THR 2.8 14.6 + - - +
202D THR* 3.1 27.1 - - + +
204D GLU* 1.3 77.2 - - - +
206D GLU* 1.3 59.7 + - + +
208D VAL* 2.9 26.5 - - - +
209D ARG* 2.9 11.3 + - - +
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Residues in contact with GLU 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PRO* 4.9 1.4 - - - +
33D ILE* 3.9 7.1 - - - +
58D GLN* 2.4 42.6 + - - +
61D ARG* 4.4 9.2 + - - +
66D LEU* 3.6 23.7 - - + +
68D TYR* 2.7 36.2 + - + +
202D THR* 4.1 9.4 - - + +
203D ALA 3.1 10.5 + - - +
204D GLU 3.1 0.6 - - - -
205D ARG* 1.3 81.2 - - + +
207D ILE* 1.3 65.1 + - - +
209D ARG* 3.2 21.9 + - - +
210D ASP* 3.0 21.0 + - - +
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Residues in contact with ILE 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ARG* 3.1 28.9 - - - +
199D PHE* 5.1 4.3 - - + -
203D ALA 3.5 1.3 + - - +
204D GLU* 2.9 29.9 + - + +
206D GLU* 1.3 76.0 - - - +
208D VAL* 1.3 62.6 + - - +
210D ASP* 3.0 18.5 + - + +
211D ILE* 3.0 16.6 + - + +
239D TYR* 4.4 18.1 + - + +
241D LEU* 4.2 28.5 - - + -
242D PRO* 3.7 29.6 - - + -
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Residues in contact with VAL 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D THR* 3.7 20.0 - - + +
188D LEU* 3.9 10.6 - - + +
189D MET* 4.3 20.0 - - + -
192D LEU* 4.1 15.9 - - + -
199D PHE* 3.3 38.6 - - + -
204D GLU 2.9 8.4 + - - +
205D ARG* 2.9 31.6 - - + +
207D ILE* 1.3 72.6 - - - +
209D ARG* 1.3 65.3 + - - +
211D ILE* 3.2 12.1 + - + +
212D LYS* 2.9 24.9 + - - +
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Residues in contact with ARG 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLY 6.2 0.2 - - - -
15D MET* 5.8 7.7 - - - +
31D PRO* 4.9 9.0 - - - +
58D GLN* 3.9 20.4 + - - +
68D TYR* 3.6 22.5 + - - -
156D ASP* 4.9 2.2 - - - -
185D THR* 4.1 21.1 - - + +
205D ARG 2.9 12.9 + - - +
206D GLU* 3.3 31.8 + - - +
208D VAL* 1.3 78.2 - - - +
210D ASP* 1.3 58.5 + - - +
212D LYS* 3.3 5.1 + - - +
213D GLU* 2.5 72.8 + - - +
401D ADP 3.7 27.7 + - - +
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Residues in contact with ASP 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D GLU 3.0 11.7 + - - +
207D ILE* 3.0 16.1 + - + +
209D ARG* 1.3 77.1 - - - +
211D ILE* 1.3 66.2 + - - +
213D GLU* 3.1 28.2 + - - +
214D LYS* 3.3 29.2 + - - +
239D TYR* 3.1 18.6 + - - +
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Residues in contact with ILE 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D LEU* 4.4 10.5 - - + -
192D LEU* 4.9 8.5 - - + -
199D PHE* 4.8 7.9 - - + -
207D ILE* 3.0 20.9 + - + +
208D VAL* 3.3 24.2 - - + +
210D ASP* 1.3 75.1 - - - +
212D LYS* 1.3 63.7 + - - +
214D LYS* 3.0 2.6 + - - -
215D LEU* 2.8 51.4 + - + +
216D CYS* 5.0 2.0 - - - -
239D TYR* 3.5 48.2 - - + -
241D LEU* 4.9 2.0 - - + -
247D ILE* 5.3 6.7 - - + -
249D ILE* 4.1 12.6 - - + -
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Residues in contact with LYS 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D ASP* 5.1 0.2 + - - -
181D GLY* 2.5 24.2 + - - -
184D LEU* 4.0 13.5 - - + -
185D THR* 2.5 34.8 + - - +
188D LEU* 3.8 7.6 - - + -
208D VAL 2.9 14.2 + - - +
209D ARG* 3.6 11.3 - - - +
211D ILE* 1.3 76.5 - - - +
213D GLU* 1.3 62.6 + - - +
214D LYS* 3.0 2.1 + - - -
216D CYS* 3.5 43.5 + - - +
256D CYS* 4.3 5.2 - - - -
305D TYR* 3.2 32.8 - - + +
401D ADP 2.6 31.2 + - - -
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Residues in contact with GLU 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D MET* 5.9 1.6 - - - +
209D ARG* 2.5 54.4 + - - +
210D ASP* 3.1 22.3 + - - +
212D LYS* 1.3 75.6 - - - +
214D LYS* 1.3 57.7 + - - +
335D LYS* 5.3 1.7 + - - -
401D ADP 2.9 79.7 + - + +
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Residues in contact with LYS 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D ASP* 3.3 32.8 + - - +
211D ILE* 3.0 4.8 + - - +
212D LYS 3.0 0.6 + - - -
213D GLU* 1.3 79.6 - - - +
215D LEU* 1.3 83.6 + - + +
216D CYS 3.3 10.3 + - - +
237D LYS* 5.8 0.7 + - - -
239D TYR* 3.4 35.3 + - - -
306D PRO* 5.2 6.1 - - - +
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Residues in contact with LEU 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D ILE* 2.8 23.3 + - + +
214D LYS* 1.3 91.7 - - + +
216D CYS* 1.3 53.7 + - - +
217D TYR* 4.0 1.7 - - - +
237D LYS* 3.8 36.7 + - + +
238D SER 5.1 3.1 - - - +
239D TYR* 3.7 35.9 - - + -
249D ILE* 3.5 36.8 - - + -
253D ARG* 2.7 35.2 + - + +
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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