Contacts of the helix formed by residues 221 - 236 (chain D) in PDB entry 5YL4
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 221 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219D THR 4.0 3.6 + - - +
220D PRO* 1.3 77.2 - - - +
222D TYR* 1.3 65.1 + - - +
223D GLY* 3.5 11.4 + - - -
224D ASP* 3.0 28.2 + - - +
225D LEU* 3.4 15.8 + - - +
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Residues in contact with TYR 222 (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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11D GLN* 4.6 13.2 - - - -
15D GLN* 5.4 7.6 - - - +
175D VAL* 3.7 20.3 + - + -
176D SER* 3.9 12.5 - - - -
221D THR* 1.3 74.2 - - - +
223D GLY* 1.3 57.2 + - - +
224D ASP 3.4 0.2 - - - -
225D LEU* 3.6 10.6 + - + +
226D ASN* 3.0 37.5 + - - +
501D GTP 3.2 79.8 + + - +
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Residues in contact with GLY 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LYS* 5.5 10.7 + - - -
221D THR* 3.2 9.4 + - - -
222D TYR* 1.3 77.4 - - - +
224D ASP* 1.3 61.9 + - - +
226D ASN* 3.7 6.4 + - - +
227D HIS* 3.3 20.1 + - - +
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Residues in contact with ASP 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D CYS* 3.7 24.8 - - - -
215D LEU* 5.4 1.6 - - + +
217D LEU* 3.4 31.6 - - + +
219D THR 4.8 0.3 - - - +
220D PRO* 3.4 11.1 - - + +
221D THR* 3.0 35.0 + - - +
223D GLY* 1.3 72.5 - - - +
225D LEU* 1.3 67.5 + - - +
227D HIS* 3.3 19.8 + - - +
228D LEU* 3.8 4.2 + - - +
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Residues in contact with LEU 225 (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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175D VAL* 3.7 35.7 - - + -
204D ASN* 3.9 16.4 - - - +
207D LEU* 3.5 40.3 - - + +
208D TYR* 3.8 8.1 - - + +
211D CYS* 3.9 9.4 - - - -
220D PRO* 4.3 11.0 - - + +
221D THR 3.4 14.7 + - - +
222D TYR* 3.9 13.0 - - + +
223D GLY 3.5 0.2 - - - -
224D ASP* 1.3 78.9 - - - +
226D ASN* 1.3 62.0 + - - +
228D LEU* 3.2 17.7 + - - +
229D VAL* 3.3 14.6 + - - +
501D GTP 4.0 14.6 - - - +
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Residues in contact with ASN 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D GLN* 4.2 19.2 + - - +
16D ILE* 3.6 16.3 - - + +
19D LYS* 4.1 26.2 - - + +
222D TYR* 3.0 18.0 + - - +
223D GLY* 4.1 4.4 - - - +
224D ASP 3.3 0.2 - - - -
225D LEU* 1.3 71.7 - - - +
227D HIS* 1.3 59.3 + - - +
228D LEU 3.1 2.0 - - - -
229D VAL* 3.7 7.1 - - + +
230D SER* 2.9 32.7 + - - -
501D GTP 2.6 48.6 + - - -
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Residues in contact with HIS 227 (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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19D LYS* 6.4 0.2 - - - -
215D LEU* 5.7 7.9 - - + -
223D GLY 3.3 12.0 + - - +
224D ASP* 3.3 14.0 + - - +
225D LEU 3.3 0.6 - - - -
226D ASN* 1.3 76.6 - - - +
228D LEU* 1.3 70.3 + - + +
230D SER* 3.3 16.5 + - - -
231D ALA* 3.4 15.6 + - + +
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Residues in contact with LEU 228 (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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207D LEU* 3.7 29.4 - - + +
210D ILE* 3.8 20.6 - - + -
211D CYS* 3.7 25.1 - - - -
215D LEU* 3.9 19.7 - - + -
224D ASP 4.1 5.6 - - - +
225D LEU 3.2 8.5 + - - +
226D ASN 3.1 0.4 - - - -
227D HIS* 1.3 84.5 - - + +
229D VAL* 1.3 59.4 + - - +
231D ALA* 3.2 7.8 + - + +
232D THR* 3.0 31.5 + - - -
270D PHE* 6.4 0.9 - - + -
273D LEU* 4.2 28.3 - - + -
300D MET* 4.4 8.7 - - + +
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Residues in contact with VAL 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ILE* 4.2 20.0 - - + -
202D ILE* 3.4 43.5 - - + -
207D LEU* 3.7 15.7 - - + -
225D LEU 3.3 15.5 + - - +
226D ASN* 3.3 10.0 + - - +
228D LEU* 1.3 75.4 - - - +
230D SER* 1.3 58.2 + - - +
232D THR* 3.2 6.5 + - - -
233D MET* 2.8 48.8 + - - +
300D MET* 5.8 0.4 - - - -
501D GTP 4.7 6.7 - - - +
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Residues in contact with SER 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LYS* 3.8 29.3 - - - +
20D PHE* 4.4 3.1 - - - +
23D VAL* 3.8 24.1 - - - +
226D ASN 2.9 19.3 + - - -
227D HIS* 3.3 11.6 + - - -
229D VAL* 1.3 77.2 - - - +
231D ALA* 1.3 59.1 + - - +
233D MET* 3.9 8.9 - - - +
234D SER* 2.9 31.4 + - - -
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Residues in contact with ALA 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D VAL* 6.0 1.1 - - - -
227D HIS* 3.4 14.3 + - + +
228D LEU* 3.2 11.8 + - + +
230D SER* 1.3 81.0 + - - +
232D THR* 1.3 60.8 + - - +
234D SER* 3.8 5.2 - - - -
235D GLY 3.2 12.3 + - - -
270D PHE* 3.2 48.0 - - + -
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Residues in contact with THR 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D PHE* 5.8 1.3 - - + -
200D TYR* 5.9 1.1 - - + -
202D ILE* 5.1 10.3 - - + -
228D LEU 3.0 13.2 + - - -
229D VAL* 3.4 11.2 - - - -
231D ALA* 1.3 73.2 - - - +
233D MET* 1.3 59.4 + - + +
235D GLY* 2.8 20.6 + - - -
236D VAL* 2.9 25.0 + - + +
268D PRO* 3.7 31.6 - - + -
269D GLY 5.0 3.6 - - - +
270D PHE* 4.3 10.3 - - - +
300D MET* 3.5 28.7 - - + +
366D THR* 4.2 3.5 - - + +
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Residues in contact with MET 233 (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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6D HIS* 5.0 1.1 - - + -
16D ILE* 4.0 22.7 - - - +
20D PHE* 3.5 40.0 - - + -
134D GLN* 5.3 0.7 - - - +
136D THR* 3.5 29.2 - - + -
167D PHE* 3.8 33.4 - - + -
202D ILE* 4.6 2.0 - - + -
229D VAL* 2.8 42.0 + - + +
230D SER* 3.9 5.2 - - - +
232D THR* 1.3 73.7 - - - +
234D SER* 1.3 61.3 + - - +
236D VAL* 3.9 8.2 - - - +
237D THR* 3.1 30.1 + - - +
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Residues in contact with SER 234 (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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20D PHE* 4.5 1.2 - - - -
23D VAL* 3.8 13.0 - - - +
24D ILE* 4.5 7.8 - - - +
27D GLU* 2.6 29.1 + - - -
230D SER 2.9 18.8 + - - -
231D ALA* 3.8 7.2 - - - -
233D MET* 1.3 76.1 - - - +
235D GLY* 1.3 59.5 + - - +
237D THR* 3.4 5.3 + - - -
238D THR* 2.9 8.7 + - - -
241D ARG* 2.7 33.3 + - - +
318D ARG* 3.4 6.4 + - - -
358D PRO* 5.3 1.5 - - - +
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Residues in contact with GLY 235 (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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231D ALA 3.2 6.8 + - - -
232D THR 2.8 14.1 + - - -
234D SER* 1.3 75.9 - - - +
236D VAL* 1.3 55.6 + - - -
237D THR 3.2 0.2 - - - -
238D THR* 3.0 28.2 + - - -
270D PHE* 4.9 0.9 - - - -
316D ILE* 3.5 12.6 - - - +
318D ARG* 4.7 6.5 - - - +
366D THR* 3.4 27.4 - - - -
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Residues in contact with VAL 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D PHE* 3.6 36.3 - - + -
200D TYR* 3.9 24.3 + - + +
232D THR* 2.9 23.2 + - + +
233D MET* 3.9 7.2 - - - +
235D GLY* 1.3 73.7 - - - +
237D THR* 1.3 59.8 + - + +
238D THR 3.5 0.4 - - - -
239D CYS* 5.0 3.3 + - - +
240D LEU* 4.5 8.8 - - - +
253D LEU* 5.5 3.8 - - - +
268D PRO* 5.4 0.9 - - + -
316D ILE* 4.3 12.0 - - - +
366D THR* 3.7 11.9 - - + -
367D PHE 5.2 1.6 - - - +
368D ILE* 3.6 34.1 - - + +
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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