Contacts of the helix formed by residues 215 - 226 (chain D) in PDB entry 4N36
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 215 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B THR* 6.5 0.2 - - + -
312B ASP* 2.7 38.1 + - + +
214D LYS* 1.3 78.5 - - - +
216D TRP* 1.3 59.3 + - - +
217D TYR* 3.9 2.2 + - - +
218D SER* 3.2 16.8 + - - -
219D ALA* 2.8 27.0 + - - +
252D TRP* 3.6 0.4 - - - -
311D CYS 3.6 9.0 - - - -
312D ASP* 3.3 27.8 - - + +
313D ILE 3.4 8.3 - - - -
314D THR* 3.7 11.8 - - + +
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Residues in contact with TRP 216 (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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217B TYR* 3.4 38.1 - + - -
215D THR* 1.3 71.4 - - - +
217D TYR* 1.3 75.0 + + - +
219D ALA* 3.2 5.5 + - - +
220D GLU* 2.9 26.5 + - + -
230D LEU* 3.5 18.2 - - + +
252D TRP* 3.3 33.6 - + + +
253D ILE 2.8 25.6 + - - -
254D GLY 3.9 7.9 - - - -
255D LEU 3.4 10.7 + - - -
256D THR* 3.5 31.0 - - + -
267D VAL* 3.7 31.6 - - + -
295D CYS* 3.4 28.5 - - + -
311D CYS* 3.1 16.4 + - + +
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Residues in contact with TYR 217 (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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216B TRP* 3.4 34.7 - + - -
217B TYR* 3.4 43.2 - + + -
256B THR* 2.6 26.5 + - - +
295B CYS* 3.8 11.9 - - - -
311B CYS* 4.1 16.2 - - + -
312B ASP* 5.5 1.8 - - - +
215D THR* 3.3 3.4 + - - +
216D TRP* 1.3 88.7 - + - +
218D SER* 1.3 60.6 + - - +
220D GLU* 3.1 14.4 + - + +
221D GLN* 2.8 54.5 + - + +
311D CYS 4.6 1.2 + - - -
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Residues in contact with SER 218 (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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292B ASN* 5.4 4.5 + - - -
294B HIS* 6.0 3.1 - - - -
311B CYS* 4.6 9.7 + - - +
312B ASP* 2.7 28.7 + - - -
214D LYS* 3.6 22.1 - - - +
215D THR* 3.2 17.5 + - - -
217D TYR* 1.3 74.7 - - - +
219D ALA* 1.3 65.0 + - - +
221D GLN* 3.4 8.4 + - - +
222D PHE* 3.0 22.7 + - - +
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Residues in contact with ALA 219 (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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214D LYS* 3.8 11.1 - - + +
215D THR 2.8 14.5 + - - +
216D TRP* 3.2 12.3 - - - +
218D SER* 1.3 78.2 - - - +
220D GLU* 1.3 61.5 + - - +
222D PHE* 3.1 5.0 + - - +
223D CYS* 3.0 24.9 + - - -
230D LEU* 3.9 9.0 - - + -
252D TRP* 4.5 2.7 - - + -
317D PHE* 3.5 38.9 - - + -
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Residues in contact with GLU 220 (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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216D TRP* 2.9 17.2 + - + +
217D TYR* 3.1 26.7 + - + +
219D ALA* 1.3 76.5 - - - +
221D GLN* 1.3 58.4 + - - +
223D CYS* 3.2 2.1 + - - +
224D VAL* 2.9 37.3 + - + +
229D HIS* 2.6 33.1 + - - -
230D LEU* 2.9 44.1 + - + +
267D VAL* 3.6 26.5 - - + +
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Residues in contact with GLN 221 (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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256B THR* 3.4 6.0 + - - -
257B LYS* 3.1 35.9 + - - +
294B HIS* 3.3 43.9 - - + +
311B CYS* 4.5 2.2 - - - -
217D TYR* 2.8 56.6 + - + +
218D SER* 3.7 7.0 - - - +
219D ALA 3.2 0.2 - - - -
220D GLU* 1.3 78.0 - - - +
222D PHE* 1.3 63.7 + - - +
224D VAL* 3.3 13.1 + - - +
225D SER* 3.0 23.3 + - - -
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Residues in contact with PHE 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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294B HIS* 5.9 0.2 - - - -
208D TYR* 3.6 39.5 - + - -
212D ILE* 6.2 3.8 - - + -
214D LYS* 4.0 19.5 - - - -
218D SER 3.0 13.8 + - - +
219D ALA 3.1 8.5 + - - +
221D GLN* 1.3 75.3 - - - +
223D CYS* 1.3 62.9 + - - +
225D SER* 2.4 25.1 + - - -
226D ARG* 3.2 61.2 + - + +
317D PHE* 3.4 28.0 - + + -
319D CYS* 4.3 3.6 - - - -
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Residues in contact with CYS 223 (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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219D ALA 3.0 16.9 + - - -
220D GLU 3.2 7.6 + - - +
222D PHE* 1.3 75.7 - - - +
224D VAL* 1.3 57.1 + - - +
226D ARG* 2.9 14.1 + - - -
228D SER* 2.7 36.7 + - - +
229D HIS* 3.7 14.8 - - - -
230D LEU* 3.7 22.2 - - - +
317D PHE* 4.1 1.1 - - - -
319D CYS* 2.0 53.6 - - - -
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Residues in contact with VAL 224 (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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257B LYS* 4.3 7.2 - - + +
258B ALA* 3.8 11.0 - - - +
259B GLY* 3.4 33.4 - - - +
260B MET* 3.7 9.9 + - - -
220D GLU* 2.9 42.3 + - + +
221D GLN* 3.6 15.9 - - - +
223D CYS* 1.3 74.7 - - - +
225D SER* 1.3 58.6 + - - +
227D ASN* 2.9 19.8 + - - -
228D SER 3.3 11.7 - - - +
229D HIS* 4.2 9.0 - - + +
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Residues in contact with SER 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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259B GLY 4.9 1.3 - - - -
260B MET* 4.1 21.0 - - - +
294B HIS* 6.4 1.6 - - - -
221D GLN 3.0 12.4 + - - -
222D PHE* 2.4 25.1 + - - -
224D VAL* 1.3 77.5 - - - +
226D ARG* 1.3 83.9 + - - +
227D ASN 3.3 1.4 + - - -
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Residues in contact with ARG 226 (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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260B MET* 5.7 0.7 - - - -
199D TRP* 3.9 23.4 - - + +
208D TYR* 5.6 2.3 + - + -
222D PHE* 3.2 57.4 - - + +
223D CYS* 2.9 10.2 + - - +
225D SER* 1.3 102.7 + - - +
227D ASN* 1.3 70.3 + - - +
228D SER* 3.3 5.9 + - - +
319D CYS* 5.9 0.2 - - - -
321D ARG* 4.1 10.2 + - - -
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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