Contacts of the helix formed by residues 215 - 226 (chain C) in PDB entry 4N32
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A ASP* 2.7 39.6 + - + +
214C LYS* 1.3 76.3 - - - +
216C TRP* 1.3 54.8 + - - +
217C TYR* 3.8 3.0 + - - +
218C SER* 3.1 18.1 + - - -
219C ALA* 2.7 31.4 + - - +
252C TRP* 3.5 0.2 - - - -
311C CYS 3.6 8.7 - - - -
312C ASP* 3.7 26.5 - - + +
313C LYS 3.3 8.3 - - - -
314C THR* 3.9 13.1 - - + +
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Residues in contact with TRP 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A TYR* 3.5 36.8 - + - -
215C THR* 1.3 73.7 - - - +
217C TYR* 1.3 75.8 + + - +
219C ALA* 3.3 2.9 + - - +
220C GLU* 2.9 26.0 + - + -
230C LEU* 3.5 17.5 - - + +
252C TRP* 3.2 41.1 - + + +
253C ILE 2.9 25.4 + - - -
254C GLY 3.9 7.2 - - - -
255C LEU 3.5 9.8 + - - -
256C THR* 3.6 29.8 - - + -
267C VAL* 3.7 32.5 - - + -
295C CYS* 3.4 21.5 - - + -
311C CYS* 3.1 17.2 + - + +
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Residues in contact with TYR 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A TRP* 3.3 32.6 - + - -
217A TYR* 3.4 43.0 - + + -
256A THR* 2.7 35.8 + - - +
295A CYS* 3.9 7.2 - - - -
311A CYS* 4.2 14.8 - - + -
312A ASP* 5.7 1.8 - - - +
215C THR* 3.3 3.7 + - - +
216C TRP* 1.3 89.8 - + - +
218C SER* 1.3 60.7 + - - +
220C GLU* 3.1 14.3 + - + +
221C GLN* 2.8 58.8 + - + +
311C CYS 4.6 1.2 + - - -
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Residues in contact with SER 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASN* 5.2 5.9 + - - -
294A HIS* 6.0 2.9 - - - -
311A CYS* 4.5 10.4 + - - +
312A ASP* 2.7 27.3 + - - -
214C LYS* 3.6 25.6 - - - +
215C THR* 3.1 18.3 + - - -
217C TYR* 1.3 78.0 - - - +
219C ALA* 1.3 56.6 + - - +
221C GLN* 3.3 9.3 + - - +
222C PHE* 3.0 22.9 + - - +
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Residues in contact with ALA 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C LYS* 3.7 11.3 - - + +
215C THR 2.7 22.8 + - - +
216C TRP* 3.3 9.0 - - - +
218C SER* 1.3 69.8 - - - +
220C GLU* 1.3 65.0 + - - +
222C PHE* 3.1 5.4 + - - +
223C CYS* 3.0 27.0 + - - -
230C LEU* 4.0 5.6 - - + -
252C TRP* 4.4 2.7 - - + -
317C PHE* 3.5 38.9 - - + -
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Residues in contact with GLU 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C TRP* 2.9 16.9 + - + +
217C TYR* 3.1 27.3 + - + +
219C ALA* 1.3 75.0 - - - +
221C GLN* 1.3 59.6 + - - +
223C CYS* 3.1 3.4 + - - +
224C VAL* 2.8 42.8 + - + +
229C HIS* 2.6 33.1 + - - -
230C LEU* 2.8 40.5 + - + +
267C VAL* 3.4 29.6 - - + +
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Residues in contact with GLN 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A THR* 4.0 5.2 - - - -
257A LYS* 3.0 36.2 + - - +
294A HIS* 3.4 38.9 - - + +
311A CYS* 4.8 2.0 - - - -
217C TYR* 2.8 57.4 + - + +
218C SER* 3.5 9.9 - - - +
219C ALA 3.2 0.2 - - - -
220C GLU* 1.3 77.9 - - - +
222C PHE* 1.3 62.2 + - - +
224C VAL* 3.4 12.8 + - - +
225C SER* 3.0 23.6 + - - -
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Residues in contact with PHE 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C TYR* 3.7 41.5 - + - -
212C ILE* 6.5 0.9 - - + -
214C LYS* 3.9 21.8 - - - -
218C SER 3.0 13.8 + - - +
219C ALA 3.1 8.7 + - - +
221C GLN* 1.3 74.5 - - - +
223C CYS* 1.3 65.6 + - - +
225C SER* 2.7 22.9 + - - -
226C ARG* 3.2 53.0 + - + +
317C PHE* 3.4 26.5 - + + -
319C CYS* 4.1 4.7 - - - -
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Residues in contact with CYS 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ALA 3.0 18.3 + - - -
220C GLU 3.1 6.9 + - - +
222C PHE* 1.3 76.2 - - - +
224C VAL* 1.3 58.8 + - - +
226C ARG* 2.9 14.3 + - - -
228C SER* 2.8 35.6 + - - +
229C HIS* 3.7 16.2 - - - -
230C LEU* 3.8 23.1 - - - +
317C PHE* 4.1 1.1 - - - -
319C CYS* 2.1 52.7 - - - -
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Residues in contact with VAL 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A LYS 4.7 3.4 - - - +
258A ALA* 4.0 11.0 - - + -
259A GLY* 3.3 40.4 - - - +
220C GLU* 2.8 44.3 + - + +
221C GLN* 3.7 13.9 - - - +
222C PHE 3.2 0.2 - - - -
223C CYS* 1.3 75.7 - - - +
225C SER* 1.3 56.6 + - - +
227C ASN* 3.0 19.9 + - - -
228C SER 3.4 11.7 - - - +
229C HIS* 4.2 9.2 - - + +
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Residues in contact with SER 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A GLY 4.3 9.6 - - - -
260A MET* 4.1 20.4 - - - +
262A GLY* 6.5 1.1 - - - -
221C GLN 3.0 13.4 + - - -
222C PHE* 2.7 22.7 + - - -
224C VAL* 1.3 76.4 - - - +
226C ARG* 1.3 86.5 + - - +
227C ASN 3.4 1.2 + - - -
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Residues in contact with ARG 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A MET* 4.7 0.7 - - - -
199C TRP* 4.0 20.2 - - + +
222C PHE* 3.2 53.3 + - + +
223C CYS* 2.9 11.0 + - - +
225C SER* 1.3 105.9 + - - +
227C ASN* 1.3 66.8 + - - +
228C SER* 3.4 3.0 + - - +
319C CYS* 5.8 0.2 - - - -
321C ARG* 2.8 29.2 + - - +
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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