Contacts of the helix formed by residues 215 - 226 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A LYS* 1.3 79.9 - - - +
216A TRP* 1.3 66.6 + - - +
217A TYR* 3.9 2.7 + - - +
218A SER* 3.2 15.2 + - - -
219A ALA* 2.9 17.8 + - - +
311A CYS 3.6 7.9 - - - -
312A ASP* 3.3 28.7 - - + +
313A ILE 3.4 8.5 - - - -
314A THR* 3.7 12.1 - - + +
312C ASP* 2.7 42.8 + - + +
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Residues in contact with TRP 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A THR* 1.3 71.2 - - - +
217A TYR* 1.3 71.7 + + - +
219A ALA* 3.2 4.0 - - - +
220A GLU* 3.0 28.1 + - + -
230A LEU* 3.4 19.9 - - + +
252A TRP* 3.3 43.5 - + + +
253A ILE 2.8 22.2 + - - -
254A GLY 4.0 6.7 - - - -
255A LEU 3.4 9.3 + - - -
256A THR* 3.7 14.8 - - + -
267A VAL* 3.8 35.7 - - + -
295A CYS* 3.4 24.7 - - + -
311A CYS* 3.0 17.5 + - + +
217C TYR* 3.4 46.4 - + - -
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Residues in contact with TYR 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A THR* 3.2 4.2 + - - +
216A TRP* 1.3 87.8 - + - +
218A SER* 1.3 62.3 + - - +
220A GLU* 3.2 12.9 + - + +
221A GLN* 2.9 56.2 + - + +
311A CYS* 4.6 0.8 + - - +
216C TRP* 3.4 31.8 - + - -
217C TYR* 3.4 45.0 - + + -
256C THR* 2.7 34.6 + - - +
257C LYS 4.2 2.1 + - - -
295C CYS* 4.0 3.6 - - - -
311C CYS* 4.2 15.5 - - + -
312C ASP* 5.4 3.1 - - - +
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Residues in contact with SER 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LYS* 3.8 20.9 - - - +
215A THR* 3.2 16.8 + - - -
217A TYR* 1.3 77.0 - - - +
219A ALA* 1.3 63.3 + - - +
221A GLN* 3.3 12.9 + - - +
222A PHE* 3.0 22.3 + - - +
292C ASN* 5.6 2.1 + - - -
311C CYS* 4.7 8.1 - - - +
312C ASP* 2.8 26.8 + - - -
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Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LYS* 3.8 12.5 - - + +
215A THR 2.9 13.5 + - - +
216A TRP* 3.2 13.0 - - - +
218A SER* 1.3 76.3 - - - +
220A GLU* 1.3 62.7 + - - +
222A PHE* 3.0 6.1 + - - +
223A CYS* 2.9 26.5 + - - -
230A LEU* 4.1 6.3 - - + -
252A TRP* 4.6 3.1 - - + -
317A PHE* 3.5 37.4 - - + -
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Residues in contact with GLU 220 (chain A).
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* 3.0 23.1 + - + +
217A TYR* 3.2 22.0 + - + +
219A ALA* 1.3 75.1 - - - +
221A GLN* 1.3 58.6 + - - +
223A CYS* 3.1 2.2 + - - +
224A VAL* 2.8 38.7 + - + +
229A HIS* 2.7 29.4 + - - -
230A LEU* 2.9 42.6 + - + +
267A VAL* 3.4 30.3 - - + +
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Residues in contact with GLN 221 (chain A).
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* 2.9 40.7 + - + +
218A SER* 3.6 11.3 + - - +
220A GLU* 1.3 77.1 - - + +
222A PHE* 1.3 63.6 + - - +
224A VAL* 3.4 8.1 + - + +
225A SER* 2.9 23.7 + - - -
256C THR* 3.0 24.5 + - - -
257C LYS* 3.2 19.5 + - - +
294C HIS* 3.2 44.9 + - + +
311C CYS* 3.6 9.9 - - - +
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Residues in contact with PHE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A TRP* 6.0 0.9 - + - -
208A TYR* 3.8 36.3 - + - -
214A LYS* 4.0 20.9 - - - -
218A SER 3.0 13.5 + - - +
219A ALA 3.0 8.0 + - - +
221A GLN* 1.3 75.9 - - - +
223A CYS* 1.3 64.6 + - - +
225A SER* 2.5 26.0 + - - -
226A ARG* 3.1 54.7 + - + +
317A PHE* 3.6 24.9 - + + -
319A CYS* 4.2 4.0 - - - -
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Residues in contact with CYS 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ALA 2.9 17.5 + - - -
220A GLU 3.1 7.6 + - - +
222A PHE* 1.3 76.9 - - - +
224A VAL* 1.3 56.4 + - - +
226A ARG* 2.8 18.2 + - - -
228A SER* 2.7 32.0 + - - +
229A HIS* 3.7 15.9 - - - -
230A LEU* 3.7 23.6 - - - +
317A PHE* 4.0 1.3 - - - -
319A CYS* 2.0 52.7 - - - -
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Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLU* 2.8 46.2 + - + +
221A GLN* 3.8 8.1 - - + +
223A CYS* 1.3 72.0 - - - +
225A SER* 1.3 58.1 + - - +
227A ASN* 3.1 17.5 + - - +
228A SER 3.3 13.9 - - - +
229A HIS* 3.9 10.3 - - + +
258C ALA* 4.1 12.1 - - + -
259C GLY* 3.2 37.6 - - - +
260C MET* 4.2 1.0 + - - +
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Residues in contact with SER 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A GLN 2.9 13.8 + - - -
222A PHE* 2.5 25.5 + - - -
224A VAL* 1.3 76.2 - - - +
226A ARG* 1.3 82.6 + - - +
227A ASN 3.4 0.7 - - - -
259C GLY 3.8 14.1 + - - -
260C MET* 3.6 22.7 - - - +
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Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A TRP* 4.0 20.9 - - + -
222A PHE* 3.4 54.7 - - + +
223A CYS 2.8 7.9 + - - +
225A SER* 1.3 97.2 + - - +
227A ASN* 1.3 65.7 + - - +
228A SER* 3.2 5.5 + - - +
319A CYS* 6.0 0.2 - - - -
321A ARG* 3.0 27.8 + - - +
260C MET* 4.7 2.0 - - - -
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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