Contacts of the helix formed by residues 221 - 235 (chain A) in PDB entry 1JYE
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 SER 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A ASP* 2.5 29.0 + - - -
220A TRP* 1.3 80.0 - - - +
222A ALA* 1.3 64.4 + - - +
223A MET* 3.7 8.1 + - - +
224A SER* 2.8 33.8 + - - -
225A GLY 3.2 4.3 + - - -
248A GLN* 4.8 3.1 - - - +
249A MET* 3.3 7.3 - - - +
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Residues in contact with ALA 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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220A TRP 4.1 0.2 + - - -
221A SER* 1.3 72.4 - - - +
223A MET* 1.3 63.2 + - - +
225A GLY 3.0 2.6 + - - -
226A PHE* 2.9 19.2 + - - +
248A GLN* 3.0 33.3 + - + +
251A LEU* 4.2 20.0 - - + -
252A GLY* 3.2 14.3 - - - +
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Residues in contact with MET 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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221A SER* 3.2 8.3 + - - +
222A ALA* 1.3 79.0 - - - +
224A SER* 1.3 56.3 + - - +
226A PHE* 3.2 26.8 + - - +
227A GLN* 2.9 56.1 + - - +
255A ARG* 4.3 13.9 - - - +
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Residues in contact with SER 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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185A LEU* 5.2 0.2 - - - -
218A GLY* 3.7 6.9 - - - -
219A ASP* 3.1 47.2 + - - -
221A SER* 2.8 23.2 + - - -
223A MET* 1.3 77.4 - - - +
225A GLY* 1.3 57.4 + - - +
227A GLN* 3.9 12.1 + - - -
228A GLN* 3.0 38.8 + - - +
249A MET* 3.6 8.3 - - - -
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Residues in contact with GLY 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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185A LEU* 3.7 16.9 - - - +
221A SER 3.2 2.4 + - - -
222A ALA 3.0 5.3 + - - -
224A SER* 1.3 83.7 + - - +
226A PHE* 1.3 59.2 + - - +
229A THR* 2.7 32.4 + - - -
249A MET* 3.4 23.3 - - - -
253A ALA 3.7 7.3 + - - -
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Residues in contact with PHE 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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222A ALA 2.9 11.9 + - - +
223A MET* 3.2 24.0 + - - +
225A GLY* 1.3 77.2 - - - +
227A GLN* 1.3 64.2 + - + +
230A MET* 2.9 56.7 + - + +
252A GLY* 3.3 15.6 - - - +
255A ARG* 3.6 40.4 - - - +
256A ALA* 3.6 34.7 - - - +
259A GLU* 3.5 25.6 - - - -
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Residues in contact with GLN 227 (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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223A MET* 2.9 45.5 + - + +
224A SER* 3.9 11.7 - - - +
226A PHE* 1.3 81.6 - - + +
228A GLN* 1.3 62.4 + - - +
230A MET* 3.3 4.1 + - - +
231A GLN* 2.9 45.5 + - + +
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Residues in contact with GLN 228 (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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185A LEU* 3.8 23.6 - - + -
216A ARG* 2.9 55.6 + - - +
217A GLU 3.5 26.7 + - - +
218A GLY* 4.5 1.8 - - - -
224A SER* 3.0 23.4 + - - +
225A GLY 4.3 0.9 - - - +
227A GLN* 1.3 80.3 + - - +
229A THR* 1.3 57.3 + - - +
231A GLN* 3.4 15.7 + - - +
232A MET* 3.0 22.7 + - - +
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Residues in contact with THR 229 (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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185A LEU* 4.2 4.0 - - - +
225A GLY 2.7 22.8 + - - -
228A GLN* 1.3 73.5 - - - +
230A MET* 1.3 61.2 + - - +
232A MET* 3.2 10.9 + - + +
233A LEU* 2.9 46.6 + - + +
242A MET* 3.5 30.3 - - + +
253A ALA* 3.3 24.8 - - - +
256A ALA* 3.6 21.1 - - + -
257A ILE* 4.2 3.6 - - + -
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Residues in contact with MET 230 (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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226A PHE* 2.9 51.0 + - + +
227A GLN* 3.7 5.4 - - - +
229A THR* 1.3 76.7 - - - +
231A GLN* 1.3 60.1 + - + +
233A LEU* 3.4 3.8 + - + +
234A ASN* 2.8 65.0 + - - +
256A ALA* 3.6 22.2 - - + +
259A GLU* 5.3 4.0 - - - -
260A SER* 3.5 27.1 - - - +
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Residues in contact with GLN 231 (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 ARG* 2.9 31.8 - - - +
227A GLN* 2.9 36.0 + - + +
228A GLN* 3.6 17.1 + - - +
230A MET* 1.3 78.2 - - + +
232A MET* 1.3 62.4 + - - +
234A ASN* 3.5 8.7 + - - +
235A GLU* 3.1 28.6 + - - +
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Residues in contact with MET 232 (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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183A ALA* 3.7 25.6 - - - -
214A ALA* 4.4 8.5 - - + -
216A ARG* 3.6 23.1 - - - +
228A GLN 3.0 14.7 + - - +
229A THR* 3.2 11.9 + - + +
231A GLN* 1.3 76.3 - - - +
233A LEU* 1.3 78.4 + - + +
235A GLU* 3.1 16.5 + - - +
237A ILE* 3.2 38.9 + - + +
239A PRO* 3.5 29.6 - - + -
242A MET* 3.9 27.4 - - + -
268A ILE* 5.6 0.4 - - + -
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Residues in contact with LEU 233 (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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229A THR* 2.9 36.6 + - + +
230A MET* 3.8 4.5 - - + +
232A MET* 1.3 88.4 - - + +
234A ASN* 1.3 58.8 + - - +
236A GLY* 3.0 19.8 + - - -
237A ILE 3.7 17.0 - - - +
238A VAL* 4.3 15.5 - - + +
256A ALA* 4.1 7.9 - - + +
257A ILE* 4.2 9.2 - - + -
260A SER* 3.4 33.4 - - - +
262A LEU* 4.7 5.6 - - + -
268A ILE* 4.1 19.7 - - + -
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Residues in contact with ASN 234 (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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230A MET* 2.8 58.3 + - - +
231A GLN* 3.9 8.3 - - - +
233A LEU* 1.3 73.6 - - - +
235A GLU* 1.3 59.8 + - - +
236A GLY 3.2 1.6 + - - -
260A SER* 5.5 0.2 + - - -
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Residues in contact with GLU 235 (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 ARG* 2.8 28.6 + - - +
231A GLN* 3.1 17.2 + - + +
232A MET* 3.1 12.3 + - - +
233A LEU 3.0 1.0 - - - -
234A ASN* 1.3 78.4 - - - +
236A GLY* 1.3 59.6 + - - +
237A ILE* 3.7 26.9 + - + +
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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