Contacts of the helix formed by residues 224 - 238 (chain A) in PDB entry 5EEA
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 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A PRO 4.0 1.4 + - - -
223A TYR* 1.3 73.4 - - - +
225A LYS* 1.3 65.1 + - - +
226A GLY* 3.4 1.7 + - - -
227A GLN* 2.7 40.3 + - - +
228A LEU* 2.8 22.7 + - - +
220B ARG 5.1 1.2 + - - -
221B ILE* 4.6 9.3 - - - +
222B PRO* 3.9 27.4 - - - -
13E A 3.8 11.9 + - - -
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Residues in contact with LYS 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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223A TYR 3.8 0.6 + - - -
224A SER* 1.3 72.7 - - - +
226A GLY* 1.3 58.3 + - - +
228A LEU* 3.8 9.6 - - - +
229A ARG* 2.9 50.9 + - - +
13E A 3.6 43.7 + - - +
14E C 4.0 22.8 + - - +
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Residues in contact with GLY 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A SER* 3.1 0.4 - - - -
225A LYS* 1.3 71.6 - - - +
227A GLN* 1.3 65.3 + - - +
229A ARG* 3.4 21.4 + - - +
230A GLU* 3.2 23.6 + - - +
219B LYS* 3.9 21.8 + - - -
13E A 2.6 24.3 + - - -
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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 TYR* 3.3 17.1 - - + -
224A SER* 2.7 43.5 + - - +
226A GLY* 1.3 73.0 - - - +
228A LEU* 1.3 67.5 + - - +
230A GLU* 3.3 4.3 + - - +
231A LEU* 3.1 27.7 + - - +
253A THR* 2.9 46.1 + - + +
254A SER 4.8 1.2 - - - -
255A LEU* 3.5 27.5 - - + +
219B LYS* 4.6 2.9 - - + +
221B ILE* 4.0 27.6 - - + +
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Residues in contact with LEU 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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223A TYR* 3.7 28.5 - - + +
224A SER 2.8 16.3 + - - +
225A LYS* 3.8 6.7 - - - +
227A GLN* 1.3 77.3 - - - +
229A ARG* 1.3 65.0 + - - +
231A LEU* 3.0 4.3 + - + -
232A GLU* 2.8 36.1 + - + +
263A TRP* 3.8 31.2 - - + +
8C T 5.6 1.6 - - - +
9C T 4.0 20.0 - - - +
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Residues in contact with ARG 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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225A LYS* 2.9 46.8 + - - +
226A GLY* 3.6 14.4 + - - +
228A LEU* 1.3 74.7 - - - +
230A GLU* 1.3 63.9 + - + +
232A GLU* 4.0 4.6 - - - +
233A ARG* 3.0 30.5 + - + +
219B LYS* 5.2 4.6 - - - +
12E A 5.4 0.6 - - - -
13E A 3.4 20.6 + - - -
10I A 5.4 12.3 - - - -
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Residues in contact with GLU 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 GLY 3.2 12.3 + - - +
227A GLN 3.6 7.6 - - - +
228A LEU 3.3 0.2 - - - -
229A ARG* 1.3 80.2 - - + +
231A LEU* 1.4 60.4 + - - +
233A ARG* 3.4 34.5 + - - +
234A GLU* 3.1 26.3 + - - +
249A ILE* 4.2 14.3 - - + +
252A ALA* 4.3 20.1 - - + +
253A THR* 3.9 21.5 - - + -
219B LYS* 5.0 8.2 + - - +
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Residues in contact with LEU 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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223A TYR* 4.0 17.5 - - + -
227A GLN 3.1 18.3 + - - +
228A LEU* 3.0 10.2 + - - +
230A GLU* 1.4 68.6 - - - +
232A GLU* 1.3 61.4 + - - +
234A GLU* 3.3 3.3 + - - +
235A TYR* 2.9 29.6 + - - +
249A ILE* 3.7 30.5 - - + -
253A THR* 5.0 0.7 - - + -
255A LEU* 3.7 23.3 - - + -
260A ILE* 4.2 15.5 - - + -
263A TRP* 3.6 46.7 - - + +
264A PHE* 4.2 12.0 - - + -
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Residues in contact with GLU 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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228A LEU* 2.8 28.2 + - + +
229A ARG* 4.0 4.9 - - - +
231A LEU* 1.3 77.7 - - - +
233A ARG* 1.3 56.4 + - - +
235A TYR* 3.3 7.0 + - - +
236A ALA* 3.0 29.3 + - - +
263A TRP* 3.4 18.8 - - + -
267A ARG* 3.2 38.3 + - - -
270A LYS* 5.0 6.2 + - - -
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Residues in contact with ARG 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 ARG* 3.0 29.0 + - + +
230A GLU* 3.4 33.9 + - - +
232A GLU* 1.3 73.0 - - - +
234A GLU* 1.3 85.3 + - - +
236A ALA* 3.6 7.2 + - - +
237A ALA* 3.2 21.0 + - - +
12H T 3.3 26.5 + - - -
13H G 2.8 35.8 + - - -
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Residues in contact with GLU 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 GLU* 3.1 12.2 + - - +
231A LEU 3.9 2.2 - - - +
233A ARG* 1.3 98.7 + - - +
235A TYR* 1.3 57.7 - - - +
237A ALA* 3.1 13.4 + - - +
238A ASN* 2.9 30.9 + - + +
241A ILE* 3.9 16.2 - - + -
245A LYS* 3.3 38.9 + - + +
249A ILE* 3.4 37.7 - - + +
264A PHE* 4.1 4.0 - - + -
14H G 5.3 2.4 + - - -
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Residues in contact with TYR 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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231A LEU 2.9 17.4 + - - +
232A GLU* 3.6 7.0 - - - +
234A GLU* 1.3 76.3 - - - +
236A ALA* 1.3 66.0 + - - +
238A ASN 3.2 22.9 - - - -
239A LYS* 3.5 42.9 + - + +
263A TRP* 3.9 10.1 - + + -
264A PHE* 4.0 15.8 - + + -
267A ARG* 3.4 51.1 - - + -
268A ARG* 3.6 29.0 - - + +
271A GLU* 3.1 34.4 + - - +
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Residues in contact with ALA 236 (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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232A GLU 3.0 17.2 + - - +
233A ARG* 3.9 7.4 - - - +
234A GLU 3.3 0.2 - - - -
235A TYR* 1.3 81.1 - - + +
237A ALA* 1.3 60.4 + - - +
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Residues in contact with ALA 237 (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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233A ARG 3.2 11.4 + - - +
234A GLU* 3.1 20.8 + - - +
236A ALA* 1.3 78.5 - - - +
238A ASN* 1.3 61.5 + - + +
245A LYS* 6.2 1.3 - - - -
14H G 5.2 9.2 - - - +
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Residues in contact with ASN 238 (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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234A GLU* 2.9 22.6 + - + +
235A TYR* 3.2 11.7 - - - +
237A ALA* 1.3 75.9 - - + +
239A LYS* 1.3 73.1 + - - +
240A PHE* 3.1 35.3 + - - +
241A ILE* 5.8 0.3 - - - +
242A THR* 4.8 12.7 - - - +
245A LYS* 6.0 8.0 - - + +
264A PHE* 3.6 7.8 - - - -
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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