Contacts of the helix formed by residues 223 - 235 (chain A) in PDB entry 2YYU
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 ASP 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A ALA* 4.1 1.2 - - - +
222A ALA* 1.3 81.7 - - + +
224A PRO* 1.3 67.0 - - - +
225A LEU* 3.8 8.1 + - - +
226A ARG* 3.2 40.9 + - + +
227A THR* 2.9 25.4 + - - +
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Residues in contact with PRO 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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22A PHE* 4.0 31.0 - - + +
25A PRO* 5.8 7.2 - - + -
26A PHE* 3.9 13.0 - - + -
218A LEU* 3.3 22.5 - - + +
219A THR 4.9 3.4 - - - +
221A ALA* 3.6 15.2 - - + +
222A ALA 3.7 4.3 - - - +
223A ASP* 1.3 85.3 - - - +
225A LEU* 1.3 57.6 + - - +
227A THR* 2.7 25.6 + - - -
228A TYR* 2.8 10.2 + - - +
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Residues in contact with LEU 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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25A PRO* 3.9 35.4 - - + +
26A PHE* 3.8 29.4 - - + -
29A THR* 4.9 9.2 - - + +
223A ASP* 3.4 6.5 - - - +
224A PRO* 1.3 78.4 - - - +
226A ARG* 1.3 62.5 + - - +
228A TYR* 3.1 15.3 + - + +
229A ALA* 3.2 12.1 + - - +
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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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223A ASP* 3.2 34.5 + - + +
224A PRO 3.2 0.6 - - - -
225A LEU* 1.3 77.0 - - - +
227A THR* 1.3 65.0 + - - +
229A ALA* 3.3 12.8 + - + +
230A ARG* 3.1 20.9 + - + +
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Residues in contact with THR 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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187A PHE* 3.6 28.5 - - + -
217A SER 3.6 13.9 - - - +
218A LEU* 3.5 19.1 - - + -
221A ALA* 3.2 16.7 - - - +
223A ASP* 2.9 15.2 + - - +
224A PRO 2.7 13.9 + - - -
226A ARG* 1.3 73.3 - - - +
228A TYR* 1.3 58.1 + - - +
230A ARG* 3.4 8.7 + - + +
231A LEU* 3.1 24.4 + - - +
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Residues in contact with TYR 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A THR* 4.6 14.2 + - - +
7A PHE* 3.6 29.1 + + + +
9A VAL* 4.3 9.0 - - + -
26A PHE* 3.8 25.1 - + + -
29A THR* 4.4 13.9 - - + -
30A PRO 4.9 1.7 + - - -
31A LEU* 3.7 29.1 - - + +
32A PHE 5.7 0.3 + - - -
218A LEU* 3.8 20.8 - - + +
224A PRO 2.8 7.6 + - - +
225A LEU* 3.3 12.1 - - + +
227A THR* 1.3 76.9 - - - +
229A ALA* 1.3 64.9 + - - +
231A LEU* 3.3 22.3 + - + +
232A GLN* 3.2 47.3 + - + +
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Residues in contact with ALA 229 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A LEU 3.2 9.0 + - - +
226A ARG* 3.5 16.4 - - + +
227A THR 3.3 0.4 - - - -
228A TYR* 1.3 80.9 - - - +
230A ARG* 1.3 59.7 + - - +
232A GLN* 3.4 16.8 + - - +
233A HIS* 3.2 37.6 + - + +
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Residues in contact with ARG 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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187A PHE* 3.5 47.4 - - + +
188A ALA* 4.5 6.1 - - - +
189A ASP* 3.4 30.7 + - - +
226A ARG 3.1 12.6 + - - +
227A THR* 3.7 11.2 - - - +
228A TYR 3.2 0.2 - - - -
229A ALA* 1.3 74.9 - - - +
231A LEU* 1.3 65.7 + - - +
233A HIS* 3.3 9.7 + - + +
234A GLU* 3.0 43.0 + - + +
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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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7A PHE* 3.5 46.9 - - + -
185A ILE* 5.2 4.3 - - + -
187A PHE* 4.2 14.8 - - + -
201A PRO* 3.5 34.0 - - + +
212A ILE* 4.2 5.4 - - + -
214A ILE* 4.3 23.8 - - + -
218A LEU* 5.3 1.8 - - + -
227A THR 3.1 14.5 + - - +
228A TYR* 3.4 24.0 - - + +
229A ALA 3.2 0.4 - - - -
230A ARG* 1.3 77.3 - - - +
232A GLN* 1.3 61.7 + - - +
234A GLU* 3.5 3.2 + - - +
235A TRP* 3.3 21.7 + - - +
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Residues in contact with GLN 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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7A PHE* 3.8 25.1 - - + -
228A TYR* 3.2 30.2 + - + +
229A ALA* 3.5 23.4 + - - +
230A ARG 3.3 0.2 - - - -
231A LEU* 1.3 76.5 - - - +
233A HIS* 1.3 65.8 + - + +
235A TRP* 2.8 29.9 + - - +
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Residues in contact with HIS 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 ALA* 3.2 24.2 + - + +
230A ARG* 3.7 10.9 - - + +
231A LEU 3.3 0.2 - - - -
232A GLN* 1.3 81.1 + - + +
234A GLU* 1.3 55.4 + - + +
235A TRP 2.8 6.0 + - - +
236A ASN* 2.5 34.8 + - - -
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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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187A PHE* 2.8 35.6 - - - -
188A ALA* 5.0 8.5 + - - +
200A THR* 5.5 5.7 - - - +
201A PRO* 3.5 21.1 - - + +
202A ARG* 2.9 39.8 - - + +
230A ARG* 3.0 40.6 + - + +
231A LEU 4.0 4.5 - - - +
233A HIS* 1.3 75.8 - - + +
235A TRP* 1.3 56.7 + - - +
236A ASN* 3.4 3.8 + - - +
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Residues in contact with TRP 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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6A PRO* 3.7 33.1 - - + +
7A PHE* 3.7 25.6 - + + -
201A PRO* 3.5 24.0 - - + -
202A ARG* 4.9 2.9 - - - +
205A ARG* 3.4 59.2 + - + +
209A SER 4.1 15.0 - - - -
210A ASP 4.9 1.6 - - - -
212A ILE* 3.6 29.6 - - + -
231A LEU 3.3 12.6 + - - +
232A GLN* 2.8 22.6 + - - +
233A HIS 2.8 1.6 - - - -
234A GLU* 1.3 73.9 - - - +
236A ASN* 1.3 61.8 + - - +
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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