Contacts of the helix formed by residues 218 - 229 (chain A) in PDB entry 4YC5
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 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A ARG* 3.4 20.7 - - - +
199A GLY* 3.0 27.5 + - - -
217A VAL* 1.3 77.7 - - - +
219A VAL* 1.3 65.4 + - - +
220A ASP* 4.0 10.5 - - + +
221A GLN* 2.7 24.9 + - + +
222A ALA* 2.9 19.6 + - - +
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Residues in contact with VAL 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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218A ASP* 1.3 72.7 - - - +
220A ASP* 1.3 70.8 + - - +
222A ALA* 3.2 8.3 + - + +
223A VAL* 3.0 33.8 + - + +
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Residues in contact with ASP 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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218A ASP* 3.2 7.4 - - + +
219A VAL* 1.3 83.9 - - - +
221A GLN* 1.3 59.5 + - + +
223A VAL* 3.5 8.7 + - - +
224A ALA* 3.0 26.2 + - - +
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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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197A LEU* 2.8 28.6 + - - +
198A ARG* 3.6 5.7 - - - -
199A GLY 3.9 0.4 - - - +
200A ALA* 3.7 22.5 + - - +
202A VAL* 5.4 1.8 - - - +
207A TRP* 3.9 26.7 - - + -
217A VAL* 3.2 19.0 - - + -
218A ASP* 2.7 48.5 + - + +
220A ASP* 1.3 77.6 - - + +
222A ALA* 1.3 59.6 + - - +
224A ALA* 3.1 7.7 + - - +
225A PHE* 2.8 28.6 + - - +
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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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217A VAL* 4.2 16.2 - - + +
218A ASP 2.9 13.2 + - - +
219A VAL* 3.2 11.9 + - + +
221A GLN* 1.3 76.3 - - - +
223A VAL* 1.3 63.9 + - + +
225A PHE* 3.2 10.9 + - - +
226A ALA* 3.1 20.4 + - - +
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Residues in contact with VAL 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 VAL* 3.0 29.5 + - + +
220A ASP* 3.7 10.5 - - - +
222A ALA* 1.3 76.3 - - + +
224A ALA* 1.3 58.7 + - - +
226A ALA* 3.1 8.0 + - - +
227A ALA* 2.9 27.2 + - + +
233A LEU* 3.7 37.8 - - + +
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Residues in contact with ALA 224 (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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204A PRO* 5.7 0.3 - - - +
207A TRP* 3.7 18.5 - - + +
220A ASP 3.0 15.2 + - - +
221A GLN* 3.1 11.2 + - - +
223A VAL* 1.3 76.5 - - - +
225A PHE* 1.3 57.4 + - - +
227A ALA* 3.7 8.1 - - - +
228A ALA* 2.8 31.4 + - - +
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Residues in contact with PHE 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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207A TRP* 3.5 57.8 - + + -
212A LEU* 3.9 16.4 - - + -
221A GLN 2.8 13.2 + - - +
222A ALA* 3.4 15.0 - - - +
224A ALA* 1.3 75.7 - - - +
226A ALA* 1.3 64.7 + - + +
228A ALA* 3.3 6.8 + - - +
229A HIS* 2.8 45.7 + + - -
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Residues in contact with ALA 226 (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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222A ALA 3.1 12.2 + - - +
223A VAL* 3.5 10.8 - - - +
225A PHE* 1.3 81.6 - - + +
227A ALA* 1.3 62.9 + - - +
229A HIS* 3.0 17.1 + - - +
231A LEU* 3.2 39.9 + - + +
233A LEU* 4.9 7.2 - - + -
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Residues in contact with ALA 227 (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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223A VAL* 2.9 17.4 + - + +
224A ALA* 3.7 9.4 - - - +
226A ALA* 1.3 76.4 - - - +
228A ALA* 1.3 57.9 + - - +
230A GLY* 2.9 20.6 + - - -
231A LEU 3.6 17.3 - - - +
233A LEU* 4.7 8.2 - - + +
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Residues in contact with ALA 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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204A PRO* 3.5 31.6 - - + +
207A TRP* 3.8 13.9 - - + -
208A ARG* 2.9 42.1 + - + +
224A ALA 2.8 18.8 + - - +
225A PHE 3.6 6.5 - - - +
226A ALA 3.2 0.2 - - - -
227A ALA* 1.3 75.5 - - - +
229A HIS* 1.3 60.2 + - - +
230A GLY 3.3 1.5 + - - -
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Residues in contact with HIS 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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207A TRP 3.2 32.0 + - - -
208A ARG* 4.4 12.5 - - + +
225A PHE* 2.8 50.1 + + - -
226A ALA* 3.0 10.6 + - - +
228A ALA* 1.3 77.6 - - - +
230A GLY* 1.3 59.1 + - - +
231A LEU* 3.4 17.9 + - + +
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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