Contacts of the helix formed by residues 218 - 234 (chain A) in PDB entry 1YQA
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 ASN 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A ALA* 3.4 2.9 - - + -
217A SER* 1.3 77.0 - - - +
219A PHE* 1.3 66.1 + - - +
221A TYR* 3.1 27.9 + - - +
222A LEU* 3.4 37.3 + - - +
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Residues in contact with PHE 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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180A TYR* 3.2 36.1 - + + +
183A MET* 5.3 0.9 - - + -
203A LYS* 4.3 4.5 - - + -
206A VAL* 3.3 26.2 - - + -
207A LYS* 3.4 29.2 - - + -
213A VAL* 3.3 38.1 - - + +
216A ALA* 3.2 27.3 + - + +
217A SER 3.1 0.2 - - - -
218A ASN* 1.3 78.3 - - - +
220A ASP* 1.3 62.1 + - - +
222A LEU* 2.9 5.8 + - - +
223A PHE* 2.6 67.9 + + + -
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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
----------------------------------------------------------
203A LYS* 2.7 46.2 + - - +
207A LYS* 3.4 24.3 + - - +
217A SER* 3.3 19.3 - - - +
218A ASN 3.2 0.8 + - - -
219A PHE* 1.3 79.1 - - - +
221A TYR* 1.3 61.1 + - - +
223A PHE* 3.2 19.5 - - - +
224A ASN* 3.3 9.0 + - - +
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Residues in contact with TYR 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 SER 4.7 0.2 + - - -
218A ASN* 3.1 20.4 + - - +
219A PHE 3.1 0.6 - - - -
220A ASP* 1.3 76.5 - - - +
222A LEU* 1.3 82.1 + - + +
224A ASN* 3.1 13.0 + - + +
225A SER* 3.0 29.3 + - - -
228A LYS* 5.5 6.4 + - - -
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Residues in contact with LEU 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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180A TYR* 3.4 38.8 - - + +
218A ASN* 3.5 34.8 - - - +
219A PHE* 2.9 8.6 + - - +
221A TYR* 1.3 91.3 - - + +
223A PHE* 1.3 53.3 + - - +
225A SER* 3.1 10.2 + - - -
226A ALA* 2.7 36.0 + - - +
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Residues in contact with PHE 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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180A TYR* 4.2 2.6 - - + -
184A ILE* 3.6 29.2 - - + -
199A ARG* 3.6 33.2 - - + -
202A LEU* 3.2 35.4 - - + -
203A LYS* 3.6 29.8 - - + -
206A VAL* 3.9 10.8 - - + -
219A PHE* 2.6 44.3 + + + +
220A ASP* 3.2 14.8 - - - +
222A LEU* 1.3 72.6 - - - +
224A ASN* 1.3 61.2 + - - +
226A ALA* 3.2 7.9 + - - +
227A ILE* 2.9 35.4 + - + +
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Residues in contact with ASN 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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199A ARG* 3.6 31.6 + - - +
220A ASP 3.3 7.5 + - - +
221A TYR* 3.1 16.9 + - + +
223A PHE* 1.3 80.5 - - + +
225A SER* 1.3 56.9 + - - +
227A ILE* 3.3 14.6 + - - +
228A LYS* 3.0 34.6 + - - +
242A PRO* 5.5 7.4 + - - +
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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 TYR* 3.0 25.7 + - - -
222A LEU* 3.1 15.9 + - - -
224A ASN* 1.3 74.9 - - - +
226A ALA* 1.3 64.2 + - - +
228A LYS* 3.3 18.3 + - - +
229A LYS* 3.0 23.2 + - - +
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Residues in contact with ALA 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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180A TYR* 3.8 35.2 - - + -
181A LYS* 4.2 5.1 - - + +
184A ILE* 4.3 8.5 - - + -
222A LEU 2.7 16.5 + - - +
223A PHE* 3.2 10.5 + - - +
225A SER* 1.3 74.2 - - - +
227A ILE* 1.3 56.8 + - - +
229A LYS* 3.1 8.7 + - - +
230A CYS* 2.8 33.8 + - - -
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Residues in contact with ILE 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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184A ILE* 3.8 12.8 - - + -
199A ARG* 5.0 5.6 - - + -
202A LEU* 4.5 0.9 - - + -
223A PHE* 2.9 47.8 + - + +
224A ASN* 3.6 12.6 - - - +
225A SER 3.3 0.2 - - - -
226A ALA* 1.3 71.5 - - - +
228A LYS* 1.3 61.0 + - - +
230A CYS* 2.9 9.3 + - - +
231A VAL* 2.9 45.5 + - + +
236A LEU* 3.9 15.9 - - + -
238A GLN* 4.6 7.4 - - + +
246A ILE* 3.8 34.3 - - + -
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Residues in contact with LYS 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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221A TYR* 5.5 7.1 + - - -
224A ASN* 3.0 22.4 + - - +
225A SER* 3.4 18.7 + - - +
227A ILE* 1.3 76.6 - - - +
229A LYS* 1.3 60.0 + - - +
231A VAL* 3.0 27.7 - - + +
232A GLU* 3.8 7.8 + - - +
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Residues in contact with LYS 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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181A LYS* 5.9 4.5 - - + -
225A SER 3.0 13.6 + - - +
226A ALA* 3.5 10.5 - - - +
227A ILE 3.1 0.2 - - - -
228A LYS* 1.3 74.6 - - + +
230A CYS* 1.3 65.1 - - - +
232A GLU* 2.7 41.9 + - - +
233A ASN* 2.9 34.9 + - - +
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Residues in contact with CYS 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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181A LYS* 3.5 39.0 - - - -
184A ILE* 5.0 0.7 - - - -
185A LEU* 5.1 0.2 - - - -
226A ALA* 2.8 28.1 + - - -
227A ILE 3.3 7.0 - - - +
229A LYS* 1.3 76.7 - - - +
231A VAL* 1.3 59.0 + - - +
233A ASN* 3.1 3.4 + - - +
234A GLY 2.8 24.9 + - - -
235A GLU* 2.8 17.7 + - + -
236A LEU* 3.4 40.6 + - + +
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Residues in contact with VAL 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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227A ILE* 2.9 23.4 + - + +
228A LYS* 3.0 31.6 - - + +
230A CYS* 1.3 76.0 - - - +
232A GLU* 1.3 62.6 + - + +
234A GLY* 3.3 11.1 + - - -
236A LEU 3.0 20.6 - - - +
237A VAL* 4.9 4.6 - - + +
238A GLN* 4.0 29.8 - - + +
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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 LYS 4.0 6.6 - - - +
229A LYS* 2.7 58.1 + - - +
231A VAL* 1.3 84.2 - - + +
233A ASN* 1.3 65.1 + - - +
234A GLY 3.5 0.3 + - - -
252A LYS* 5.6 1.2 - - - -
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Residues in contact with ASN 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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181A LYS* 5.0 8.6 - - - +
229A LYS* 2.9 41.8 + - - +
230A CYS* 3.1 5.5 + - - +
232A GLU* 1.3 87.7 - - - +
234A GLY* 1.3 61.6 + - - +
235A GLU* 3.4 23.3 + - + +
252A LYS* 3.1 31.5 + - - +
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Residues in contact with GLY 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 CYS 2.8 5.1 + - - -
231A VAL 3.3 7.6 + - - -
232A GLU 3.2 4.6 - - - -
233A ASN* 1.3 79.7 - - - +
235A GLU* 1.3 62.9 + - - +
236A LEU 3.6 3.1 - - - -
237A VAL* 5.3 1.3 - - - -
249A ASN* 3.4 18.2 - - - +
250A LYS* 3.4 17.7 + - - -
252A LYS* 3.7 20.1 - - - +
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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