Contacts of the helix formed by residues 197 - 220 (chain A) in PDB entry 1Y5D
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 LEU 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A LYS* 1.3 86.8 - - + +
198A PHE* 1.3 58.4 + - - +
200A ALA* 3.0 11.9 + - - +
201A LEU* 3.0 39.1 + - + +
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Residues in contact with PHE 198 (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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162A ILE 4.1 15.5 - - - -
163A LEU* 4.3 13.9 - - + -
166A MET* 3.4 47.3 - - + -
196A LYS 3.4 3.0 - - - +
197A LEU* 1.3 76.8 - - - +
199A GLN* 1.3 61.5 + - + +
201A LEU* 3.2 22.4 + - + +
202A LYS* 2.8 71.9 + - + +
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Residues in contact with GLN 199 (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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196A LYS* 3.0 19.9 + - - +
198A PHE* 1.3 78.3 - - + +
200A ALA* 1.3 52.4 + - - +
202A LYS* 3.1 18.6 + - - +
203A LEU* 2.7 61.4 + - + +
258A THR* 4.7 16.4 - - - +
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Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LYS 3.4 4.9 + - - +
197A LEU* 3.0 14.4 + - - +
199A GLN* 1.3 75.3 - - - +
201A LEU* 1.3 58.2 + - + +
203A LEU* 4.2 8.7 - - - +
204A ASN* 2.8 49.0 + - - +
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 5.0 5.6 - - + -
197A LEU* 3.0 30.9 + - + +
198A PHE* 3.2 30.5 + - + +
200A ALA* 1.3 77.1 - - + +
202A LYS* 1.3 55.2 + - - +
205A LEU* 2.8 63.5 + - + +
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Residues in contact with LYS 202 (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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111A GLY 5.3 0.8 + - - -
112A PHE* 3.4 27.3 - - - -
115A THR* 4.0 29.6 - - + +
163A LEU* 3.6 35.0 - - + -
166A MET* 5.4 0.6 - - - +
198A PHE* 2.8 49.6 + - + +
199A GLN* 3.5 21.0 + - - +
201A LEU* 1.3 68.4 - - - +
203A LEU* 1.3 66.2 + - + +
206A PHE* 2.8 39.0 + - + +
207A GLY* 3.0 6.7 + - - -
255A TYR* 5.7 0.2 - - - -
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Residues in contact with LEU 203 (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 GLN* 2.7 55.7 + - + +
200A ALA* 3.7 7.6 - - - +
202A LYS* 1.3 74.1 - - + +
204A ASN* 1.3 62.2 + - - +
207A GLY* 3.2 3.9 - - - +
208A LEU* 3.0 33.0 + - - +
255A TYR* 3.1 36.3 - - + +
258A THR* 5.0 10.5 - - + -
259A ILE* 4.2 25.6 - - + -
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Residues in contact with ASN 204 (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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200A ALA* 2.8 32.3 + - - +
202A LYS 3.1 0.2 + - - -
203A LEU* 1.3 73.2 - - - +
205A LEU* 1.3 65.6 + - + +
206A PHE 3.0 8.5 + - - -
208A LEU* 3.0 33.8 + - + +
209A VAL* 2.8 36.1 + - + -
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Residues in contact with LEU 205 (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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162A ILE* 5.9 5.8 - - + -
163A LEU* 5.1 14.3 - - + +
201A LEU* 2.8 47.9 + - + +
204A ASN* 1.3 83.2 - - + +
206A PHE* 1.3 59.1 + - + +
209A VAL* 3.9 14.3 - - + +
210A LEU* 3.1 21.1 - - - +
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Residues in contact with PHE 206 (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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115A THR* 4.5 11.9 - - + -
118A TYR* 4.8 9.6 - + - -
119A SER* 3.0 53.4 - - - -
122A PHE* 4.6 11.6 - + - -
123A PHE* 5.4 1.3 - + + -
159A ALA* 4.8 14.1 - - + -
160A LEU* 4.8 3.4 - - + -
163A LEU* 3.4 33.0 - - + -
202A LYS* 2.8 23.9 + - + +
204A ASN 3.0 0.4 + - - -
205A LEU* 1.3 82.8 - - - +
207A GLY* 1.3 56.8 + - - -
208A LEU 3.6 1.1 - - - -
210A LEU* 3.4 53.3 - - + +
211A PRO* 3.8 1.6 - - - +
251A PHE* 6.3 3.8 - + - -
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Residues in contact with GLY 207 (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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202A LYS 3.0 11.0 + - - -
203A LEU* 3.2 11.4 - - - -
206A PHE* 1.3 75.7 - - - +
208A LEU* 1.3 67.3 + - - +
211A PRO* 3.1 18.1 - - - +
251A PHE* 5.3 9.6 - - - -
255A TYR* 4.4 18.2 - - - -
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Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 3.0 21.9 + - + +
204A ASN* 3.0 28.4 + - - +
207A GLY* 1.3 86.4 - - - +
209A VAL* 1.3 66.6 + - + +
210A LEU 3.5 0.4 - - - -
211A PRO* 3.3 2.7 - - - +
212A LEU* 3.0 46.1 + - + +
255A TYR* 3.4 21.8 - - + +
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Residues in contact with VAL 209 (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 ASN* 2.8 32.7 + - + +
205A LEU* 3.9 16.4 - - + +
208A LEU* 1.3 73.5 - - + +
210A LEU* 1.3 66.4 + - + +
212A LEU* 3.1 6.2 + - - +
213A LEU* 2.9 51.6 + - + +
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PHE* 3.7 29.8 - - + -
123A PHE* 4.8 8.5 - - + -
126A LEU* 4.3 23.1 - - + +
159A ALA* 6.0 2.7 - - + -
205A LEU 3.1 27.8 - - - +
206A PHE* 3.4 42.6 + - + +
209A VAL* 1.3 86.2 - - + +
211A PRO* 1.3 58.7 - - + +
213A LEU* 3.3 11.4 + - + +
214A VAL* 3.0 32.7 + - - +
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Residues in contact with PRO 211 (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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122A PHE* 5.6 4.2 - - + -
206A PHE 3.8 1.8 - - - +
207A GLY* 3.1 30.7 - - - +
208A LEU* 3.3 17.0 - - - +
210A LEU* 1.3 89.6 - - + +
212A LEU* 1.3 56.9 + - + +
214A VAL* 3.1 9.0 + - + +
215A MET* 2.7 47.6 + - + +
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Residues in contact with LEU 212 (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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208A LEU* 3.0 42.8 + - + +
209A VAL* 3.4 7.0 - - - +
211A PRO* 1.3 77.3 - - + +
213A LEU* 1.3 61.8 + - + +
215A MET* 3.8 5.7 - - + +
216A ILE* 2.9 52.3 + - + +
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Residues in contact with LEU 213 (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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126A LEU* 6.2 3.8 - - + -
209A VAL* 2.9 43.1 + - + +
210A LEU* 3.4 15.0 - - + +
212A LEU* 1.3 79.0 - - + +
214A VAL* 1.3 58.6 + - + +
216A ILE* 3.8 5.2 - - + +
217A ILE* 2.9 50.1 + - + +
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Residues in contact with VAL 214 (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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122A PHE* 4.8 15.3 - - + -
126A LEU* 5.1 9.9 - - + -
129A ILE* 5.0 17.3 - - + -
210A LEU* 3.0 17.7 + - - +
211A PRO* 3.4 11.2 - - + +
213A LEU* 1.3 74.0 - - + +
215A MET* 1.3 62.5 + - - +
217A ILE* 3.4 8.8 + - + +
218A CYS* 3.0 30.1 + - + +
244A ILE* 3.8 44.0 - - + -
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Residues in contact with MET 215 (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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211A PRO* 2.7 31.9 + - + +
212A LEU* 3.8 6.3 - - + +
214A VAL* 1.3 80.2 - - - +
216A ILE* 1.3 63.0 + - + +
218A CYS* 3.2 13.6 + - + +
219A TYR* 3.1 20.8 + - - +
244A ILE* 5.1 10.1 - - - -
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Residues in contact with ILE 216 (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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212A LEU* 2.9 43.1 + - + +
213A LEU* 4.0 4.3 - - + +
215A MET* 1.3 73.9 - - + +
217A ILE* 1.3 65.0 + - + +
219A TYR* 3.1 26.1 + - + +
220A THR* 3.5 9.6 + - - +
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Residues in contact with ILE 217 (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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129A ILE* 5.6 13.7 - - + -
130A ASP* 5.4 7.4 - - - +
213A LEU* 2.9 39.4 + - + +
214A VAL* 3.7 7.4 - - + +
216A ILE* 1.3 73.7 - - + +
218A CYS* 1.3 62.3 + - - +
220A THR* 3.1 27.4 + - - +
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Residues in contact with CYS 218 (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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214A VAL* 3.0 14.8 + - + +
215A MET* 3.2 18.4 + - - +
217A ILE* 1.3 76.8 - - - +
219A TYR* 1.3 59.9 + - - +
220A THR 3.5 8.1 + - - +
241A ILE* 5.7 13.9 - - - -
244A ILE* 6.0 5.8 - - + -
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Residues in contact with TYR 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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215A MET 3.1 11.0 + - - +
216A ILE* 3.1 19.9 + - + +
218A CYS* 1.3 76.4 - - - +
220A THR* 1.3 63.4 + - - +
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Residues in contact with THR 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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216A ILE* 3.5 9.0 + - - +
217A ILE* 3.1 20.5 + - - +
218A CYS* 3.5 9.1 - - - +
219A TYR* 1.3 83.3 - - - +
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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