Contacts of the helix formed by residues 186 - 203 (chain A) in PDB entry 1YFL
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 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A LEU* 3.9 14.1 - - - +
185A TRP* 1.3 79.3 - - - +
187A GLU* 1.3 59.9 + - - +
188A ASP* 3.2 20.1 + - - +
189A GLU* 3.0 26.2 + - - +
190A GLU* 2.9 23.9 + - - +
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Residues in contact with GLU 187 (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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175A LEU* 4.0 22.8 - - + +
186A SER* 1.3 71.0 - - - +
188A ASP* 1.3 60.1 + - - +
189A GLU 2.9 2.0 - - - -
190A GLU* 2.9 9.1 + - + +
191A LYS* 2.7 37.1 + - - +
222A LEU* 5.7 7.0 - - + +
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Residues in contact with ASP 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A SER* 3.4 15.2 + - - +
187A GLU* 1.3 78.9 + - - +
189A GLU* 1.3 61.1 + - + +
191A LYS* 3.5 7.9 - - - +
192A ASP* 2.8 33.0 + - - +
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Residues in contact with GLU 189 (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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156A HIS* 2.9 28.5 + - - -
157A PHE* 3.5 20.6 - - - -
184A PHE 3.9 11.8 - - - +
185A TRP* 3.4 32.0 - - + -
186A SER* 3.0 28.5 + - - +
187A GLU 2.9 0.6 - - - -
188A ASP* 1.3 75.6 - - + +
190A GLU* 1.3 64.3 + - - +
191A LYS 3.0 1.6 - - - -
192A ASP* 3.3 10.7 + - - +
193A LEU* 3.0 25.6 + - - +
300A SFG 4.5 0.3 + - - -
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Residues in contact with GLU 190 (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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172A PRO* 5.4 0.3 - - - +
173A PRO 4.5 0.5 - - - +
175A LEU* 3.7 31.4 - - + +
185A TRP* 3.2 29.7 + - - -
186A SER 2.9 9.5 + - - +
187A GLU* 2.9 8.3 + - - +
189A GLU* 1.3 75.0 - - - +
191A LYS* 1.3 58.0 + - - +
193A LEU* 3.5 6.6 + - - +
194A LEU* 2.9 67.2 + - + +
209A LEU* 5.6 1.7 - - - +
211A ASN* 4.1 20.6 + - - -
220A ASN* 4.1 13.2 + - - +
222A LEU* 5.0 8.3 - - + -
223A LEU* 4.3 6.1 - - - +
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Residues in contact with LYS 191 (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 GLU 2.7 16.1 + - - +
188A ASP* 3.5 10.1 - - - +
189A GLU 3.0 0.6 - - - -
190A GLU* 1.3 73.7 - - - +
192A ASP* 1.3 58.1 + - - +
194A LEU* 2.8 9.7 + - - +
195A ASN* 2.7 48.4 + - - +
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Residues in contact with ASP 192 (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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156A HIS* 5.8 0.6 - - + -
157A PHE* 4.2 14.6 - - + -
158A LYS* 5.6 8.1 - - + +
188A ASP* 2.8 20.2 + - - +
189A GLU* 3.6 14.1 - - - +
191A LYS* 1.3 76.3 - - - +
193A LEU* 1.3 57.4 + - - +
195A ASN* 4.3 9.7 + - - +
196A LEU* 2.8 34.1 + - - +
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Residues in contact with LEU 193 (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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31A LEU* 4.6 3.1 - - + -
32A PHE* 4.2 19.5 - - + -
157A PHE* 3.8 22.6 - - + -
170A VAL* 3.9 15.3 - - + -
172A PRO* 3.5 32.1 - - + -
185A TRP* 3.8 13.7 - - + -
189A GLU 3.0 17.5 + - - +
190A GLU* 3.6 11.0 - - - +
192A ASP* 1.3 78.2 - - - +
194A LEU* 1.3 52.9 + - + +
196A LEU* 3.7 4.6 - - + +
197A LEU* 2.7 57.7 + - + +
209A LEU* 4.1 6.5 - - + -
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Residues in contact with LEU 194 (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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190A GLU* 2.9 54.7 + - + +
191A LYS* 2.8 7.6 + - - +
193A LEU* 1.3 76.6 - - + +
195A ASN* 1.3 65.8 + - - +
197A LEU* 3.3 10.7 + - + -
198A ASP* 3.0 16.1 + - - -
209A LEU* 5.1 7.6 - - + -
222A LEU* 4.5 7.0 - - + +
223A LEU* 4.3 17.7 - - + +
226A TRP* 3.3 70.5 + - + +
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Residues in contact with ASN 195 (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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191A LYS* 2.7 37.6 + - - +
192A ASP* 4.0 9.0 + - - +
194A LEU* 1.3 72.4 - - - +
196A LEU* 1.3 60.0 + - - +
198A ASP* 2.7 37.2 + - - +
199A SER* 3.1 7.3 + - - -
226A TRP* 5.5 2.1 + - - -
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Residues in contact with LEU 196 (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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31A LEU* 5.6 6.1 - - + -
157A PHE* 5.2 11.0 - - + +
158A LYS* 4.6 24.7 - - + +
162A ILE* 5.6 4.7 - - + -
192A ASP 2.8 21.0 + - - +
193A LEU* 4.5 10.3 - - + +
195A ASN* 1.3 71.0 - - - +
197A LEU* 1.3 72.0 + - + +
199A SER* 3.0 15.5 + - - -
200A LEU* 2.9 45.2 + - + +
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Residues in contact with LEU 197 (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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168A VAL* 5.9 0.2 - - + -
170A VAL* 4.4 13.9 - - + -
193A LEU* 2.7 40.7 + - + +
194A LEU* 3.4 11.0 - - + +
195A ASN 3.1 0.2 - - - -
196A LEU* 1.3 77.7 - - + +
198A ASP* 1.3 64.2 + - - +
200A LEU* 3.5 12.7 + - + +
201A ASN 3.4 3.6 + - - -
207A PHE* 2.9 62.9 - - + -
209A LEU* 3.7 35.4 - - + -
226A TRP* 3.8 23.3 - - + -
230A TYR* 4.4 0.2 - - - -
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Residues in contact with ASP 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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194A LEU 3.0 12.6 + - - +
195A ASN* 2.7 23.0 + - - +
197A LEU* 1.3 74.6 - - - +
199A SER* 1.3 54.0 + - - +
201A ASN* 2.5 35.2 + - - +
202A ASP* 3.1 12.8 - - - +
226A TRP* 3.5 8.7 + - - -
229A LYS* 2.5 35.5 + - - -
230A TYR* 2.4 30.5 + - - +
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Residues in contact with SER 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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195A ASN 3.4 9.7 + - - -
196A LEU* 3.2 18.9 - - - -
198A ASP* 1.3 78.0 - - - +
200A LEU* 1.3 64.4 + - - -
201A ASN 3.1 0.2 + - - -
202A ASP* 3.2 10.3 + - - +
203A ARG* 3.1 32.7 + - - +
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Residues in contact with LEU 200 (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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31A LEU* 6.0 3.6 - - + -
162A ILE* 3.8 32.8 - - + -
168A VAL* 4.5 18.6 - - + -
196A LEU* 2.9 36.0 + - + +
197A LEU* 3.7 20.0 - - + +
198A ASP 2.9 0.2 + - - -
199A SER* 1.3 77.4 - - - +
201A ASN* 1.3 59.1 + - - +
203A ARG* 3.4 32.9 + - - +
205A ILE* 2.8 51.7 + - + +
207A PHE* 4.5 4.9 - - + -
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Residues in contact with ASN 201 (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 3.4 4.3 + - - +
198A ASP 2.5 19.9 + - - +
200A LEU* 1.3 70.7 - - - +
202A ASP* 1.3 57.9 + - - +
203A ARG 3.1 1.6 - - - -
204A GLY* 2.7 26.6 + - - -
205A ILE 4.0 6.7 + - - +
206A LYS* 6.2 0.2 - - - +
230A TYR* 3.1 39.7 + - + +
259A ASN* 3.5 20.6 - - - +
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Residues in contact with ASP 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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198A ASP* 3.1 22.1 + - - +
199A SER* 3.2 10.5 + - - +
201A ASN* 1.3 74.7 - - - +
203A ARG* 1.3 58.8 + - + +
204A GLY* 2.9 9.0 + - - -
230A TYR* 5.2 0.5 + - - -
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Residues in contact with ARG 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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162A ILE* 3.0 28.7 + - - +
163A LEU* 4.4 0.2 - - - +
164A ASP* 3.2 39.5 + - - +
199A SER* 3.1 21.2 + - - +
200A LEU* 3.6 28.9 - - - +
201A ASN 3.1 1.0 - - - -
202A ASP* 1.3 75.6 - - + +
204A GLY* 1.3 61.8 + - - +
205A ILE* 3.1 26.8 + - + +
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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