Contacts of the helix formed by residues 204 - 223 (chain A) in PDB entry 6U17
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 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A ASP 3.9 1.2 + - - -
203A LEU* 1.3 73.6 - - - +
205A SER* 1.3 63.6 + - - +
206A LYS* 3.6 8.7 + - - +
207A GLU* 3.0 37.6 + - - +
208A PHE* 3.2 26.3 + - - -
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Residues in contact with SER 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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204A SER* 1.3 73.0 - - - +
206A LYS* 1.4 58.0 + - - +
208A PHE* 3.2 11.8 + - - +
209A ARG* 3.0 55.9 + - - +
237A ILE* 6.2 0.7 - - - -
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Residues in contact with LYS 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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204A SER* 3.4 7.5 + - - +
205A SER* 1.4 73.7 - - - +
207A GLU* 1.3 60.6 + - + +
209A ARG* 3.3 23.6 + - - +
210A GLU* 2.9 31.1 + - - +
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Residues in contact with GLU 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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193A VAL* 3.7 22.3 - - + +
195A ARG* 2.8 52.9 + - - +
203A LEU* 3.7 10.9 - - + +
204A SER* 3.0 38.1 + - - +
205A SER 3.3 0.2 - - - -
206A LYS* 1.3 76.9 - - + +
208A PHE* 1.3 57.0 + - - +
210A GLU* 3.5 16.0 + - - +
211A GLY 2.9 23.4 + - - -
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Residues in contact with PHE 208 (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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139A ILE* 3.8 9.2 - - + -
192A MET* 3.5 13.7 - - + +
193A VAL* 3.8 14.1 - - + -
200A SER* 4.2 9.2 - - - -
203A LEU* 3.6 46.7 - - + -
204A SER 3.2 20.8 + - - -
205A SER* 3.2 10.8 + - - +
207A GLU* 1.3 78.5 - - - +
209A ARG* 1.3 57.2 + - - +
211A GLY* 3.2 1.7 + - - -
212A GLY 2.8 24.4 + - - -
233A CYS* 5.0 8.5 - - + -
234A ILE* 3.7 29.2 - - + -
237A ILE* 3.5 39.5 - - + -
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Residues in contact with ARG 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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205A SER* 3.0 40.4 + - - +
206A LYS* 3.8 29.3 - - - +
208A PHE* 1.3 70.7 - - - +
210A GLU* 1.3 64.4 + - - +
213A ARG* 3.1 12.8 + - - +
237A ILE* 4.1 17.0 - - + -
241A GLU* 2.5 43.1 - - + +
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Residues in contact with GLU 210 (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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206A LYS 2.9 17.4 + - - +
207A GLU* 3.7 15.2 - - - +
209A ARG* 1.3 73.4 - - - +
211A GLY* 1.3 62.9 + - - +
213A ARG* 3.2 27.4 + - - +
214A ILE* 3.1 43.2 + - + +
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Residues in contact with GLY 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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192A MET* 3.0 30.6 - - - +
193A VAL* 4.8 1.6 - - - -
207A GLU 2.9 15.4 + - - -
208A PHE 3.2 4.2 + - - -
210A GLU* 1.3 78.1 - - - +
212A GLY* 1.3 50.1 - - - +
214A ILE* 3.3 10.9 + - - +
215A LEU* 2.8 35.9 + - - +
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Residues in contact with GLY 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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192A MET* 3.8 17.6 - - - +
208A PHE 2.8 15.0 + - - -
209A ARG 3.3 0.2 + - - -
210A GLU 3.3 0.6 - - - -
211A GLY* 1.3 72.1 - - - +
213A ARG* 1.4 56.4 + - - +
215A LEU* 3.3 3.1 + - - +
216A VAL* 2.9 31.7 + - - +
238A PHE* 4.0 8.6 - - - -
241A GLU* 3.3 22.0 - - - -
242A VAL* 5.2 1.1 - - - -
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Residues in contact with ARG 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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209A ARG 3.1 12.0 + - - +
210A GLU* 3.2 34.2 + - - +
212A GLY* 1.4 73.5 - - - +
214A ILE* 1.3 79.2 + - - +
216A VAL* 3.4 11.2 - - + +
217A GLN* 3.3 20.8 + - - +
241A GLU* 3.8 7.4 + - - +
242A VAL* 6.1 0.4 - - - -
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Residues in contact with ILE 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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192A MET 6.1 0.4 - - - +
210A GLU* 3.1 39.6 + - + +
211A GLY* 3.7 9.0 - - - +
213A ARG* 1.3 94.5 - - - +
215A LEU* 1.3 62.1 + - - +
217A GLN* 3.4 8.4 + - - +
218A LYS* 3.1 49.3 + - + +
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Residues in contact with LEU 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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137A ILE* 3.9 25.6 - - + -
190A THR* 3.8 29.4 - - + +
191A ASN 4.9 5.2 - - - +
192A MET* 3.8 27.1 - - - +
211A GLY 2.8 21.7 + - - +
212A GLY 3.6 3.8 - - - +
214A ILE* 1.3 72.9 - - - +
216A VAL* 1.3 68.3 + - - +
218A LYS* 3.1 12.3 + - + +
219A LEU* 3.0 39.7 + - + +
229A PHE* 3.9 9.4 - - + -
238A PHE* 3.8 18.4 - - + -
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Residues in contact with VAL 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 GLY 2.9 14.8 + - - +
213A ARG* 3.4 15.9 - - + +
215A LEU* 1.3 75.1 - - - +
217A GLN* 1.4 60.2 + - + +
219A LEU* 3.2 5.3 + - - +
220A GLN* 3.0 47.0 + - - +
238A PHE* 4.0 15.4 - - + -
242A VAL* 3.9 31.0 - - + -
259A ILE* 4.0 22.0 - - + -
260A PRO* 4.1 4.9 - - + -
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Residues in contact with GLN 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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213A ARG 3.3 12.9 + - - +
214A ILE* 3.5 11.4 - - - +
215A LEU 3.2 0.2 - - - -
216A VAL* 1.4 78.6 - - + +
218A LYS* 1.3 62.7 + - + +
220A GLN* 3.3 15.3 + - - +
221A LYS* 3.1 21.8 + - + +
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Residues in contact with LYS 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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126A ASP* 2.7 33.1 + - - +
128A LEU* 4.1 18.8 - - + -
190A THR* 3.8 12.0 + - + +
191A ASN 5.2 4.0 + - - -
214A ILE* 3.1 38.2 + - + +
215A LEU* 3.1 15.2 + - + +
217A GLN* 1.3 77.4 - - + +
219A LEU* 1.3 59.3 + - + +
221A LYS* 3.2 6.9 + - + +
222A TYR* 3.0 41.3 + - + +
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Residues in contact with LEU 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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128A LEU* 6.3 0.9 - - + -
135A VAL* 4.6 11.9 - - + -
137A ILE* 4.2 11.7 - - + -
190A THR* 5.6 0.9 - - + -
215A LEU* 3.0 40.7 + - + +
216A VAL* 3.8 4.0 - - - +
218A LYS* 1.3 76.7 - - + +
220A GLN* 1.3 57.3 + - - +
222A TYR* 5.3 0.4 - - + -
223A GLN* 2.8 32.1 + - - +
224A PRO* 3.9 29.3 - - + +
227A ALA* 3.9 21.3 - - + -
229A PHE* 5.0 0.4 - - + -
238A PHE* 4.5 5.8 - - + -
259A ILE* 3.7 39.9 - - + -
262A THR* 4.3 2.3 - - - +
264A THR* 4.4 2.1 + - + -
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Residues in contact with GLN 220 (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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216A VAL* 3.0 37.0 + - - +
217A GLN* 3.6 10.6 - - - +
218A LYS 3.2 0.2 - - - -
219A LEU* 1.3 75.7 - - - +
221A LYS* 1.3 58.4 + - - +
223A GLN* 3.0 24.9 + - - -
259A ILE* 4.1 5.4 - - + -
260A PRO* 2.9 40.3 + - - +
261A ASP* 4.4 7.1 - - + +
262A THR* 4.0 12.7 - - + +
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Residues in contact with LYS 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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130A PHE* 3.4 34.8 - - + -
217A GLN* 3.1 14.4 + - + +
218A LYS* 3.2 10.5 + - + +
220A GLN* 1.3 79.6 - - - +
222A TYR* 1.3 101.1 + - + +
223A GLN* 3.7 6.9 + - - -
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Residues in contact with TYR 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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128A LEU* 3.9 49.0 + - + +
129A THR* 3.4 36.4 - - - +
130A PHE* 3.8 45.2 - + - +
131A ASN 4.1 4.7 + - - -
132A LEU* 5.7 2.0 - - + +
135A VAL* 5.8 0.9 - - + -
218A LYS* 3.0 33.2 + - + +
219A LEU* 5.3 0.7 - - + -
221A LYS* 1.3 108.6 + - + +
223A GLN* 1.3 71.4 + - - +
224A PRO* 3.5 8.0 - - + +
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Residues in contact with GLN 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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131A ASN* 5.2 4.3 + - - -
132A LEU 4.6 0.9 - - - +
219A LEU 2.8 17.3 + - - +
220A GLN 3.0 24.9 + - - +
221A LYS 4.1 7.0 + - - +
222A TYR* 1.3 77.8 - - - +
224A PRO* 1.3 72.7 - - - +
225A ARG 3.8 0.3 + - - -
261A ASP 4.8 3.3 + - - +
262A THR* 3.8 28.9 - - + +
263A GLU 5.0 1.8 + - - +
264A THR* 3.7 6.7 - - - +
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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