Contacts of the helix formed by residues 206 - 224 (chain A) in PDB entry 1D0N
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 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ARG* 3.9 15.9 - - - +
204A LYS 3.8 1.4 + - - -
205A SER* 1.3 72.8 - - - +
207A ARG* 1.3 81.4 + - - +
208A PHE* 3.2 11.9 + - - +
209A GLU* 3.0 36.1 + - + +
210A ARG* 3.2 15.1 + - - +
669A ASP* 3.5 23.8 + - - +
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Residues in contact with ARG 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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205A SER 4.0 0.8 + - - -
206A ASN* 1.3 79.1 + - - +
208A PHE* 1.3 61.5 + - - +
210A ARG* 3.3 26.4 + - - +
211A LEU* 3.0 21.1 + - - +
235A GLU* 5.9 0.2 + - - -
744A ASP* 2.8 38.0 + - - +
746A LEU* 3.4 34.1 - - + +
747A ASP* 3.5 18.8 + - - -
750A LEU* 6.3 0.2 - - - +
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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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168A ARG* 3.5 67.8 - - + +
169A ARG* 4.3 3.6 - - - -
206A ASN* 3.2 5.2 + - - +
207A ARG* 1.3 78.5 - - - +
209A GLU* 1.3 62.7 + - - +
211A LEU* 3.1 26.1 + - + +
212A LYS* 3.1 39.9 + - + +
664A GLU 3.3 26.5 - - - -
665A ASP* 4.1 15.0 - - - -
666A LEU 4.8 1.1 - - - -
667A ALA* 4.2 26.5 - - + -
668A THR 5.6 0.2 - - - -
669A ASP* 5.0 1.3 - - - +
745A PRO* 6.1 2.5 - - + -
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Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A VAL* 5.5 1.7 - - - +
167A GLY 4.5 15.5 - - - +
168A ARG* 4.0 22.6 + - + +
186A GLY 3.7 9.9 - - - +
187A ASP* 5.5 2.2 - - - -
188A CYS* 4.4 7.5 - - - -
204A LYS 4.7 0.9 - - - +
205A SER* 3.7 7.4 - - - -
206A ASN* 3.0 35.2 + - - +
208A PHE* 1.3 79.5 - - - +
210A ARG* 1.3 57.8 + - + +
212A LYS* 3.2 10.1 + - - +
213A ALA* 2.9 26.5 + - - +
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Residues in contact with ARG 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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188A CYS* 3.9 10.5 - - - -
199A GLN* 3.6 2.6 + - - +
201A CYS* 3.6 23.3 - - - +
202A GLY 4.7 3.4 + - - -
203A SER 4.7 6.1 + - - -
205A SER* 2.6 47.5 + - - +
206A ASN 3.2 10.2 + - - +
207A ARG* 3.6 35.4 - - - +
209A GLU* 1.3 73.4 - - - +
211A LEU* 1.3 64.8 + - - +
213A ALA* 3.4 2.0 + - - +
214A THR* 2.8 29.5 + - - -
233A VAL* 6.3 2.0 - - + -
235A GLU* 3.6 35.7 + - - -
746A LEU* 4.0 21.3 - - + +
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Residues in contact with LEU 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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207A ARG 3.0 13.4 + - - +
208A PHE* 3.1 34.7 + - + +
210A ARG* 1.3 77.5 - - - +
212A LYS* 1.3 69.3 + - + +
214A THR* 3.2 18.2 + - - -
215A GLN* 3.5 14.4 + - + +
664A GLU* 5.0 5.6 - - + +
740A TYR* 4.6 7.2 - - - +
745A PRO* 3.8 33.7 - - + +
746A LEU* 3.9 13.6 - - + +
749A ALA* 3.4 31.2 - - + -
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Residues in contact with LYS 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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135A LYS 5.7 2.0 + - - -
165A VAL* 5.1 2.9 - - + -
167A GLY 4.5 9.0 - - - +
168A ARG 3.6 23.8 - - - +
169A ARG 5.2 3.8 + - - -
171A VAL* 3.7 32.0 - - + +
208A PHE* 3.1 36.3 + - + +
209A GLU* 3.4 9.4 - - - +
211A LEU* 1.3 81.3 - - + +
213A ALA* 1.3 65.9 + - - +
215A GLN* 3.0 40.6 + - - +
216A VAL* 3.6 10.0 + - - +
664A GLU* 4.9 8.7 + - - +
665A ASP* 3.4 21.6 + - - -
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Residues in contact with ALA 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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165A VAL* 4.2 22.3 - - + +
188A CYS* 3.7 29.8 - - + -
190A ILE* 4.1 1.8 - - + +
199A GLN* 3.4 18.0 - - + +
209A GLU 2.9 12.9 + - - +
210A ARG 3.6 8.1 - - - +
211A LEU 3.3 0.2 - - - -
212A LYS* 1.3 75.4 - - - +
214A THR* 1.3 62.3 + - - +
216A VAL* 3.1 16.3 + - - +
217A SER* 3.2 11.3 + - - -
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Residues in contact with THR 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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199A GLN* 3.1 21.5 + - - +
210A ARG 2.8 18.1 + - - -
211A LEU* 3.2 15.0 - - - -
213A ALA* 1.3 78.4 - - - +
215A GLN* 1.3 56.2 + - + +
217A SER* 3.3 2.0 + - - -
218A LYS* 2.9 31.0 + - - +
233A VAL* 5.7 0.2 - - - +
746A LEU* 4.5 0.9 - - - +
749A ALA* 4.3 15.9 - - + +
750A LEU* 4.2 16.1 - - + +
753A LEU* 3.3 36.1 - - + -
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Residues in contact with GLN 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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135A LYS 4.8 9.2 - - - +
136A SER* 4.6 23.9 - - - +
171A VAL* 5.6 1.0 - - - +
211A LEU* 3.8 17.3 - - + +
212A LYS* 3.0 38.0 + - - +
214A THR* 1.3 77.4 - - + +
216A VAL* 1.3 57.3 + - - +
218A LYS* 3.8 12.0 - - + +
219A GLY* 2.9 24.3 + - - -
664A GLU* 6.0 5.1 - - - +
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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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136A SER* 4.4 6.1 - - - +
137A GLY* 5.7 0.4 - - - -
138A LEU 5.8 0.7 - - - +
139A LYS* 5.0 9.1 - - - -
163A LEU* 5.8 1.1 - - + -
165A VAL* 4.5 13.0 - - + -
171A VAL* 3.9 25.1 - - + -
173A ALA* 4.0 23.6 - - + -
190A ILE* 3.7 18.8 - - + -
212A LYS 3.9 11.9 - - - +
213A ALA 3.1 8.0 + - - +
215A GLN* 1.3 76.0 - - - +
217A SER* 1.3 59.0 + - - +
219A GLY* 3.2 2.0 + - - -
220A ILE* 3.0 43.0 + - + +
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Residues in contact with SER 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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190A ILE* 3.4 24.5 - - - +
197A ILE* 4.2 7.7 - - - +
199A GLN* 2.8 32.1 + - - +
213A ALA 3.2 1.2 + - - -
214A THR* 3.6 4.7 - - - -
216A VAL* 1.3 76.8 - - - +
218A LYS* 1.3 64.2 + - - +
220A ILE* 3.2 9.9 + - - +
221A ARG* 3.0 22.5 + - - +
231A VAL* 4.0 26.3 - - - +
753A LEU* 5.3 0.7 - - - -
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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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214A THR* 2.9 21.2 + - - +
215A GLN* 3.8 11.3 - - + +
217A SER* 1.3 72.5 - - - +
219A GLY* 1.3 60.8 + - - +
221A ARG* 3.2 17.2 + - - +
222A ASP* 2.8 51.9 + - - +
749A ALA* 4.1 8.9 + - - +
752A GLU* 3.6 30.5 + - - +
753A LEU* 3.4 42.7 - - + +
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Residues in contact with GLY 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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136A SER* 6.0 3.6 - - - -
139A LYS* 5.5 2.7 - - - -
215A GLN 2.9 16.9 + - - -
216A VAL* 3.6 4.0 - - - -
217A SER 3.2 0.2 - - - -
218A LYS* 1.3 77.6 - - - +
220A ILE* 1.3 52.6 + - - +
222A ASP* 4.8 1.6 - - - -
223A ASN* 2.7 54.0 + - - +
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Residues in contact with ILE 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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139A LYS* 3.9 21.3 - - - +
161A ARG* 3.9 10.1 - - - +
163A LEU* 4.0 27.1 - - + -
190A ILE* 4.4 15.5 - - + -
192A ASP* 4.2 3.8 - - + +
197A ILE* 3.7 19.3 - - + -
216A VAL* 3.0 27.0 + - + +
217A SER* 3.6 7.6 - - - +
218A LYS 3.2 0.2 - - - -
219A GLY* 1.3 76.0 - - - +
221A ARG* 1.3 52.4 + - - +
224A GLU* 2.5 51.8 + - - +
225A ARG* 3.5 16.9 - - - +
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Residues in contact with ARG 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 ILE* 3.9 8.2 - - + +
217A SER 3.0 13.0 + - - +
218A LYS* 3.2 24.9 + - - +
220A ILE* 1.3 77.1 - - - +
222A ASP* 1.3 83.4 + - - +
224A GLU 2.6 15.6 - - - +
225A ARG* 3.5 6.3 - - - +
226A SER 3.3 0.9 + - - -
227A GLY* 2.6 35.8 + - - -
229A ALA* 3.5 32.1 - - + +
231A VAL* 4.0 16.3 - - + +
752A GLU* 4.2 6.7 + - - +
753A LEU* 3.9 34.4 + - - +
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Residues in contact with ASP 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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218A LYS* 2.8 31.9 + - - +
219A GLY* 4.2 1.8 - - - +
221A ARG* 1.3 112.0 + - - +
223A ASN* 1.3 67.3 + - - +
226A SER* 3.2 21.1 + - - -
227A GLY* 3.7 12.5 + - - +
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Residues in contact with ASN 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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57A ASN* 3.3 56.0 + - + +
58A LEU* 5.4 0.4 - - + -
136A SER* 5.5 7.1 + - - -
139A LYS* 6.3 0.4 - - - +
153A VAL* 4.9 1.4 - - - +
219A GLY* 2.7 37.6 + - - +
222A ASP* 1.3 76.7 - - - +
224A GLU* 1.3 64.2 + - + +
226A SER* 4.4 5.6 + - - -
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Residues in contact with GLU 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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58A LEU* 3.8 20.9 - - + +
61A ASP* 4.4 7.8 - - - +
139A LYS* 2.8 23.0 + - - +
141A LYS* 5.2 3.1 + - - -
153A VAL* 3.8 25.1 - - + +
161A ARG* 2.7 34.9 + - - -
220A ILE* 2.5 31.0 + - + +
221A ARG 2.6 8.7 - - - +
223A ASN* 1.3 75.8 - - + +
225A ARG* 1.3 71.4 + - - +
226A SER 2.6 18.2 + - - -
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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
------------------------------------------------------------
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