Contacts of the helix formed by residues 201 - 220 (chain A) in PDB entry 3KDO
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 ARG 201 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A SER* 2.8 36.3 + - - +
197A PRO* 3.2 14.6 + - - +
198A TRP* 3.5 32.5 + - - +
200A ASN* 1.3 72.9 - - - +
202A PHE* 1.3 66.6 + - - +
203A GLU* 4.4 4.0 - - + +
204A GLU* 3.2 39.7 + - + +
205A ARG* 2.9 23.8 + - - +
98E GLU* 5.6 3.8 + - - -
131E LYS* 5.5 2.6 - - - +
97H GLU* 4.8 6.1 - - - +
98H GLU* 5.5 5.1 + - - +
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Residues in contact with PHE 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A THR 4.3 2.0 - - - +
196A SER* 2.9 27.1 + - - +
200A ASN 3.7 0.8 + - - -
201A ARG* 1.3 69.6 - - - +
203A GLU* 1.3 53.6 + - - +
205A ARG* 3.1 22.3 + - - +
206A ALA* 2.8 37.7 + - + +
226A TRP* 4.5 4.1 - + - -
228A ALA* 3.8 26.2 - - + -
229A ASN 3.3 36.1 - - - -
230A ILE* 3.9 8.3 - - + -
240A ARG* 3.5 50.7 - - + +
243A VAL* 4.0 20.2 - - + -
244A LEU* 3.9 10.8 - - + -
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Residues in contact with GLU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A SER* 4.8 0.2 + - - -
201A ARG* 3.3 4.3 - - + +
202A PHE* 1.3 82.8 - - - +
204A GLU* 1.3 59.5 + - + +
206A ALA* 3.3 7.9 + - - +
207A GLU* 2.9 37.7 + - + +
243A VAL* 4.7 15.5 - - + -
247A LEU* 5.0 0.2 - - - +
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Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PRO* 3.5 29.0 - - + +
198A TRP 5.2 2.3 - - - +
200A ASN* 4.9 0.3 + - - -
201A ARG* 3.2 36.6 + - + +
203A GLU* 1.3 79.0 - - + +
205A ARG* 1.3 62.8 + - - +
207A GLU* 3.6 7.7 + - - +
208A ILE* 3.2 32.2 + - + +
134E ARG* 5.3 6.8 + - - +
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Residues in contact with ARG 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PRO* 5.2 1.5 - - - +
173A PHE* 3.6 28.7 - - + -
190A ASP* 3.1 38.1 + - - -
194A LEU* 3.7 26.4 + - - +
195A THR* 2.7 25.5 + - - +
200A ASN* 2.6 61.4 + - - +
201A ARG 2.9 14.8 + - - +
202A PHE* 3.4 23.4 - - - +
204A GLU* 1.3 75.9 - - - +
206A ALA* 1.3 63.3 + - - +
208A ILE* 3.5 8.9 + - - +
209A MET* 3.1 24.3 + - - +
226A TRP* 3.7 10.5 - - + -
229A ASN 4.4 0.2 + - - -
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PHE* 2.8 18.2 + - + +
203A GLU 3.3 4.9 + - - +
205A ARG* 1.3 75.8 - - - +
207A GLU* 1.3 65.5 + - - +
209A MET* 3.4 0.9 + - - +
210A ALA* 3.0 27.7 + - - +
226A TRP* 3.6 23.1 - - + -
243A VAL* 3.8 17.0 - - + -
247A LEU* 3.4 20.4 - - + +
249A LEU* 4.1 4.5 - - + +
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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
----------------------------------------------------------
203A GLU* 2.9 31.7 + - + +
204A GLU* 3.8 8.3 - - - +
205A ARG 3.4 0.2 - - - -
206A ALA* 1.3 76.6 - - - +
208A ILE* 1.3 63.7 + - + +
210A ALA* 3.9 2.3 - - - +
211A LYS* 3.3 22.2 + - - +
247A LEU* 2.9 34.2 - - - +
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Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PRO* 3.3 41.5 - - + +
171A GLU* 4.5 1.1 - - - +
173A PHE* 4.6 8.5 - - + -
174A GLU* 3.5 44.4 - - + +
204A GLU* 3.2 19.2 + - + +
205A ARG* 3.8 6.5 - - - +
206A ALA 3.2 0.4 - - - -
207A GLU* 1.3 78.0 - - + +
209A MET* 1.3 59.7 + - - +
211A LYS* 3.2 8.5 + - - +
212A ILE* 2.8 38.8 + - + +
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Residues in contact with MET 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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173A PHE* 3.4 34.1 - - + -
177A ALA* 3.8 13.9 - - + -
181A LEU* 3.9 28.5 - - + -
188A MET* 3.9 9.0 - - + -
205A ARG 3.1 19.4 + - - +
206A ALA 3.4 0.9 + - - +
208A ILE* 1.3 80.3 - - - +
210A ALA* 1.3 57.2 + - - +
212A ILE* 4.0 3.8 - - + +
213A ILE* 2.8 44.4 + - + +
225A THR 4.6 1.1 - - - +
226A TRP* 3.5 52.9 - - + -
249A LEU* 4.9 0.9 - - + -
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Residues in contact with ALA 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 ALA 3.0 17.7 + - - +
207A GLU 3.9 3.6 - - - +
209A MET* 1.3 77.6 - - - +
211A LYS* 1.3 61.0 + - - +
213A ILE* 3.8 3.7 - - - +
214A ASP* 3.4 26.7 + - - +
247A LEU* 4.2 30.5 - - + +
249A LEU* 3.8 23.2 - - + +
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Residues in contact with LYS 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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174A GLU* 2.6 31.8 + - - +
207A GLU 3.3 14.0 + - - +
208A ILE* 3.2 7.5 + - - +
209A MET 3.2 0.2 - - - -
210A ALA* 1.3 79.1 - - - +
212A ILE* 1.3 69.5 + - + +
214A ASP* 3.7 6.8 + - - +
215A LYS* 3.2 29.2 + - + +
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLU* 3.0 49.6 - - + +
177A ALA* 3.9 9.9 - - + -
178A TYR* 4.1 24.0 - - + +
181A LEU* 4.3 14.4 - - + -
208A ILE* 2.8 29.5 + - + +
209A MET* 4.0 5.4 - - + +
211A LYS* 1.3 81.5 - - + +
213A ILE* 1.3 67.2 + - - +
215A LYS* 3.2 8.3 + - + +
216A VAL* 2.9 36.6 + - + +
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Residues in contact with ILE 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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181A LEU* 4.9 2.0 - - + -
209A MET* 2.8 40.3 + - + +
210A ALA* 3.8 4.9 - - - +
212A ILE* 1.3 76.9 - - - +
214A ASP* 1.3 68.0 + - - +
216A VAL* 3.1 4.4 + - - -
217A GLU* 2.8 55.2 + - + +
224A LYS* 3.8 17.3 - - + +
225A THR* 3.9 29.6 - - - +
226A TRP* 4.4 2.2 - - + +
249A LEU* 4.1 21.3 - - + -
250A LYS* 4.7 8.1 - - - +
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Residues in contact with ASP 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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210A ALA 3.4 16.8 + - - +
211A LYS* 3.9 7.5 - - - +
213A ILE* 1.3 83.8 - - - +
215A LYS* 1.3 51.1 - - - +
217A GLU* 4.2 8.1 - - - +
218A ASN* 2.8 41.2 + - - +
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Residues in contact with LYS 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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178A TYR* 3.3 42.4 - - + -
211A LYS* 3.2 20.5 + - + +
212A ILE* 3.4 13.7 - - + +
213A ILE 3.1 0.8 - - - -
214A ASP* 1.3 78.9 - - - +
216A VAL* 1.3 57.5 + - - +
218A ASN* 3.2 7.4 + - - +
219A GLU* 3.0 46.7 + - + +
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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
----------------------------------------------------------
178A TYR* 3.8 16.8 - - + +
181A LEU* 4.1 24.7 - - + +
182A SER* 3.6 19.5 - - - +
212A ILE* 2.9 28.3 + - + +
213A ILE* 3.8 2.0 - - - +
215A LYS* 1.3 70.3 - - - +
217A GLU* 1.3 55.5 + - - +
218A ASN 2.5 6.8 + - - -
219A GLU* 2.4 32.3 + - - +
220A THR* 2.8 35.9 + - + +
224A LYS* 4.1 20.6 - - + -
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Residues in contact with GLU 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 ILE* 2.8 36.6 + - + +
214A ASP* 4.2 9.3 - - - +
216A VAL* 1.3 72.1 - - - +
218A ASN* 1.3 57.8 + - - +
221A GLY* 3.1 26.0 + - - +
222A GLU 3.0 25.8 - - - +
223A LYS* 3.3 20.8 + - + +
224A LYS* 2.6 39.9 + - + +
250A LYS* 3.1 13.2 + - - -
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Residues in contact with ASN 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 ASP* 2.8 22.4 + - - +
215A LYS* 3.2 8.7 - - - +
216A VAL 2.5 5.3 + - - -
217A GLU* 1.3 76.9 - - - +
219A GLU* 1.3 59.2 + - + +
221A GLY* 4.5 1.4 + - - -
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Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A TYR* 2.3 36.0 + - - -
182A SER* 4.7 2.8 + - - -
215A LYS* 3.0 39.0 + - + +
216A VAL* 2.4 18.7 + - - +
218A ASN* 1.3 76.2 - - + +
220A THR* 1.3 63.7 + - + +
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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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181A LEU 5.3 0.9 - - - +
182A SER* 4.7 19.3 - - - +
216A VAL* 2.8 29.7 + - + +
219A GLU* 1.3 84.0 - - + +
221A GLY* 1.3 59.7 + - - +
222A GLU* 2.9 39.9 + - - +
224A LYS* 4.8 0.4 - - - -
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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