Contacts of the helix formed by residues 210 - 224 (chain Z) in PDB entry 1KD1
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 GLY 210 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1313A A 2.7 24.4 + - - -
1314A U 4.0 13.7 - - - -
1316A G 3.7 15.5 - - - -
209Z VAL* 1.3 73.8 - - - +
211Z ALA* 1.3 67.6 + - - -
212Z ARG 3.1 3.6 - - - -
213Z LYS 3.0 3.8 + - - -
214Z ARG* 2.8 22.4 + - - +
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Residues in contact with ALA 211 (chain Z).
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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1315A G 3.3 31.0 + - - +
1316A G 2.9 16.5 + - - +
100Z ARG* 5.3 0.5 + - - -
210Z GLY* 1.3 72.0 - - - -
212Z ARG* 1.3 63.3 + - - +
214Z ARG* 3.5 13.3 - - - +
215Z GLU* 3.0 25.8 + - - +
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Residues in contact with ARG 212 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A U 5.6 2.0 + - - -
313A U 5.6 1.4 + - - -
319A A 4.5 17.0 + - - -
320A G 3.1 52.1 + - - -
1313A A 6.0 0.2 - - - +
1314A U 4.7 12.9 + - - +
1315A G 3.1 90.9 + - + +
210Z GLY 3.0 0.8 + - - -
211Z ALA* 1.3 79.6 - - - +
213Z LYS* 1.3 61.2 + - - +
215Z GLU* 3.7 6.5 + - - +
216Z ARG* 3.7 41.5 + - - +
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Residues in contact with LYS 213 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1312A G 2.6 34.8 + - - +
1313A A 2.9 41.0 + - - +
188Z HIS 3.9 19.1 - - - +
189Z ASN* 4.5 5.8 - - + -
190Z VAL* 5.5 3.6 - - + +
209Z VAL* 3.6 8.7 - - + -
210Z GLY 3.0 2.2 + - - -
212Z ARG* 1.3 79.3 - - + +
214Z ARG* 1.3 66.6 + - - +
216Z ARG* 3.2 16.4 + - + +
217Z ILE* 3.0 36.8 + - + +
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Residues in contact with ARG 214 (chain Z).
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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1316A G 5.8 0.2 - - - -
1335A C 4.3 9.2 + - - -
100Z ARG* 5.3 0.2 - - - +
205Z ILE* 3.5 35.6 + - + +
206Z ALA 5.0 1.2 + - - -
207Z SER 6.0 0.2 - - - -
209Z VAL* 3.9 27.5 - - + +
210Z GLY 2.8 16.6 + - - +
211Z ALA* 3.5 13.9 - - - +
213Z LYS* 1.3 76.9 - - - +
215Z GLU* 1.3 54.5 + - - +
217Z ILE* 2.9 7.4 + - - +
218Z GLU* 2.6 50.6 + - - +
230Z ASN* 2.9 33.1 + - - +
231Z PRO 3.4 2.8 + - - -
232Z THR* 2.9 35.8 + - - +
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Residues in contact with GLU 215 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1315A G 3.4 26.5 + - - +
100Z ARG* 3.5 37.0 + - - +
211Z ALA 3.0 15.9 + - - +
212Z ARG 3.8 6.8 - - - +
213Z LYS 3.3 0.2 - - - -
214Z ARG* 1.3 76.7 - - - +
216Z ARG* 1.3 63.7 + - + +
218Z GLU* 4.1 1.1 - - - +
219Z GLU* 3.2 31.1 + - + +
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Residues in contact with ARG 216 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A G 4.3 19.8 + - - -
321A A 5.1 13.9 + - - -
190Z VAL* 4.2 17.1 - - + +
212Z ARG* 3.7 32.0 + - - +
213Z LYS* 3.2 17.9 + - + +
214Z ARG 3.2 0.6 - - - -
215Z GLU* 1.3 77.2 - - + +
217Z ILE* 1.3 66.6 + - - +
219Z GLU* 3.2 19.3 - - - +
220Z GLU* 3.2 26.1 + - - +
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Residues in contact with ILE 217 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187Z VAL* 4.4 4.7 - - + -
188Z HIS 4.0 7.0 - - - +
189Z ASN* 3.4 42.4 - - - +
190Z VAL* 3.9 12.3 - - + +
193Z LEU* 3.7 26.0 - - + +
203Z VAL* 5.5 1.6 - - + -
205Z ILE* 3.7 30.1 - - + -
209Z VAL* 4.3 9.6 - - + -
213Z LYS* 3.0 25.0 + - + +
214Z ARG 2.9 7.5 + - - +
216Z ARG* 1.3 76.8 - - - +
218Z GLU* 1.3 63.0 + - - +
221Z ALA* 3.0 29.5 + - + +
228Z VAL* 5.7 0.2 - - + -
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Residues in contact with GLU 218 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Z ARG* 3.0 40.6 + - + +
101Z GLY* 5.2 4.0 + - - -
205Z ILE* 3.9 15.7 - - + -
214Z ARG* 2.6 32.8 + - - +
215Z GLU 4.1 3.6 - - - +
217Z ILE* 1.3 74.7 - - - +
219Z GLU* 1.3 60.5 + - - +
221Z ALA* 3.9 5.0 - - - +
222Z GLU* 3.4 23.4 + - - +
228Z VAL* 4.5 12.8 - - + +
231Z PRO* 3.3 12.4 - - - +
232Z THR* 2.7 49.4 + - - -
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Residues in contact with GLU 219 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Z ARG* 5.9 0.2 - - - +
215Z GLU* 3.2 17.9 + - - +
216Z ARG* 3.2 29.5 - - - +
218Z GLU* 1.3 76.6 - - - +
220Z GLU* 1.3 68.0 + - + +
222Z GLU* 3.7 8.3 + - - +
223Z ASP* 2.8 36.2 + - - +
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Residues in contact with GLU 220 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190Z VAL* 3.9 24.7 - - + +
193Z LEU* 4.2 11.8 - - + +
216Z ARG* 3.2 14.9 + - - +
217Z ILE 4.3 1.3 - - - +
219Z GLU* 1.3 82.6 - - + +
221Z ALA* 1.3 65.2 + - - +
223Z ASP* 3.5 10.8 + - + +
224Z ALA* 3.2 21.7 + - - +
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Residues in contact with ALA 221 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193Z LEU* 3.8 24.0 - - + +
203Z VAL* 5.1 0.2 - - + -
217Z ILE* 3.0 19.0 + - + +
218Z GLU 3.9 3.6 - - - +
219Z GLU 3.3 0.2 - - - -
220Z GLU* 1.3 77.2 - - - +
222Z GLU* 1.3 60.6 + - - +
224Z ALA* 2.9 20.5 + - - +
226Z ILE* 2.9 32.7 + - + +
228Z VAL* 4.0 22.0 - - + -
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Residues in contact with GLU 222 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Z ARG* 5.4 0.7 - - - +
101Z GLY* 3.6 36.0 + - - +
102Z LEU* 4.1 24.7 - - + +
218Z GLU 3.4 15.7 + - - +
219Z GLU* 3.8 8.7 - - - +
221Z ALA* 1.3 80.1 - - - +
223Z ASP* 1.3 67.4 + - - +
225Z GLY* 3.0 13.9 + - - -
226Z ILE 3.9 9.1 + - - -
228Z VAL* 5.6 0.2 - - - +
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Residues in contact with ASP 223 (chain Z).
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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219Z GLU* 2.8 26.1 + - - +
220Z GLU* 3.9 12.3 - - + +
221Z ALA 3.2 0.4 - - - -
222Z GLU* 1.3 86.1 - - - +
224Z ALA* 1.3 58.2 + - - +
225Z GLY 3.2 1.3 + - - -
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Residues in contact with ALA 224 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193Z LEU* 5.8 3.4 - - + +
196Z VAL 5.3 1.2 - - - +
198Z GLY* 4.9 3.3 + - - -
220Z GLU 3.2 15.6 + - - +
221Z ALA* 2.9 7.6 + - - +
223Z ASP* 1.3 76.4 - - - +
225Z GLY* 1.3 61.9 + - - +
226Z ILE* 3.3 23.3 + - + +
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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