Contacts of the helix formed by residues 210 - 230 (chain J) in PDB entry 6XAV
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 210 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208J THR* 3.2 15.8 + - - +
209J ASN* 1.3 73.9 - - - +
211J GLU* 1.3 55.3 + - - +
212J THR 3.1 0.4 + - - -
213J LYS* 3.2 20.8 - - - +
214J ARG* 2.6 35.0 + - - +
1T G 4.0 6.0 - - - -
2T G 3.4 33.3 + - - -
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Residues in contact with GLU 211 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209J ASN* 3.2 7.4 + - - +
210J SER* 1.3 71.4 - - - +
212J THR* 1.3 62.9 + - - +
214J ARG* 3.8 17.9 - - - +
215J LYS* 3.1 33.6 + - + +
2T G 5.0 1.4 - - - -
3T G 4.3 21.8 + - - +
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Residues in contact with THR 212 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210J SER* 4.1 0.2 - - - -
211J GLU* 1.3 78.8 - - - +
213J LYS* 1.3 58.2 + - - +
215J LYS* 3.9 1.7 - - - +
216J LYS* 3.0 42.3 + - - +
2T G 2.3 52.4 + - + +
3T G 3.3 24.7 + - + +
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Residues in contact with LYS 213 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208J THR* 4.2 13.0 - - + -
210J SER* 3.1 16.0 + - - +
212J THR* 1.3 81.7 + - - +
214J ARG* 1.3 64.7 + - - +
216J LYS* 4.4 21.5 - - + +
217J LEU* 3.0 41.5 + - + +
1T G 5.1 6.2 + - - -
2T G 3.3 24.6 + - - +
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Residues in contact with ARG 214 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205J LEU* 3.0 38.3 + - - +
206J ASN* 4.6 9.4 + - - +
207J GLU 4.9 0.2 - - - -
208J THR* 2.4 33.9 + - - +
209J ASN* 3.5 23.1 + - - +
210J SER 2.6 23.6 + - - +
211J GLU* 3.7 22.7 - - - +
213J LYS* 1.3 72.6 - - - +
215J LYS* 1.3 56.4 + - - +
217J LEU* 5.5 0.2 - - - -
218J THR* 3.2 24.5 + - + +
1276J GLU* 5.2 8.5 + - - +
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Residues in contact with LYS 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211J GLU* 3.1 27.2 + - + +
212J THR* 4.0 2.0 - - - +
214J ARG* 1.3 74.9 - - - +
216J LYS* 1.3 63.6 + - + +
217J LEU 3.3 0.9 - - - -
218J THR* 2.3 28.2 + - - +
219J LYS* 3.3 35.0 + - + +
23N A 5.8 3.8 - - - -
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Residues in contact with LYS 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212J THR* 3.0 29.6 + - - +
213J LYS* 4.3 22.0 - - + +
215J LYS* 1.3 77.7 - - + +
217J LEU* 1.3 62.9 + - + +
219J LYS* 3.3 11.3 + - - +
220J ARG* 3.2 26.2 + - + +
24N A 5.4 8.5 + - - -
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Residues in contact with LEU 217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201J LEU* 3.9 38.5 - - + +
204J GLU* 3.8 20.9 - - + +
205J LEU* 3.7 40.7 - - + +
208J THR* 4.9 2.0 - - + -
213J LYS* 3.0 35.9 + - + +
216J LYS* 1.3 76.0 - - + +
218J THR* 1.3 61.3 - - - +
220J ARG* 3.2 12.6 + - + +
221J ILE* 3.0 29.7 + - - +
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Residues in contact with THR 218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205J LEU* 3.7 19.1 - - + -
214J ARG* 3.2 18.8 + - - +
215J LYS* 2.3 36.9 + - - +
217J LEU* 1.3 75.8 - - - +
219J LYS* 1.3 62.6 + - - +
221J ILE* 3.2 8.8 - - + +
222J LYS* 2.9 46.1 + - - +
1275J LEU* 5.8 7.6 - - + -
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Residues in contact with LYS 219 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J LEU* 4.5 12.6 - - + +
215J LYS* 3.3 42.6 + - + +
216J LYS* 3.3 10.3 + - - +
218J THR* 1.3 79.5 + - - +
220J ARG* 1.3 64.6 + - + +
222J LYS* 3.6 31.4 - - - +
223J LEU* 3.3 20.4 + - - +
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Residues in contact with ARG 220 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J LEU* 2.8 38.6 + - - +
127J LEU* 3.1 24.7 + - - +
129J ASP* 2.5 37.8 + - - +
192J MET* 5.1 4.2 - - - +
197J GLU* 5.2 3.0 - - - +
201J LEU* 3.7 37.6 - - + +
216J LYS* 3.2 16.3 + - + +
217J LEU* 3.4 17.4 - - + +
218J THR 3.1 0.6 - - - -
219J LYS* 1.3 74.8 - - - +
221J ILE* 1.3 61.0 + - - +
223J LEU* 3.2 4.7 + - - +
224J LEU* 2.9 44.5 + - - +
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Residues in contact with ILE 221 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198J CYS* 3.9 38.6 - - + +
201J LEU* 5.4 6.0 - - + +
202J ARG* 3.7 32.8 - - + +
205J LEU* 4.5 15.5 - - + -
217J LEU 3.0 15.9 + - - +
218J THR* 3.2 18.6 - - + +
220J ARG* 1.3 75.8 - - - +
222J LYS* 1.3 62.9 + - + +
224J LEU* 4.2 5.2 - - + -
225J GLU* 2.8 35.2 + - + +
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Residues in contact with LYS 222 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218J THR* 2.9 34.1 + - - +
219J LYS* 3.6 35.0 - - + +
220J ARG 3.1 0.2 - - - -
221J ILE* 1.3 82.1 - - + +
223J LEU* 1.3 56.4 + - - +
225J GLU* 3.9 7.9 - - - +
226J ALA* 3.0 27.0 + - - +
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Residues in contact with LEU 223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J ARG* 4.4 27.8 - - + +
126J LEU* 3.7 25.4 - - + -
127J LEU* 4.3 15.9 - - + -
219J LYS 3.3 14.1 + - - +
220J ARG 3.2 4.3 + - - +
222J LYS* 1.3 75.9 - - - +
224J LEU* 1.3 61.5 + - + +
226J ALA* 3.1 9.7 + - + +
227J PHE* 2.9 63.4 + - + -
1337J VAL* 4.0 22.4 - - + -
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Residues in contact with LEU 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J LEU* 3.7 28.7 - - + +
192J MET* 6.5 0.2 - - + -
193J ASP 5.4 0.4 - - - +
194J LEU* 3.8 19.4 - - + +
197J GLU* 3.9 36.1 - - + +
198J CYS* 3.6 20.4 - - - +
201J LEU* 3.9 22.4 - - + -
220J ARG* 2.9 30.2 + - - +
221J ILE* 3.9 6.7 - - + +
223J LEU* 1.3 76.2 - - + +
225J GLU* 1.3 61.1 + - - +
227J PHE* 3.2 7.1 + - + +
228J VAL* 3.1 26.7 + - - +
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Residues in contact with GLU 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198J CYS* 4.5 3.5 - - - -
221J ILE* 2.8 28.9 + - + +
222J LYS* 3.9 7.3 - - - +
224J LEU* 1.3 73.1 - - - +
226J ALA* 1.3 62.2 + - - +
228J VAL* 3.2 7.5 + - + +
229J GLN* 2.9 53.0 + - + +
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Residues in contact with ALA 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222J LYS 3.0 16.2 + - - +
223J LEU* 3.1 17.5 + - + +
225J GLU* 1.3 83.2 + - - +
227J PHE* 1.3 51.0 + - - +
229J GLN* 4.2 3.9 - - - +
230J SER* 2.4 41.1 + - - -
1337J VAL 4.4 3.4 - - - +
1338J ALA* 4.1 29.6 - - + +
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Residues in contact with PHE 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J LEU* 4.7 6.1 - - + -
123J ARG* 6.2 0.2 - - + -
127J LEU* 4.5 15.5 - - + -
194J LEU* 4.0 20.1 - - + +
223J LEU* 2.9 56.5 + - + -
224J LEU* 3.2 9.2 + - - +
226J ALA* 1.3 77.0 - - - +
228J VAL* 1.3 58.3 + - - +
230J SER* 2.9 18.8 - - - +
232J ASN* 3.5 30.3 - - + +
233J LYS 4.3 3.1 - - - -
234J PRO* 3.9 34.5 - - + -
237J MET* 3.8 27.6 - - + -
1337J VAL* 4.3 17.0 - - + -
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Residues in contact with VAL 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194J LEU* 3.8 28.3 - - + -
195J GLU* 5.2 7.2 - - - +
198J CYS* 4.4 10.8 - - - -
224J LEU 3.1 16.4 + - - +
225J GLU* 3.7 9.6 - - + +
227J PHE* 1.3 77.8 - - - +
229J GLN* 1.3 66.8 + - - +
230J SER 3.4 4.4 - - - +
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Residues in contact with GLN 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225J GLU* 2.9 40.0 + - + +
226J ALA* 4.2 4.0 - - - +
228J VAL* 1.3 79.7 - - - +
230J SER* 1.3 61.2 + - - +
231J GLY 3.9 0.9 + - - -
1338J ALA 5.9 2.9 - - - +
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Residues in contact with SER 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226J ALA 2.4 27.7 + - - -
227J PHE* 2.9 25.6 - - - +
228J VAL 3.6 3.7 - - - +
229J GLN* 1.3 80.0 - - - +
231J GLY* 1.3 59.2 + - - +
232J ASN* 3.1 18.9 + - - +
1337J VAL 3.5 12.1 + - - -
1338J ALA 3.5 22.2 - - - -
1339J GLY* 4.1 7.9 - - - -
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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