Contacts of the helix formed by residues 217 - 230 (chain J) in PDB entry 3V6K
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 ILE 217 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186J ILE* 6.0 2.2 - - + -
190J THR* 4.5 16.4 - - + +
193J LYS* 4.7 10.3 - - + +
194J LEU* 3.7 32.5 - - + -
213J LEU* 3.1 36.6 + - + +
216J MET* 1.3 83.7 - - + +
218J GLY* 1.3 66.4 + - - +
221J LYS* 3.0 37.8 + - + +
222J ALA* 3.5 30.1 - - + +
225J LEU* 5.3 4.0 - - + -
12M T 4.7 0.2 + - - -
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Residues in contact with GLY 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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213J LEU 3.8 2.2 + - - +
214J LYS 3.8 12.4 + - - -
216J MET 3.5 4.0 + - - -
217J ILE* 1.3 84.2 - - - +
219J GLU* 1.3 65.1 + - - -
220J ALA 3.2 2.0 - - - -
221J LYS 4.7 0.2 - - - -
222J ALA* 3.2 18.2 + - - +
12M T 3.0 25.6 - - - -
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Residues in contact with GLU 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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214J LYS* 3.7 46.7 + - + +
218J GLY* 1.3 72.5 - - - -
220J ALA* 1.3 61.6 + - - +
222J ALA* 3.4 4.5 + - - +
223J LYS* 3.2 24.4 + - - +
12M T 4.0 7.2 + - - +
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Residues in contact with ALA 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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218J GLY 3.2 0.2 - - - -
219J GLU* 1.3 79.8 - - - +
221J LYS* 1.3 61.8 + - - +
223J LYS* 3.8 4.4 + - - +
224J TYR* 3.7 16.3 + - - +
11M C 3.4 39.6 + - + +
12M T 3.8 15.7 + - - +
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Residues in contact with LYS 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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185J GLY* 3.6 24.0 - - - +
186J ILE* 4.6 12.1 - - + +
190J THR* 3.7 23.5 + - + +
217J ILE* 3.0 34.1 + - + +
218J GLY* 3.6 2.2 + - - -
219J GLU 3.5 0.2 - - - -
220J ALA* 1.3 76.3 - - + +
222J ALA* 1.3 63.1 + - - +
224J TYR* 3.4 22.1 - - + +
225J LEU* 3.4 7.6 + - - +
11K T 4.0 24.8 + - - -
12K T 4.0 10.9 - - - -
10M C 5.3 0.4 + - - -
11M C 3.9 30.0 + - - +
12M T 6.1 0.4 - - - +
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Residues in contact with ALA 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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210J PHE 5.3 0.9 - - - +
213J LEU* 3.8 31.1 - - + +
214J LYS* 4.4 3.6 - - + +
217J ILE* 3.5 9.1 - - + +
218J GLY 3.2 18.9 + - - +
219J GLU* 3.6 8.7 - - - +
220J ALA 3.3 0.4 - - - -
221J LYS* 1.3 75.3 - - - +
223J LYS* 1.3 64.9 + - - +
225J LEU* 3.0 14.4 + - - +
226J ILE* 3.2 24.0 + - + +
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Residues in contact with LYS 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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219J GLU 3.2 13.7 + - - +
220J ALA* 4.2 4.9 - - - +
222J ALA* 1.3 77.1 - - - +
224J TYR* 1.3 63.0 + - - +
226J ILE* 4.1 10.4 - - - +
227J SER* 3.0 28.0 + - - -
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Residues in contact with TYR 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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149J VAL* 2.9 34.6 - - + +
183J VAL* 3.6 17.7 - - + +
184J PRO* 2.7 32.9 + - - +
185J GLY* 5.0 1.8 - - - -
186J ILE* 4.8 13.5 - - + -
220J ALA 3.7 10.7 + - - +
221J LYS* 3.4 15.5 + - + +
223J LYS* 1.3 80.5 - - - +
225J LEU* 1.3 63.8 + - + +
227J SER* 3.8 4.8 - - - -
228J LEU* 3.4 35.1 + - + +
233J TYR* 3.6 33.0 - + - -
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Residues in contact with LEU 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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180J ILE* 6.3 2.9 - - + -
183J VAL* 6.4 0.2 - - - -
186J ILE* 6.2 3.4 - - + -
199J ILE* 6.2 4.0 - - + -
202J LEU* 4.5 6.7 - - + +
205J THR* 4.1 12.2 + - - +
213J LEU* 5.1 8.5 - - + -
217J ILE* 5.3 3.4 - - + -
221J LYS 3.4 8.6 + - - +
222J ALA* 3.0 12.9 + - - +
224J TYR* 1.3 82.8 - - + +
226J ILE* 1.3 66.4 + - + +
228J LEU* 3.2 9.8 + - - +
229J ALA* 3.0 19.8 + - - +
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Residues in contact with ILE 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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205J THR* 4.7 8.1 - - + +
206J LEU* 6.2 3.4 - - - +
210J PHE* 5.4 14.4 - - + +
213J LEU* 5.1 9.6 - - + -
222J ALA* 3.2 28.4 + - + +
223J LYS* 4.1 8.3 - - - +
225J LEU* 1.3 76.4 - - + +
227J SER* 1.3 57.6 + - - +
229J ALA* 3.0 10.9 + - + +
230J ARG* 2.9 31.6 + - + +
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Residues in contact with SER 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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223J LYS 3.0 18.5 + - - -
224J TYR* 3.8 6.3 - - - -
225J LEU 3.2 0.2 - - - -
226J ILE* 1.3 77.3 - - - +
228J LEU* 1.3 54.6 + - - +
230J ARG* 3.5 3.6 + - - -
231J ASP 3.1 5.4 + - - -
232J GLU* 2.7 39.5 + - - +
233J TYR* 3.0 39.3 + - - -
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Residues in contact with LEU 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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147J ASN* 3.8 19.5 - - - +
149J VAL* 3.9 15.5 - - + -
150J PHE* 5.4 0.4 - - + +
174J LEU* 5.7 1.2 - - - +
175J ILE* 3.3 12.6 - - - +
183J VAL* 4.1 13.0 - - + -
202J LEU* 3.9 16.6 - - + +
224J TYR* 3.4 48.4 + - + +
225J LEU* 3.2 7.4 + - - +
227J SER* 1.3 75.2 - - - +
229J ALA* 1.3 65.4 + - - +
231J ASP* 3.1 14.0 + - - +
233J TYR* 3.6 30.3 - - + -
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Residues in contact with ALA 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175J ILE* 3.4 29.2 - - - +
202J LEU* 4.0 3.1 - - + +
205J THR* 3.4 35.7 - - + +
206J LEU* 5.6 1.6 - - + -
225J LEU 3.0 12.0 + - - +
226J ILE* 3.0 15.8 + - + +
228J LEU* 1.3 80.0 - - - +
230J ARG* 1.3 59.9 + - - +
231J ASP 3.1 1.3 + - - -
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Residues in contact with ARG 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 ILE* 2.9 17.0 + - + +
227J SER* 4.0 4.5 - - - +
228J LEU 3.4 0.2 - - - -
229J ALA* 1.3 74.2 - - - +
231J ASP* 1.3 68.7 + - - +
232J GLU* 3.5 15.1 + - + +
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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