Contacts of the helix formed by residues 211 - 225 (chain J) in PDB entry 3FKS
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 LYS 211 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209J GLY 4.1 0.6 + - - -
210J GLN* 1.3 77.1 - - - +
212J ARG* 1.3 64.2 + - - +
213J SER* 3.3 27.1 - - - +
214J THR* 3.2 42.4 + - - +
215J VAL* 3.5 7.8 + - - +
237J THR* 4.4 0.4 - - - -
238J ALA* 5.1 0.6 - - - +
152M LYS* 4.3 13.6 - - + +
294M GLU* 3.4 21.1 - - - +
327M ALA 4.0 11.5 + - - +
328M HIS* 3.8 48.0 + - - +
329M LEU 4.2 4.0 - - - +
330M ASP* 2.9 30.8 + - - -
356M ARG* 5.5 3.2 - - - +
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Residues in contact with ARG 212 (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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211J LYS* 1.3 71.7 - - - +
213J SER* 1.3 60.2 + - - +
215J VAL* 3.1 5.2 + - - +
216J ALA* 2.8 31.4 + - - +
237J THR* 3.3 27.1 + - + +
239J SER* 4.4 10.5 + - - -
240J GLU* 3.9 28.5 + - - +
121M PRO* 3.9 20.0 + - - +
122M PRO 2.7 40.8 + - - -
123M SER* 3.7 8.2 - - - +
124M PHE* 4.1 25.5 - - + +
127M GLN* 3.4 24.4 - - + +
294M GLU* 3.0 21.4 + - - +
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Residues in contact with SER 213 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211J LYS* 3.3 26.7 - - - +
212J ARG* 1.3 77.8 - - - +
214J THR* 1.3 57.7 + - - +
216J ALA* 3.6 6.2 + - - +
217J GLN* 3.2 26.7 + - - +
127M GLN* 2.9 20.6 + - - -
128M SER 5.6 5.0 + - - -
129M THR* 4.7 4.7 - - - +
152M LYS* 5.5 3.3 - - - +
294M GLU* 4.8 1.8 + - - -
297M THR* 3.1 17.0 + - - -
330M ASP* 5.6 1.8 - - - -
356M ARG* 5.2 1.0 + - - -
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Residues in contact with THR 214 (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 GLN* 3.7 26.6 - - + +
211J LYS* 3.2 38.2 + - - +
212J ARG 3.1 0.2 - - - -
213J SER* 1.3 77.6 - - - +
215J VAL* 1.3 60.1 + - - +
217J GLN* 3.4 6.0 + - - +
218J LEU* 3.0 33.5 + - + +
327M ALA 4.8 2.8 + - - -
356M ARG* 5.0 10.1 + - - +
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Residues in contact with VAL 215 (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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109J VAL* 5.1 0.4 - - + -
207J ALA* 3.8 25.4 - - + -
210J GLN* 3.9 10.3 - - + +
211J LYS 3.7 12.8 - - - +
212J ARG* 3.1 7.0 + - - +
214J THR* 1.3 73.2 - - - +
216J ALA* 1.3 63.4 - - - +
218J LEU* 3.9 9.1 - - + +
219J VAL* 3.1 26.7 + - + +
233J ILE* 4.3 24.2 - - + -
235J ALA* 4.6 10.8 - - + -
237J THR* 4.2 16.6 - - + -
124M PHE* 3.8 19.5 - - + -
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Residues in contact with ALA 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212J ARG 2.8 15.5 + - - +
213J SER* 3.8 5.6 - - - +
215J VAL* 1.3 78.3 - - - +
217J GLN* 1.3 60.4 + - - +
219J VAL* 4.2 1.8 - - - +
220J GLN* 3.4 22.5 + - - +
124M PHE* 3.8 17.9 - - + +
127M GLN* 3.8 26.7 - - + +
129M THR* 4.4 13.8 - - + +
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Residues in contact with GLN 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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213J SER 3.2 17.5 + - - +
214J THR 3.7 4.5 - - - +
215J VAL 3.2 0.2 - - - -
216J ALA* 1.3 76.5 - - - +
218J LEU* 1.3 65.9 + - - +
220J GLN* 3.2 11.3 + - - +
221J THR* 2.9 45.8 + - - +
129M THR* 3.5 27.4 - - + +
356M ARG* 3.7 37.6 + - - +
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Residues in contact with LEU 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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178J THR* 4.1 25.1 - - + -
182J LEU* 4.2 29.3 - - + +
205J TYR* 3.3 46.9 - - + +
210J GLN* 5.7 2.0 - - - +
214J THR* 3.0 21.9 + - + +
215J VAL* 3.9 9.4 - - + +
216J ALA 3.5 0.2 - - - -
217J GLN* 1.3 77.0 - - - +
219J VAL* 1.3 63.5 + - + +
221J THR* 3.2 8.4 + - - -
222J LEU* 3.1 30.9 + - + +
233J ILE* 5.2 3.4 - - + -
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Residues in contact with VAL 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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109J VAL* 4.2 16.2 - - + -
215J VAL* 3.1 28.1 + - + +
216J ALA 4.2 3.4 - - - +
218J LEU* 1.3 78.2 - - + +
220J GLN* 1.3 59.6 + - - +
222J LEU* 3.2 10.6 + - - +
223J GLU* 2.8 41.2 + - - +
228J MET* 3.6 12.6 - - + +
233J ILE* 4.1 26.7 - - + -
124M PHE* 4.4 9.4 - - + -
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Residues in contact with GLN 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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216J ALA 3.4 15.8 + - - +
217J GLN* 3.2 14.6 + - - +
219J VAL* 1.3 80.6 - - - +
221J THR* 1.3 57.5 + - - +
223J GLU* 3.3 10.0 + - + +
224J GLN* 3.1 45.0 + - + +
129M THR* 2.9 32.6 + - - +
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Residues in contact with THR 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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182J LEU* 4.5 11.0 - - + -
186J LEU* 4.6 2.2 - - + +
217J GLN* 2.9 30.6 + - - +
218J LEU* 3.2 10.6 + - - -
220J GLN* 1.3 74.7 - - - +
222J LEU* 1.3 63.6 + - - +
224J GLN* 3.6 10.8 + - - +
225J HIS* 3.0 40.6 + - + +
435J TYR* 3.6 36.2 + - + -
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Residues in contact with LEU 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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182J LEU* 4.1 16.2 - - + -
185J ILE* 4.0 27.1 - - + -
186J LEU* 3.9 24.7 - - + -
205J TYR* 5.7 0.4 - - + -
218J LEU* 3.1 26.8 + - + +
219J VAL* 3.5 11.7 - - - +
221J THR* 1.3 76.9 - - - +
223J GLU* 1.3 61.9 + - - +
225J HIS 3.6 0.7 + - - -
226J ASP 3.2 1.9 + - - -
227J ALA* 3.1 21.4 + - + +
228J MET* 3.0 34.2 + - + -
231J SER* 4.2 11.7 - - - +
233J ILE* 4.1 24.9 - - + -
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Residues in contact with GLU 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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120J LYS* 4.3 15.1 + - - -
219J VAL* 2.8 21.1 + - - +
220J GLN* 3.5 15.3 - - + +
221J THR 3.2 0.4 - - - -
222J LEU* 1.3 79.9 - - - +
224J GLN* 1.3 60.6 + - + +
225J HIS 3.4 0.2 - - - -
226J ASP* 3.5 13.7 + - - +
228J MET* 3.2 43.2 - - - +
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Residues in contact with GLN 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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220J GLN* 3.1 29.2 + - + +
221J THR* 3.6 11.9 + - - +
222J LEU 3.3 0.4 - - - -
223J GLU* 1.3 77.4 - - + +
225J HIS* 1.3 64.9 + - + +
226J ASP* 3.2 5.8 + - - +
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Residues in contact with HIS 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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186J LEU* 3.7 44.7 - - + +
189J LYS* 3.3 40.0 + - + +
221J THR* 3.0 27.5 + - + +
222J LEU 3.6 0.4 + - - +
223J GLU 3.4 0.4 - - - -
224J GLN* 1.3 83.4 - - + +
226J ASP* 1.3 67.8 + - - +
227J ALA* 2.9 6.9 + - + +
435J TYR* 4.3 29.5 + + + +
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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