Contacts of the helix formed by residues 211 - 223 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210C GLN* 1.3 75.9 - - - +
212C ARG* 1.3 65.2 + - - +
213C SER* 3.4 26.0 + - - +
214C THR* 2.9 44.6 + - - +
215C VAL* 3.4 11.1 + - - +
237C THR* 4.0 2.2 - - - -
238C ALA* 5.0 0.4 - - - +
152F LYS* 4.4 11.1 - - + +
294F GLU* 3.5 19.7 - - - +
327F ALA 3.8 10.2 + - - +
328F HIS* 3.2 54.3 - - - +
329F LEU 4.3 4.0 - - - +
330F ASP* 3.3 26.0 + - - -
356F ARG* 4.1 3.8 - - - +
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Residues in contact with ARG 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C LYS* 1.3 71.6 - - - +
213C SER* 1.3 61.8 + - - +
215C VAL* 3.5 3.2 + - - -
216C ALA* 3.2 22.5 + - - +
237C THR* 3.3 32.5 + - + +
239C SER* 4.4 13.5 + - - -
240C GLU* 4.0 26.1 + - - +
121F PRO* 3.6 13.9 + - - +
122F PRO 2.8 30.5 + - - -
123F SER* 3.2 17.0 - - - +
124F PHE* 3.8 26.0 - - + +
127F GLN* 3.5 19.8 - - + +
294F GLU* 2.6 25.3 + - - +
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Residues in contact with SER 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C LYS* 3.1 24.7 + - - +
212C ARG* 1.3 77.8 - - - +
214C THR* 1.3 60.7 + - - +
216C ALA* 3.4 7.0 + - - +
217C GLN* 3.2 17.2 + - - +
127F GLN* 3.8 21.0 + - - +
128F SER 5.4 2.1 + - - -
129F THR* 3.7 14.2 - - - +
152F LYS* 5.7 4.7 - - - -
294F GLU* 4.6 3.2 + - - -
297F THR* 4.5 9.6 + - - -
330F ASP* 4.9 3.5 + - - -
356F ARG* 4.5 6.9 + - - -
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Residues in contact with THR 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C GLN* 4.7 19.1 - - + +
211C LYS* 2.9 41.5 + - - +
213C SER* 1.3 74.3 - - - +
215C VAL* 1.3 60.7 - - - +
216C ALA 3.0 1.8 - - - -
217C GLN* 2.8 20.8 + - + +
218C LEU* 3.0 13.9 + - + +
327F ALA 5.1 0.9 + - - -
356F ARG* 3.8 20.3 + - - +
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Residues in contact with VAL 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C VAL* 5.1 0.9 - - + -
205C TYR* 5.9 2.5 - - + -
207C ALA* 3.8 24.2 - - + -
210C GLN* 4.0 9.6 - - + +
211C LYS 3.4 13.2 + - - +
212C ARG 3.5 2.2 + - - +
214C THR* 1.3 77.3 - - - +
216C ALA* 1.3 59.7 + - - +
218C LEU* 3.6 8.6 + - + +
219C VAL* 3.3 25.0 + - + +
233C ILE* 4.3 16.8 - - + -
235C ALA* 3.9 18.6 - - + -
237C THR* 4.0 18.4 - - + -
124F PHE* 3.4 23.8 - - + -
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Residues in contact with ALA 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C ARG 3.2 13.4 + - - +
213C SER 3.5 10.3 - - - +
214C THR 3.0 0.6 - - - -
215C VAL* 1.3 76.3 - - - +
217C GLN* 1.3 60.3 + - - +
219C VAL* 3.1 20.1 - - + +
220C GLN* 3.4 11.4 + - - +
124F PHE* 3.4 14.1 - - + +
127F GLN* 3.8 21.1 - - + -
129F THR* 3.8 16.9 + - + +
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Residues in contact with GLN 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C SER 3.2 7.1 + - - +
214C THR* 2.8 11.7 + - + +
216C ALA* 1.3 76.0 - - - +
218C LEU* 1.3 65.1 + - - +
220C GLN* 3.2 28.6 + - - +
221C THR* 3.1 32.7 + - - +
129F THR* 3.7 18.6 - - + -
130F SER 5.1 2.8 + - - -
131F ALA* 5.8 6.9 - - - +
356F ARG* 2.8 39.9 + - - +
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Residues in contact with LEU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C THR* 4.8 11.2 - - + -
182C LEU* 3.6 43.3 - - + -
205C TYR* 3.5 49.1 - - + +
214C THR* 3.0 12.6 + - + +
215C VAL* 3.9 11.7 - - + +
217C GLN* 1.3 77.8 - - - +
219C VAL* 1.3 57.9 + - - +
221C THR* 2.9 9.4 + - - -
222C LEU* 2.8 41.9 + - + +
233C ILE* 5.1 4.7 - - + -
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Residues in contact with VAL 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C VAL* 4.3 9.6 - - + -
215C VAL* 3.3 19.3 - - + +
216C ALA* 3.1 25.4 - - - +
218C LEU* 1.3 76.6 - - + +
220C GLN* 1.3 62.5 + - + +
222C LEU* 3.7 2.7 - - - +
223C GLU* 3.1 32.9 + - - +
228C MET* 3.9 14.8 - - + -
233C ILE* 3.4 28.7 - - + -
124F PHE* 4.0 17.7 - - + -
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Residues in contact with GLN 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ALA 3.5 11.0 - - - +
217C GLN* 3.2 32.6 + - - +
218C LEU 3.1 0.2 - - - -
219C VAL* 1.3 82.2 - - - +
221C THR* 1.3 59.4 + - - +
223C GLU* 3.8 5.9 + - - +
224C GLN* 3.0 49.0 + - + +
129F THR* 3.3 31.6 + - - +
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Residues in contact with THR 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C LEU* 4.6 10.5 - - + -
186C LEU* 4.8 2.9 - - + +
217C GLN* 3.1 24.1 + - - +
218C LEU* 2.9 11.8 + - - -
220C GLN* 1.3 76.5 + - - +
222C LEU* 1.3 63.5 + - - +
224C GLN* 3.2 16.9 + - - +
225C HIS* 3.1 34.4 - - + +
435C TYR* 3.4 41.0 + - + +
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Residues in contact with LEU 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C LEU* 3.7 28.3 - - + -
185C ILE* 4.2 17.0 - - + -
186C LEU* 4.0 15.5 - - + -
205C TYR* 6.1 1.6 - - + -
218C LEU* 2.8 25.4 + - + +
219C VAL* 3.7 6.7 - - - +
221C THR* 1.3 77.8 - - - +
223C GLU* 1.3 57.2 + - - +
224C GLN 3.0 0.2 - - - -
225C HIS* 3.1 12.6 + - - -
227C ALA* 2.9 30.0 + - + +
228C MET* 3.6 18.8 - - + +
231C SER* 4.7 11.9 - - - -
233C ILE* 3.6 32.5 - - + -
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Residues in contact with GLU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LYS* 3.9 19.2 + - - -
219C VAL* 3.1 22.4 + - - +
220C GLN* 4.4 5.0 - - - +
222C LEU* 1.3 76.3 - - - +
224C GLN* 1.3 61.2 + - - +
225C HIS 3.3 0.4 - - - -
226C ASP* 3.7 11.3 + - - +
227C ALA 4.5 2.7 - - - +
228C MET* 3.4 36.6 - - + +
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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