Contacts of the helix formed by residues 211 - 225 (chain A) in PDB entry 1F4L
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 GLN 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A ALA 3.7 1.0 + - - -
210A LEU* 1.3 76.3 - - - +
212A GLU* 1.3 66.7 + - - +
213A GLN* 4.3 6.5 - - + +
214A VAL* 3.0 16.1 + - + +
215A ALA* 3.0 20.1 + - - +
319A ASN* 4.7 1.4 + - - -
320A LEU 3.6 11.2 + - - +
321A PHE* 5.7 0.4 - - + -
322A VAL* 2.8 56.1 + - - +
365A SER 2.9 31.0 + - - +
366A ARG 3.9 1.0 + - - -
367A ILE* 3.9 12.4 - - + +
435A ARG* 3.9 17.1 - - - +
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU 3.5 3.1 + - - -
211A GLN* 1.3 71.5 - - - +
213A GLN* 1.3 63.3 + - + +
215A ALA* 3.3 8.7 + - + +
216A ASN* 3.0 51.0 + - - +
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Residues in contact with GLN 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLN* 3.3 4.5 - - + +
212A GLU* 1.3 81.7 - - + +
214A VAL* 1.3 62.5 + - - +
216A ASN* 3.5 6.5 + - - +
217A LYS* 2.8 46.5 + - + +
366A ARG* 3.4 23.3 - - - +
367A ILE* 2.8 60.7 + - + +
368A ASP* 3.8 8.1 + - - -
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU* 4.3 13.2 - - + -
211A GLN* 3.0 31.1 + - + +
213A GLN* 1.3 73.4 - - - +
215A ALA* 1.3 69.3 + - - +
217A LYS* 3.1 8.4 + - - +
218A MET* 2.8 38.5 + - + +
298A VAL* 3.9 26.5 - - + -
302A SER* 5.0 1.8 - - - -
320A LEU* 5.2 1.3 - - + -
322A VAL* 3.9 13.5 - - + -
367A ILE* 3.4 27.1 - - + -
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Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A THR* 3.9 24.0 - - + +
210A LEU* 4.8 4.9 - - + +
211A GLN 3.0 12.6 + - - +
212A GLU* 3.5 12.1 - - + +
214A VAL* 1.3 77.3 - - - +
216A ASN* 1.3 64.5 + - - +
218A MET* 3.1 18.5 + - + +
219A GLN* 3.0 27.6 + - - +
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Residues in contact with ASN 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A GLU* 3.0 43.3 + - - +
213A GLN* 3.7 8.9 - - - +
214A VAL 3.2 0.2 - - - -
215A ALA* 1.3 77.4 - - - +
217A LYS* 1.3 72.7 + - - +
219A GLN* 3.1 19.3 + - - +
220A GLU* 3.4 15.6 + - - +
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Residues in contact with LYS 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLN* 2.8 44.8 + - + +
214A VAL* 3.1 12.0 + - + +
216A ASN* 1.3 84.6 - - - +
218A MET* 1.3 65.3 + - - +
220A GLU* 3.1 35.9 + - - +
221A TRP* 3.2 38.0 + - + -
298A VAL* 5.9 1.3 - - + -
367A ILE* 5.7 4.3 - - + -
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Residues in contact with MET 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A TRP* 5.2 1.3 - - - -
205A THR* 3.3 31.4 - - + +
210A LEU* 3.1 35.2 - - + -
214A VAL* 2.8 16.8 + - + +
215A ALA* 3.1 31.8 + - - +
217A LYS* 1.3 78.2 - - - +
219A GLN* 1.3 61.6 + - - +
221A TRP* 3.1 26.4 + - + +
222A PHE* 2.9 35.7 + - + -
302A SER* 3.8 27.8 - - - +
303A LEU* 5.0 5.4 - - + -
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Residues in contact with GLN 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A GLN* 5.1 9.0 + - - +
205A THR* 3.5 25.5 - - - +
206A ARG* 5.2 11.5 - - - +
215A ALA* 3.0 19.0 + - - +
216A ASN* 3.1 11.3 + - - +
218A MET* 1.3 77.9 - - - +
220A GLU* 1.3 61.5 + - - +
222A PHE* 3.4 16.7 + - - +
223A GLU* 2.9 24.8 + - - +
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Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ASN* 3.4 10.2 + - - +
217A LYS* 3.1 32.9 + - - +
219A GLN* 1.3 78.1 - - - +
221A TRP* 1.3 65.9 + - + +
223A GLU* 3.4 6.9 + - - +
224A SER* 3.0 28.1 + - - -
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Residues in contact with TRP 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A LYS* 3.2 24.6 + - + +
218A MET* 3.1 29.4 + - + +
220A GLU* 1.3 83.6 + - + +
222A PHE* 1.3 66.8 + - - +
224A SER* 3.1 11.6 + - - -
225A GLY 3.1 16.8 + - - +
226A LEU* 3.9 10.5 - - + +
295A LYS 5.6 2.2 - - - -
298A VAL* 3.9 17.3 - - + -
299A TYR* 3.4 58.5 + + + +
302A SER* 3.8 18.6 - - - -
303A LEU* 3.7 23.3 - - + -
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Residues in contact with PHE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A SER* 4.5 3.4 - - - -
201A LEU* 3.9 17.0 - - + -
202A GLN* 3.7 44.0 - - + +
205A THR* 3.5 31.2 - - + -
218A MET* 2.9 33.4 + - + +
219A GLN* 3.9 18.2 - - - +
221A TRP* 1.3 75.9 - - - +
223A GLU* 1.3 63.5 + - - +
225A GLY* 3.0 14.2 + - - -
226A LEU* 4.0 25.2 + - + +
303A LEU* 3.7 29.2 - - + -
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Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A GLN 2.9 17.8 + - - +
220A GLU* 3.5 8.3 - - - +
222A PHE* 1.3 77.5 - - - +
224A SER* 1.3 63.4 + - - +
225A GLY* 3.3 1.0 + - - -
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Residues in contact with SER 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLU 3.0 14.5 + - - -
221A TRP* 3.1 18.8 + - - -
222A PHE 3.3 0.2 - - - -
223A GLU* 1.3 78.2 - - - +
225A GLY* 1.3 63.8 + - - +
227A GLN* 5.7 1.2 + - - -
299A TYR* 5.7 1.2 + - - -
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Residues in contact with GLY 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A TRP 3.1 7.0 + - - +
222A PHE 3.0 15.6 + - - -
223A GLU 4.2 0.9 - - - -
224A SER* 1.3 85.9 + - - +
226A LEU* 1.3 66.7 + - - +
227A GLN* 3.7 12.1 + - - +
299A TYR* 4.9 0.9 + - - -
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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