Contacts of the helix formed by residues 210 - 226 (chain A) in PDB entry 1LVK
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 VAL 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A GLY* 1.3 69.6 - - - -
211A LEU* 1.3 68.1 + - + +
212A GLU* 3.3 1.2 + - - -
213A GLN* 3.3 5.3 - - + +
214A GLN* 2.8 49.0 + - + +
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Residues in contact with LEU 211 (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 ARG* 5.9 0.4 - - - +
210A VAL* 1.3 81.2 - - + +
212A GLU* 1.3 61.6 + - - +
214A GLN* 2.9 18.1 + - - +
215A ILE* 2.7 43.1 + - + +
253A ILE* 4.0 20.2 - - + +
254A SER* 3.6 32.5 - - - +
255A GLY* 3.8 4.0 - - - +
440A VAL 5.0 1.8 - - - +
441A LEU* 3.9 31.6 - - + +
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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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197A ALA* 4.9 11.7 - - + +
201A GLY* 3.4 15.9 - - - -
202A ARG* 2.8 45.9 + - - +
209A GLY* 3.5 25.7 - - - +
210A VAL 3.3 0.7 + - - -
211A LEU* 1.3 96.2 + - + +
213A GLN* 1.3 56.5 + - - +
215A ILE* 3.2 10.1 + - - +
216A LEU* 2.8 41.8 + - + +
253A ILE* 4.3 19.7 - - + +
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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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209A GLY 2.9 22.6 + - - +
210A VAL* 3.3 9.2 - - + +
212A GLU* 1.3 74.7 - - - +
214A GLN* 1.3 58.7 + - - +
216A LEU* 3.2 13.1 + - - +
217A GLN* 2.8 43.2 + - + +
333A ILE* 4.0 22.6 - - + +
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Residues in contact with GLN 214 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A VAL* 2.8 37.7 - - + +
211A LEU* 2.9 23.9 + - - +
213A GLN* 1.3 76.6 - - - +
215A ILE* 1.3 61.3 + - - +
217A GLN 3.2 1.9 + - - -
218A ALA* 3.1 21.1 + - - +
333A ILE* 3.7 27.6 + - + +
334A VAL* 3.3 35.0 + - + +
440A VAL* 3.4 17.6 - - + +
441A LEU* 3.5 14.2 - - + +
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Residues in contact with ILE 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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193A ILE* 4.3 24.2 - - + +
197A ALA* 6.5 0.7 - - + -
211A LEU* 2.7 30.3 + - + +
212A GLU* 3.3 12.8 - - - +
214A GLN* 1.3 74.2 - - - +
216A LEU* 1.3 64.5 + - + +
218A ALA* 3.2 13.2 + - - +
219A ASN* 4.2 6.6 + - - -
243A ILE* 6.2 0.4 - - + -
245A ILE* 4.4 14.6 - - + -
253A ILE* 3.7 34.5 - - + -
255A GLY 4.0 12.3 - - - +
256A ALA* 4.2 7.6 - - + -
441A LEU* 3.9 23.7 - - + +
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Residues in contact with LEU 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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190A LYS 5.8 0.4 - - - +
193A ILE* 4.0 26.9 - - + +
194A GLN* 4.7 8.1 - - + -
197A ALA* 4.4 22.4 - - + -
212A GLU* 2.8 31.8 + - + +
213A GLN* 3.8 12.1 - - - +
215A ILE* 1.3 74.0 - - + +
217A GLN* 1.3 73.3 + - - +
218A ALA 3.2 0.7 + - - -
219A ASN* 3.6 4.7 + - - +
220A PRO* 3.2 16.5 - - - +
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Residues in contact with GLN 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 29.3 + - + +
214A GLN 3.2 4.7 + - - +
216A LEU* 1.3 88.0 + - - +
218A ALA* 1.3 63.0 + - - +
219A ASN 3.4 0.4 - - - -
220A PRO* 3.1 20.7 - - - +
221A ILE* 3.3 15.8 - - - +
326A ILE* 4.9 4.9 - - - +
329A GLN* 4.9 3.3 - - - +
330A ALA* 3.4 26.9 + - + +
333A ILE* 3.8 33.6 - - + +
334A VAL* 4.1 4.7 - - + -
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Residues in contact with ALA 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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214A GLN 3.1 11.9 + - - +
215A ILE 3.2 9.8 + - - +
216A LEU 3.2 2.0 - - - -
217A GLN* 1.3 76.8 - - - +
219A ASN* 1.3 68.1 + - - +
221A ILE* 3.1 13.7 + - - +
222A LEU* 3.0 22.4 + - - +
258A ILE* 4.3 10.1 - - + -
334A VAL* 4.4 2.0 - - + -
437A ILE* 3.8 33.0 - - + -
441A LEU* 4.3 6.7 - - + -
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Residues in contact with ASN 219 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A THR* 5.2 0.2 - - - +
189A THR* 5.5 1.3 - - - +
190A LYS* 4.6 18.2 - - + +
193A ILE* 5.0 8.4 - - - +
215A ILE 4.2 5.9 + - - -
216A LEU 3.6 5.8 + - - +
218A ALA* 1.3 76.7 - - - +
220A PRO* 1.3 61.0 - - + +
222A LEU* 2.8 14.8 + - - +
223A GLU* 2.6 55.3 + - - +
241A LYS* 4.0 22.3 + - - +
243A ILE* 4.2 20.2 - - - +
258A ILE* 5.0 8.3 - - - +
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Residues in contact with PRO 220 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A LEU 3.2 13.7 - - - +
217A GLN* 3.1 31.9 - - - +
218A ALA 3.3 0.4 - - - -
219A ASN* 1.3 93.3 - - + +
221A ILE* 1.3 64.2 + - - +
223A GLU* 4.1 8.0 - - + +
224A ALA* 3.1 22.9 + - - +
326A ILE* 4.8 17.0 - - + +
327A THR* 4.2 7.7 + - - +
330A ALA* 4.1 13.0 - - + -
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Residues in contact with ILE 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 GLN 3.3 18.6 - - - +
218A ALA* 3.2 9.2 - - - +
220A PRO* 1.3 76.0 - - - +
222A LEU* 1.3 69.1 + - + +
224A ALA* 3.3 7.4 + - - +
225A PHE* 3.1 39.6 - - + -
327A THR* 4.7 6.5 - - + +
330A ALA* 3.7 28.7 - - + +
331A MET* 3.9 22.2 - - + +
334A VAL* 3.8 14.8 - - + -
336A PHE* 4.1 13.5 - - + -
433A LEU* 4.7 13.2 - - + -
437A ILE* 4.2 16.4 - - + -
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A ALA 3.0 10.5 + - - +
219A ASN* 2.8 16.9 + - - +
221A ILE* 1.3 87.3 - - + +
223A GLU* 1.3 57.0 + - + +
225A PHE 3.4 0.9 + - - -
226A GLY* 2.7 28.9 + - - -
239A PHE* 3.8 25.8 - - + -
241A LYS* 5.8 2.2 - - + -
258A ILE* 3.8 39.3 - - + -
260A SER* 6.3 0.2 - - - -
430A PHE* 3.9 16.6 - - + -
433A LEU* 4.6 8.1 - - + -
434A VAL* 4.0 26.5 - - + -
437A ILE* 4.0 16.8 - - + -
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Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A THR* 3.3 14.9 - - - +
190A LYS* 3.1 33.5 + - - -
219A ASN* 2.6 35.9 + - - +
220A PRO* 4.1 6.7 - - + +
221A ILE 3.3 0.4 - - - -
222A LEU* 1.3 75.5 - - + +
224A ALA* 1.3 59.5 + - - +
227A ASN* 2.9 56.7 + - + +
235A ASN* 3.3 20.3 + - - +
239A PHE* 5.5 3.4 - - + -
241A LYS* 5.3 0.7 + - - +
279A HIS* 3.4 7.3 - - + -
999A MNT 4.8 3.6 - - - -
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A PRO 3.1 18.2 + - - +
221A ILE 3.6 5.4 - - - +
222A LEU 3.2 0.4 - - - -
223A GLU* 1.3 79.0 - - - +
225A PHE* 1.3 65.6 + - + +
278A TYR* 4.0 0.3 - - - +
279A HIS* 3.5 19.1 + - - -
280A ILE* 2.9 30.8 + - + +
283A GLN* 4.0 14.6 - - - +
327A THR* 3.7 27.6 - - + +
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Residues in contact with PHE 225 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A ILE* 3.1 30.6 + - + +
223A GLU 3.2 0.2 - - - -
224A ALA* 1.3 86.5 - - + +
226A GLY* 1.3 55.8 + - - +
227A ASN 3.7 0.7 - - - -
278A TYR* 3.2 7.8 - - - -
280A ILE* 3.7 29.2 - - + -
327A THR* 4.7 9.4 - - + -
331A MET* 5.2 5.4 - - - -
344A ILE* 3.3 34.5 - - + -
345A PHE* 5.0 2.7 - + - -
348A ILE* 3.9 13.0 - - + -
426A TYR* 2.6 39.2 + + + +
429A LEU* 3.8 19.1 - - + -
430A PHE* 3.8 24.0 - + + -
433A LEU* 3.5 24.5 - - + -
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Residues in contact with GLY 226 (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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222A LEU 2.7 19.0 + - - -
225A PHE* 1.3 73.7 - - - +
227A ASN* 1.3 59.2 + - - +
238A ARG* 2.7 37.2 + - - +
239A PHE* 3.3 19.0 - - - -
263A LEU* 4.1 2.7 - - - -
278A TYR* 3.4 11.2 - - - -
430A PHE* 3.7 6.5 - - - -
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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