Contacts of the helix formed by residues 207 - 221 (chain O) in PDB entry 3V3K
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 THR 207 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205O ASP 3.8 1.2 + - - -
206O LEU* 1.3 74.9 - - - +
208O ALA* 1.3 66.0 + - - +
209O LYS* 4.0 9.7 + - + +
210O LYS* 3.1 42.9 + - + +
211O MET* 2.8 28.2 + - - +
245O GLY* 4.1 2.0 - - - -
246O THR* 3.6 16.8 + - - +
247O ASP* 3.2 24.6 + - - +
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Residues in contact with ALA 208 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207O THR* 1.3 79.2 + - - +
209O LYS* 1.3 62.6 - - + +
210O LYS 3.5 0.3 + - - -
211O MET* 3.5 4.2 + - - +
212O VAL* 3.5 25.5 + - - +
245O GLY* 3.9 5.2 - - - -
247O ASP* 3.1 16.3 + - - +
254O CYS* 3.2 40.6 - - + +
255O PRO 5.3 0.2 - - - +
256O VAL* 3.8 15.4 - - + +
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Residues in contact with LYS 209 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207O THR* 3.3 9.4 + - + +
208O ALA* 1.3 79.2 - - + +
210O LYS* 1.3 59.1 + - + +
212O VAL* 3.9 7.1 + - - +
213O LEU* 3.4 33.3 + - + +
247O ASP* 5.3 7.0 + - - +
254O CYS* 5.7 6.1 - - - -
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Residues in contact with LYS 210 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206O LEU* 4.3 20.0 - - + +
207O THR* 3.1 34.0 + - + +
209O LYS* 1.3 79.0 - - + +
211O MET* 1.3 54.4 + - - +
212O VAL 3.3 0.4 - - - -
213O LEU* 3.7 13.1 - - + +
214O ALA* 2.7 37.5 + - - +
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Residues in contact with MET 211 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168O ILE* 3.8 29.9 - - + +
170O ASN* 3.4 27.4 - - - +
206O LEU* 3.7 19.3 - - + +
207O THR 2.8 15.7 + - - +
208O ALA 3.7 4.7 - - - +
210O LYS* 1.3 76.2 - - - +
212O VAL* 1.3 57.5 + - - +
214O ALA* 3.5 1.4 + - - +
215O LEU* 3.1 38.3 + - + +
234O ILE* 4.3 10.3 - - + -
243O VAL* 3.7 31.6 - - + +
244O TYR 3.8 2.2 - - - +
245O GLY* 3.7 20.2 - - - -
256O VAL* 4.5 15.3 - - + -
261O ILE* 5.0 2.2 - - + -
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Residues in contact with VAL 212 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208O ALA 3.5 14.7 + - - +
209O LYS* 3.9 9.2 - - - +
210O LYS 3.3 0.2 - - - -
211O MET* 1.3 75.9 - - - +
213O LEU* 1.3 59.9 + - + +
215O LEU* 3.4 8.8 + - - +
216O LEU* 2.9 47.8 + - + +
256O VAL* 4.4 23.1 - - + -
260O LYS* 4.4 29.4 - - + +
264O ILE* 4.4 8.2 - - + +
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Residues in contact with LEU 213 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209O LYS* 3.4 23.0 + - + +
210O LYS* 3.3 14.1 + - + +
212O VAL* 1.3 79.3 - - + +
214O ALA* 1.3 57.8 + - - +
216O LEU* 3.7 16.6 - - + +
217O GLU* 2.9 30.0 + - - +
220O ARG* 5.3 6.3 + - - +
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Residues in contact with ALA 214 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166O LEU* 3.8 21.8 - - + +
168O ILE* 4.9 0.7 - - + -
203O LYS* 4.3 23.2 + - + +
206O LEU* 4.1 20.6 - - + -
210O LYS 2.7 21.5 + - - +
211O MET 3.8 4.5 - - - +
213O LEU* 1.3 73.2 - - - +
215O LEU* 1.3 61.2 + - - +
217O GLU* 3.6 8.2 - - - +
218O LEU* 3.3 15.9 + - - +
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Residues in contact with LEU 215 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166O LEU* 3.6 16.6 - - + -
168O ILE* 4.5 11.2 - - + -
211O MET* 3.1 26.2 + - + +
212O VAL* 3.8 4.9 - - + +
214O ALA* 1.3 74.4 - - - +
216O LEU* 1.3 64.6 + - - +
218O LEU* 3.3 1.4 + - - -
219O ALA* 3.1 19.6 + - - +
232O VAL* 3.4 33.0 - - + -
234O ILE* 4.9 0.9 - - + -
256O VAL* 5.5 1.1 - - + -
261O ILE* 3.6 39.3 - - + -
264O ILE* 3.9 16.6 - - + +
265O PHE* 3.5 29.9 - - + -
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Residues in contact with LEU 216 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212O VAL* 2.9 39.5 + - + +
213O LEU* 3.7 17.5 - - + +
215O LEU* 1.3 76.0 - - - +
217O GLU* 1.3 56.9 + - - +
219O ALA* 3.3 3.4 + - + +
220O ARG* 2.9 45.8 + - - +
264O ILE* 3.9 31.4 - - + -
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Residues in contact with GLU 217 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203O LYS* 5.5 8.1 - - - +
213O LEU 2.9 17.9 + - - +
214O ALA* 3.6 10.1 - - - +
215O LEU 3.3 0.2 - - - -
216O LEU* 1.3 77.4 - - - +
218O LEU* 1.3 60.3 + - - +
220O ARG* 2.8 33.9 + - - +
221O GLN* 3.3 46.9 + - + +
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Residues in contact with LEU 218 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164O HIS* 3.3 41.7 - - + +
165O CYS 5.1 0.2 - - - +
166O LEU* 3.8 25.4 - - + +
214O ALA 3.3 10.2 + - - +
215O LEU* 3.3 9.5 + - - +
217O GLU* 1.3 78.3 - - - +
219O ALA* 1.3 59.3 + - - +
221O GLN* 3.4 13.0 + - + +
224O HIS* 2.9 26.4 + - + -
230O CYS* 4.1 10.1 - - - -
231O VAL 4.2 3.1 - - - +
232O VAL* 3.7 29.4 - - + -
265O PHE* 3.8 13.9 - - + -
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Residues in contact with ALA 219 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215O LEU 3.1 7.4 + - - +
216O LEU* 3.8 4.9 - - + +
218O LEU* 1.3 74.9 - - - +
220O ARG* 1.3 63.4 + - - +
221O GLN 3.4 7.4 + - - +
224O HIS* 4.5 0.2 - - - -
264O ILE* 3.6 40.4 - - + +
265O PHE* 3.8 14.3 - - + -
269O SER 5.3 1.6 - - - +
270O CYS* 3.5 29.5 - - + +
271O PRO* 5.8 0.5 - - - +
272O SER* 5.4 0.3 + - - -
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Residues in contact with ARG 220 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213O LEU* 5.3 6.1 + - - +
216O LEU* 2.9 34.3 + - - +
217O GLU* 2.8 51.9 + - - +
218O LEU 3.3 0.6 - - - -
219O ALA* 1.3 74.4 - - - +
221O GLN* 1.3 65.6 + - - +
222O ASP 3.8 0.5 + - - -
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Residues in contact with GLN 221 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164O HIS* 4.2 27.9 + - + +
217O GLU* 3.3 36.8 + - + +
218O LEU* 3.5 14.8 - - + +
219O ALA 3.2 4.8 - - - +
220O ARG* 1.3 84.4 - - - +
222O ASP* 1.3 62.4 + - - +
224O HIS* 3.2 22.8 + - + +
272O SER* 4.0 6.6 + - - -
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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