Contacts of the helix formed by residues 207 - 221 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL* 6.1 1.6 - - + -
51B SER* 5.1 2.2 - - - -
205M ASP 4.0 1.8 + - - -
206M LEU* 1.3 75.5 - - - +
208M ALA* 1.3 62.1 + - - +
209M LYS* 4.0 9.9 + - + +
210M LYS* 3.0 49.0 + - + +
211M MET* 2.8 32.8 + - - +
245M GLY* 4.2 0.4 - - - -
246M THR* 3.8 12.0 + - - +
247M ASP* 3.0 30.5 + - - +
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Residues in contact with ALA 208 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207M THR* 1.3 78.3 + - - +
209M LYS* 1.3 61.0 + - + +
211M MET* 3.5 5.4 + - - +
212M VAL* 3.4 26.3 + - - +
245M GLY* 3.9 6.9 - - - -
247M ASP* 3.4 6.5 + - - +
254M CYS* 3.4 45.8 - - - +
255M PRO 4.6 0.7 - - - +
256M VAL* 3.7 21.2 - - + +
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Residues in contact with LYS 209 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ASP* 4.4 11.9 + - - -
47B ASP* 3.7 33.9 - - + +
48B VAL* 4.0 25.9 - - - +
51B SER* 3.8 15.9 - - - +
207M THR* 3.2 8.2 + - + +
208M ALA* 1.3 77.7 - - + +
210M LYS* 1.3 61.0 + - - +
212M VAL* 3.4 8.4 + - - +
213M LEU* 3.1 32.6 + - + +
247M ASP* 5.5 2.7 - - - +
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Residues in contact with LYS 210 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B VAL* 4.2 18.8 + - - +
51B SER* 4.2 10.3 - - - +
54B SER* 3.0 33.0 + - - +
55B CYS* 3.9 22.3 - - - -
127B SER* 4.3 8.3 + - - -
205M ASP 5.5 1.6 - - - +
206M LEU* 4.3 18.5 - - + +
207M THR* 3.0 39.9 + - + +
209M LYS* 1.3 74.0 - - - +
211M MET* 1.3 58.8 + - - +
212M VAL 3.4 0.2 - - - -
213M LEU* 3.9 7.2 - - - +
214M ALA* 2.9 31.2 + - - +
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Residues in contact with MET 211 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168M ILE* 3.7 30.2 - - + +
170M ASN* 3.5 22.7 - - - +
206M LEU* 3.6 23.5 - - + +
207M THR 2.8 18.3 + - - +
208M ALA* 3.6 9.2 - - - +
209M LYS 3.3 0.2 - - - -
210M LYS* 1.3 72.9 - - - +
212M VAL* 1.3 57.2 + - + +
214M ALA* 3.5 1.6 + - - +
215M LEU* 3.0 38.9 + - + +
234M ILE* 4.1 14.4 - - + -
243M VAL* 3.8 26.5 - - + -
244M TYR 3.8 9.9 - - - +
245M GLY* 4.1 9.0 - - - -
256M VAL* 4.7 13.5 - - + -
261M ILE* 5.0 3.6 - - + -
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Residues in contact with VAL 212 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208M ALA 3.4 15.4 + - - +
209M LYS* 3.8 8.5 - - - +
210M LYS 3.4 0.2 - - - -
211M MET* 1.3 74.2 - - - +
213M LEU* 1.3 60.2 + - + +
215M LEU* 3.4 7.9 + - + +
216M LEU* 2.8 50.7 + - + +
256M VAL* 4.3 22.0 - - + -
260M LYS* 4.4 28.5 - - + +
264M ILE* 4.6 8.1 - - + -
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Residues in contact with LEU 213 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B SER* 3.6 41.1 - - - +
52B ILE* 4.4 11.4 - - + +
55B CYS* 4.3 19.1 - - + -
209M LYS* 3.1 21.7 + - + +
210M LYS* 3.9 4.3 - - - +
211M MET 3.4 0.2 - - - -
212M VAL* 1.3 75.7 - - + +
214M ALA* 1.3 57.6 + - - +
216M LEU* 3.5 13.7 + - + +
217M GLU* 3.1 29.3 + - - +
220M ARG* 4.9 5.5 + - - +
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Residues in contact with ALA 214 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B CYS* 5.2 3.1 - - - -
166M LEU* 4.0 14.9 - - + +
203M LYS* 3.5 40.2 + - + +
206M LEU* 4.2 10.5 - - + -
210M LYS 2.9 19.0 + - - +
211M MET 3.8 4.3 - - - +
213M LEU* 1.3 76.6 - - - +
215M LEU* 1.3 61.5 + - - +
217M GLU* 3.6 5.1 + - - +
218M LEU* 3.4 19.6 + - - +
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Residues in contact with LEU 215 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166M LEU* 3.8 16.2 - - + -
168M ILE* 4.4 11.0 - - + -
211M MET* 3.0 28.7 + - + +
212M VAL* 3.8 4.9 - - + +
214M ALA* 1.3 74.6 - - - +
216M LEU* 1.3 63.5 + - - +
218M LEU* 3.2 5.1 + - - +
219M ALA* 3.1 19.1 + - - +
232M VAL* 3.5 32.3 - - + -
234M ILE* 5.0 0.7 - - + -
256M VAL* 5.6 1.6 - - + -
261M ILE* 3.8 36.1 - - + -
264M ILE* 4.0 17.7 - - + -
265M PHE* 3.6 25.4 - - + -
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Residues in contact with LEU 216 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212M VAL* 2.8 48.6 + - + +
213M LEU* 3.8 15.9 - - + +
215M LEU* 1.3 72.2 - - - +
217M GLU* 1.3 57.1 + - - +
219M ALA* 3.4 5.0 + - + +
220M ARG* 3.0 46.5 + - - +
264M ILE* 3.9 27.8 - - + -
269M SER* 6.5 0.7 - - - -
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Residues in contact with GLU 217 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ARG* 2.7 43.1 + - - -
57D ARG* 5.6 3.0 + - - -
203M LYS* 4.2 10.9 + - - -
213M LEU 3.1 18.3 + - - +
214M ALA* 3.9 5.3 - - - +
215M LEU 3.3 0.2 - - - -
216M LEU* 1.3 73.8 - - - +
218M LEU* 1.3 62.8 + - - +
220M ARG* 3.3 28.8 + - + +
221M GLN* 3.3 31.8 + - - +
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Residues in contact with LEU 218 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164M HIS* 3.4 39.3 - - + +
166M LEU* 3.6 37.9 - - + +
214M ALA 3.4 11.7 + - - +
215M LEU* 3.2 9.5 + - - +
217M GLU* 1.3 77.4 - - - +
219M ALA* 1.3 60.5 + - - +
221M GLN* 3.4 12.4 + - + +
224M HIS* 3.0 28.6 + - + -
230M CYS* 4.3 9.4 - - - -
231M VAL 4.4 0.4 - - - +
232M VAL* 3.9 22.2 - - + -
265M PHE* 3.9 11.7 - - + -
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Residues in contact with ALA 219 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215M LEU 3.1 6.4 + - - +
216M LEU* 3.6 6.7 - - + +
218M LEU* 1.3 75.7 - - - +
220M ARG* 1.3 61.3 + - - +
221M GLN 3.5 4.2 + - - +
224M HIS* 4.7 0.2 - - - -
264M ILE* 3.6 41.3 - - + +
265M PHE* 3.8 16.0 - - + -
269M SER* 5.1 2.6 - - - +
270M CYS* 3.4 31.2 - - + +
271M PRO* 5.6 0.5 - - - +
272M SER* 5.4 0.2 + - - -
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Residues in contact with ARG 220 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213M LEU* 4.9 4.6 + - - +
216M LEU* 3.0 31.9 + - - +
217M GLU* 3.5 37.4 - - + +
218M LEU 3.2 0.8 - - - -
219M ALA* 1.3 73.8 - - - +
221M GLN* 1.3 65.7 + - - +
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Residues in contact with GLN 221 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164M HIS* 4.4 25.8 + - + +
217M GLU* 3.3 37.9 + - - +
218M LEU* 3.6 16.8 - - + +
219M ALA 3.3 4.2 - - - +
220M ARG* 1.3 83.9 - - - +
222M ASP* 1.3 62.6 + - - +
224M HIS* 3.3 22.3 + - + +
272M SER* 3.8 9.0 + - - -
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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