Contacts of the helix formed by residues 209 - 224 (chain B) in PDB entry 3RC0
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 SER 209 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B TYR* 3.1 8.7 + - - -
206B ARG 4.4 10.5 - - - -
207B VAL 3.1 6.3 + - - +
208B ARG* 1.3 77.4 - - - +
210B LEU* 1.3 64.9 + - - +
211B GLU* 3.6 9.9 + - - +
212B LEU* 3.2 29.5 + - - +
213B TYR* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ARG* 4.6 17.3 - - + -
188B TYR* 3.5 49.4 + - + -
189B GLN* 4.9 13.5 - - - +
209B SER* 1.3 71.6 + - - +
211B GLU* 1.3 64.3 + - - +
213B TYR* 2.9 16.4 + - + +
214B HIS* 3.0 47.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B SER* 3.3 7.7 + - - +
210B LEU* 1.3 79.6 - - - +
212B LEU* 1.3 63.7 + - - +
214B HIS* 3.1 11.3 + - - +
215B GLN* 3.1 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 3.9 12.3 - - + -
133B LEU* 5.5 5.4 - - + -
150B LEU* 3.6 29.8 - - + -
206B ARG 4.4 4.3 - - - +
207B VAL* 3.8 39.5 - - + +
209B SER* 3.2 21.6 + - - +
211B GLU* 1.3 79.1 - - - +
213B TYR* 1.3 57.8 + - - +
215B GLN* 3.3 12.2 + - - +
216B LEU* 2.9 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B VAL* 4.2 1.6 - - - +
126B LEU* 3.5 35.9 - - + +
130B LEU* 4.2 13.9 - - + -
184B ILE* 3.5 38.1 - - + -
187B GLU* 2.7 26.3 + - - +
188B TYR* 3.7 30.3 - + + -
192B VAL* 3.5 39.0 - - + +
209B SER 3.0 12.7 + - - +
210B LEU* 2.9 13.0 + - + +
212B LEU* 1.3 77.4 - - - +
214B HIS* 1.3 59.1 + - - +
216B LEU* 3.4 5.1 + - + +
217B VAL* 3.0 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B MET* 3.9 12.1 - - + +
158B PHE* 3.8 18.0 - + + -
181B LEU* 3.8 33.4 + - + +
184B ILE* 3.6 27.3 - - + +
185B ARG* 5.0 5.8 - - + +
210B LEU* 3.0 56.1 + - + +
211B GLU* 3.4 10.5 - - + +
213B TYR* 1.3 76.0 - - - +
215B GLN* 1.3 58.2 + - - +
217B VAL* 3.4 4.9 + - - +
218B ALA* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU* 3.4 52.7 + - + +
151B GLY* 4.1 8.1 - - - -
153B LEU* 3.5 7.7 - - + +
158B PHE* 4.2 19.1 - - + -
211B GLU* 3.1 42.7 + - + +
212B LEU* 3.6 24.7 - - - +
214B HIS* 1.3 77.0 - - - +
216B LEU* 1.3 57.7 + - - +
218B ALA* 3.3 3.5 + - - +
219B LEU* 2.9 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.8 13.7 - - + +
129B LEU* 4.7 8.7 - - + -
130B LEU* 3.3 44.6 - - + +
133B LEU* 3.9 28.7 - - + -
147B TRP* 4.3 3.1 - - + -
150B LEU* 4.0 17.3 - - + -
212B LEU* 2.9 26.8 + - + +
213B TYR* 4.0 5.2 - - + +
215B GLN* 1.3 74.5 - - - +
217B VAL* 1.3 60.4 + - - +
219B LEU* 3.3 23.0 + - + +
220B VAL* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TRP* 4.1 10.5 - - + -
126B LEU* 3.9 28.0 - - + -
180B ASP* 6.3 0.2 - - + -
184B ILE* 3.9 25.6 - - + -
213B TYR* 3.0 38.0 + - + +
214B HIS 3.7 4.7 - - - +
216B LEU* 1.3 75.8 - - - +
218B ALA* 1.3 58.9 + - - +
220B VAL* 3.3 4.6 + - - +
221B MET* 3.0 42.0 + - + +
478B EDO 4.1 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 3.7 7.6 - - + -
155B HIS* 3.4 19.1 + - + +
157B MET* 4.2 0.7 - - - -
158B PHE* 3.7 27.6 - - + -
214B HIS 3.0 13.6 + - - +
215B GLN 3.4 9.0 - - - +
217B VAL* 1.3 78.4 - - - +
219B LEU* 1.3 56.7 + - - +
221B MET* 3.2 21.5 + - + +
222B ALA* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 4.5 6.5 - - + -
147B TRP* 3.4 48.5 - - + -
148B PRO* 3.9 27.4 - - + -
150B LEU* 4.2 14.6 - - + -
153B LEU* 4.5 4.4 - - + +
155B HIS* 5.5 0.2 - - - -
215B GLN 2.9 14.7 + - - +
216B LEU* 3.5 18.6 - - + +
217B VAL 3.3 0.2 - - - -
218B ALA* 1.3 74.3 - - - +
220B VAL* 1.3 60.4 + - - +
222B ALA* 4.9 0.4 - - - -
223B TYR* 2.8 59.7 + - + +
243B MET* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TRP* 3.7 35.7 - - + -
125B LEU* 3.8 20.9 - - + -
126B LEU* 3.7 19.3 - - + -
129B LEU* 3.7 20.4 - - + -
216B LEU 2.9 20.4 + - - +
217B VAL 3.7 4.7 - - - +
219B LEU* 1.3 75.3 - - - +
221B MET* 1.3 63.2 + - - +
224B SER* 2.6 47.5 + - - +
241B PRO* 4.2 1.3 - - + -
243B MET* 4.7 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TRP* 3.5 18.6 - - + -
155B HIS* 4.5 4.5 - - + -
157B MET* 3.4 33.7 - - - -
180B ASP* 4.3 18.6 - - - +
184B ILE* 5.4 0.4 - - + -
217B VAL* 3.0 21.9 + - + +
218B ALA* 3.2 31.4 + - + +
220B VAL* 1.3 79.6 - - - +
222B ALA* 1.3 58.9 + - - +
223B TYR 3.8 0.2 + - - -
295B HIS* 4.4 10.5 - - + +
296B MET* 3.5 54.2 - - + +
297B TYR* 3.7 17.3 + - - -
310Q LYS* 4.4 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B HIS* 3.6 10.1 - - + +
218B ALA 3.0 14.6 + - - +
219B LEU* 3.2 0.4 + - - -
221B MET* 1.3 76.4 - - - +
223B TYR* 1.3 73.6 + - + +
296B MET 3.5 11.9 - - - +
297B TYR* 3.1 27.6 - - + -
480B SAM 3.4 38.3 - - - +
310Q LYS* 3.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B TRP* 4.9 8.7 - + - -
148B PRO* 3.3 39.0 - - + +
153B LEU* 5.5 4.7 - - + -
219B LEU* 2.8 32.0 + - + +
222B ALA* 1.3 97.6 - - + +
224B SER* 1.3 64.5 - - - +
225B PHE* 3.4 21.0 - - - -
243B MET* 3.6 18.3 - - + +
244B VAL 5.1 0.3 + - - -
248B ASP* 3.7 30.9 - - + +
480B SAM 2.8 64.3 + + + -
310Q LYS* 3.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TRP* 5.4 2.1 - - - -
125B LEU* 4.5 0.4 - - - -
219B LEU 4.1 0.2 + - - -
220B VAL* 2.6 30.5 + - - +
221B MET 5.0 0.2 + - - -
223B TYR* 1.3 80.2 - - - +
225B PHE* 1.3 60.4 + - - +
241B PRO* 3.4 27.4 - - - +
242B VAL 3.4 9.4 - - - -
243B MET* 3.8 18.1 - - - +
310Q LYS* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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