Contacts of the strand formed by residues 214 - 222 (chain B) in PDB entry 6VSU
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 ALA 214 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B PRO* 4.0 4.4 - - - +
179B VAL 3.0 7.4 - - - +
181B ILE* 3.6 32.3 - - + -
208B ILE* 3.9 5.7 + - + -
209B MET* 3.7 31.9 - - - +
212B GLY* 3.3 7.5 - - - -
213B TYR* 1.3 78.8 - - - +
215B ARG* 1.3 65.1 + - - +
216B ARG 4.1 6.1 - - - +
217B LEU* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B PRO* 3.8 16.3 - - + +
179B VAL 2.6 12.9 + - - +
180B ASP* 2.9 35.4 + - - +
209B MET* 4.2 9.9 - - - +
214B ALA* 1.3 77.4 - - - +
216B ARG* 1.3 71.9 + - + +
217B LEU 4.1 0.7 + - - -
236B PHE 5.2 1.4 - - - +
237B GLY 5.7 0.7 - - - +
259B GLY 3.9 2.0 - - - +
260B GLU* 3.0 36.5 + - - +
261B GLY* 4.4 3.2 - - - -
262B VAL* 3.6 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL 4.1 1.6 - - - +
180B ASP* 3.1 29.3 + - + +
181B ILE* 3.0 26.1 + - - +
214B ALA* 4.1 3.1 - - - +
215B ARG* 1.3 97.7 - - + +
217B LEU* 1.3 59.1 + - - +
218B LEU* 4.1 16.5 - - + +
237B GLY 5.7 2.7 - - - -
239B GLU* 3.0 40.0 + - - +
252B MET* 5.2 8.5 - - - +
257B LYS 3.9 9.1 + - - -
258B LEU* 3.7 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ILE* 3.5 32.8 - - + -
183B HIS* 3.8 19.5 - - + -
190B ILE* 5.0 1.8 - - + -
205B PHE* 3.9 25.4 - - + -
209B MET* 4.0 33.1 - - + +
215B ARG 4.1 1.0 + - - -
216B ARG* 1.3 72.1 - - - +
218B LEU* 1.3 56.9 + - - +
219B GLN* 3.8 16.6 - - + +
237B GLY 5.3 1.8 + - - -
238B VAL* 3.4 31.6 - - + +
239B GLU* 2.8 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ILE 2.9 15.6 + - - +
182B LEU* 3.5 12.6 - - + +
183B HIS* 2.6 35.3 + - - +
216B ARG* 4.1 24.0 - - + +
217B LEU* 1.3 72.1 - - - +
219B GLN* 1.3 57.4 + - - +
220B VAL* 4.0 6.1 - - + -
239B GLU* 3.5 35.4 - - - +
241B TYR* 4.2 16.6 - - + +
252B MET* 5.4 0.9 - - + -
256B LEU* 3.9 35.0 - - + -
258B LEU* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B HIS* 2.9 27.8 + - - +
188B PRO* 2.7 37.7 + - - +
190B ILE* 4.2 3.3 - - - +
205B PHE* 4.5 0.4 - - - +
217B LEU* 3.8 15.5 - - + +
218B LEU* 1.3 73.0 - - - +
220B VAL* 1.3 60.7 + - - +
222B ILE* 3.9 17.7 - - + -
238B VAL* 3.3 23.6 - - + +
239B GLU 2.9 10.4 + - - +
240B GLN* 2.7 33.8 + - - -
241B TYR* 2.9 32.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
182B LEU* 3.8 23.1 - - + -
183B HIS 2.8 9.4 + - - +
184B LEU* 3.3 30.3 - - + +
185B ASP 2.9 24.2 + - - +
218B LEU* 4.4 4.7 - - + -
219B GLN* 1.3 77.7 - - - +
221B GLY* 1.3 64.1 + - - +
222B ILE* 3.5 1.8 - - - +
241B TYR* 3.9 9.4 - - + -
246B PHE* 5.3 3.6 - - + -
253B LEU* 3.7 38.1 - - + -
256B LEU* 5.2 0.2 - - + -
273B CYS* 4.4 0.2 - - - +
290B LEU* 4.5 3.6 - - + -
298B ILE* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ASP 3.1 11.0 - - - +
186B ALA* 3.3 1.2 - - - -
220B VAL* 1.3 76.2 - - - +
222B ILE* 1.3 65.1 + - - +
223B ARG* 3.0 27.6 + - - -
241B TYR 3.4 5.5 + - - -
243B MET* 3.6 26.7 - - - +
273B CYS* 4.9 0.9 - - - -
290B LEU* 4.2 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ASP* 3.5 9.2 - - + +
186B ALA 3.4 6.3 - - - +
187B HIS 3.4 32.1 - - - +
188B PRO* 3.4 13.9 - - + -
219B GLN* 3.9 29.4 - - + +
221B GLY* 1.3 75.9 - - - +
223B ARG* 1.3 60.4 + - - +
225B ILE* 3.9 38.6 - - + -
240B GLN* 5.0 3.4 - - + -
241B TYR 3.3 18.1 + - - +
242B GLU* 3.1 17.5 - - + +
243B MET 3.0 24.9 + - - -
----------------------------------------------------------
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