Contacts of the strand formed by residues 206 - 222 (chain A) in PDB entry 2VDY
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 206 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASN* 3.7 37.0 - - + +
199A PHE 3.6 10.3 - - - +
200A TYR* 3.6 26.0 - - + -
202A ASP 5.0 2.2 - - - +
203A GLU 6.3 1.1 - - - -
204A THR 4.3 1.5 + - - -
205A THR* 1.3 82.0 - - - +
207A VAL* 1.3 68.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASN* 3.6 3.6 - - - -
199A PHE* 2.8 54.8 + - + +
201A VAL* 3.8 12.1 - - + -
205A THR* 4.7 8.1 - - + -
206A VAL* 1.3 79.7 - - - +
208A LYS* 1.3 66.2 + - - +
381A ASN* 3.5 35.7 - - - +
382A PRO* 4.6 2.7 - - + -
383A VAL* 4.6 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLU* 3.5 32.3 + - + +
197A GLU* 3.5 9.8 - - - +
198A ASN* 3.3 34.9 + - - +
207A VAL* 1.3 74.7 - - - +
209A VAL* 1.3 61.5 + - - +
210A PRO* 4.8 0.9 - - - +
383A VAL* 4.0 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLU* 3.3 7.3 + - - -
197A GLU 2.9 37.6 + - - +
199A PHE* 3.9 20.9 - - + -
207A VAL* 5.4 0.2 - - + -
208A LYS* 1.3 75.8 - - - +
210A PRO* 1.3 77.8 - - + +
211A MET* 3.2 12.3 + - + -
280A PRO* 3.8 27.8 - - + -
281A LYS 4.3 8.1 - - - +
382A PRO* 3.7 28.0 - - + -
383A VAL* 4.6 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A THR* 4.2 8.5 - - + -
195A ARG 3.8 5.8 - - - +
196A GLU* 3.5 20.2 - - + +
208A LYS 4.8 0.9 - - - +
209A VAL* 1.3 91.9 - - + +
211A MET* 1.3 59.9 + - - +
212A MET 4.1 0.2 - - - -
280A PRO* 3.4 2.9 - - - +
281A LYS* 2.8 60.4 + - + +
383A VAL* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A SER 4.2 1.7 - - - +
194A THR* 3.3 6.6 - - - +
195A ARG* 2.7 38.5 + - + +
197A GLU* 3.4 45.8 - - + +
198A ASN 4.7 0.7 - - - +
199A PHE* 5.2 0.2 - - + -
209A VAL* 3.2 14.7 + - + +
210A PRO* 1.3 72.3 - - - +
212A MET* 1.3 67.4 + - - +
213A LEU* 5.1 0.2 - - - +
278A TYR* 3.8 21.4 - - + +
279A ILE* 3.5 6.5 - - - -
280A PRO* 3.5 22.9 - - + -
356A ARG* 4.7 2.2 - - + -
357A PHE 3.7 18.2 - - - +
358A ASN* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PHE* 3.7 21.3 - - + -
194A THR* 4.0 15.5 - - - +
211A MET* 1.3 76.9 - - - +
213A LEU* 1.3 62.4 + - - +
278A TYR* 3.2 25.6 - - - +
279A ILE* 2.9 39.3 + - + +
280A PRO 3.5 25.6 - - - +
281A LYS* 3.6 22.7 - - + +
331A LEU* 4.3 2.7 - - + -
332A ASN* 3.3 44.0 - - - +
333A GLU* 3.4 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PHE* 3.8 4.2 - - - +
190A ASP* 3.1 31.0 + - - +
193A SER* 3.6 39.1 + - - +
211A MET 4.1 0.4 + - - +
212A MET* 1.3 78.5 - - - +
214A GLN* 1.3 79.4 + - - +
215A SER* 4.7 2.0 - - - +
276A ASP* 4.2 10.5 - - + +
277A LEU 3.4 9.4 - - - +
278A TYR* 3.5 47.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLN* 2.8 38.0 + - - +
188A PRO 3.8 8.6 + - - +
189A PHE* 3.6 36.0 - - + -
190A ASP* 4.3 6.3 - - + +
213A LEU* 1.3 80.6 - - - +
215A SER* 1.3 60.0 + - - +
216A SER* 2.6 30.2 + - - +
218A ILE* 4.4 7.4 - - + +
233A MET* 3.4 18.8 - - - +
275A VAL 3.2 2.9 - - - +
276A ASP* 3.7 0.9 - - - -
277A LEU* 3.0 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU* 4.7 3.2 - - - +
214A GLN* 1.3 70.7 - - - +
216A SER* 1.3 60.0 + - - +
274A GLN* 4.4 11.7 + - - -
275A VAL 3.4 6.3 + - - -
276A ASP* 2.7 23.5 + - - -
352A PRO* 4.2 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLN* 3.5 17.4 - - - +
214A GLN* 2.6 33.4 + - - +
215A SER* 1.3 76.0 + - - +
217A THR* 1.3 59.9 + - - +
218A ILE* 3.3 12.2 + - - +
273A SER 3.4 0.2 - - - +
274A GLN* 3.7 9.0 - - - +
275A VAL 3.1 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLN* 3.0 21.3 + - - +
216A SER* 1.3 69.9 - - - +
218A ILE* 1.3 59.5 + - - +
272A SER* 3.9 28.0 - - - +
273A SER 3.2 12.1 - - - +
274A GLN* 2.6 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLN* 3.9 18.4 - - - +
214A GLN* 4.4 8.1 - - - +
216A SER* 3.3 23.1 + - - +
217A THR* 1.3 79.5 - - - +
219A SER* 1.3 76.7 + - - +
220A TYR* 3.2 4.3 + - - +
231A VAL* 3.8 21.5 - - + -
232A GLN 3.9 10.8 - - - +
233A MET* 4.6 10.1 - - + -
272A SER* 4.4 2.0 - - - -
273A SER* 2.8 29.8 + - - +
275A VAL* 4.0 17.5 - - + +
277A LEU* 3.9 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLN* 5.6 0.6 - - - +
218A ILE* 1.3 71.2 - - - +
220A TYR* 1.3 59.3 + - - +
231A VAL* 3.2 10.0 - - - +
232A GLN* 3.2 41.6 + - - -
270A LEU* 3.5 24.5 + - - +
271A THR 3.6 8.7 - - - -
272A SER* 4.4 9.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE 3.2 8.3 + - - +
219A SER* 1.3 75.2 - - - +
221A LEU* 1.3 64.7 + - - +
222A HIS* 3.4 31.0 - - + +
229A GLN* 2.7 43.9 + - + -
230A LEU 3.5 11.7 - - - -
231A VAL* 4.1 11.2 - - + -
270A LEU* 3.7 2.8 - - - +
271A THR* 2.8 38.7 + - + +
273A SER* 3.9 16.4 - - - -
275A VAL* 4.0 15.9 - - + -
353A ILE* 3.9 38.0 - - + +
355A LEU* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 1.3 81.7 - - - +
222A HIS* 1.3 74.0 + - - +
223A ASP* 4.2 6.7 - - - +
229A GLN* 3.5 0.9 - - - -
230A LEU* 2.9 47.1 + - + +
265A ARG* 4.5 2.5 - - - +
266A TRP* 3.6 48.9 - - + +
269A GLY* 3.4 26.2 - - - +
270A LEU* 3.8 14.1 - - + +
271A THR* 5.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 3.4 25.0 - - + +
221A LEU* 1.3 80.0 - - - +
223A ASP* 1.3 78.5 + - - +
224A SER* 3.5 7.3 + - - -
228A CYS 5.1 1.1 - - - -
229A GLN* 3.3 39.3 + - + +
247A ASP* 5.9 0.4 + - - -
----------------------------------------------------------
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