Contacts of the strand formed by residues 211 - 218 (chain A) in PDB entry 3NYN
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 MET 211 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 5.2 6.3 - - - -
15A ALA* 3.9 30.3 - - - +
16A ARG* 4.2 10.1 - - + -
189A TYR* 3.7 12.6 - - + -
202A ALA* 5.9 0.7 - - + -
203A CYS 3.0 29.4 - - - +
204A GLN* 3.1 37.9 - - + +
209A GLY 4.4 5.8 - - - +
210A LYS* 1.3 85.8 - - - +
212A TYR* 1.3 69.6 + - - +
265A LEU* 4.0 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PHE* 5.4 0.2 - + - -
202A ALA 3.7 0.5 - - - -
203A CYS* 2.8 37.4 + - - +
205A VAL* 3.7 25.1 - - + -
210A LYS* 3.6 29.2 + - + +
211A MET* 1.3 79.5 - - - +
213A ALA* 1.3 58.4 + - - +
248A SER* 5.7 3.4 - - - -
250A ALA* 3.6 22.9 - - + +
251A TYR* 3.9 3.1 - + - -
262A VAL* 3.2 28.9 - - + -
263A LEU 3.5 21.1 - - - +
264A THR* 4.3 7.2 - - - -
265A LEU* 3.7 13.9 - - - +
510A PRO* 4.5 4.5 + - + +
514A GLU* 2.8 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 5.2 0.4 - - + -
200A VAL* 4.9 6.3 - - + -
201A CYS 3.7 5.4 - - - +
203A CYS* 4.2 0.2 - - - -
212A TYR* 1.3 74.8 - - - +
214A CYS* 1.3 60.6 + - - +
215A LYS 4.0 0.9 - - - +
261A LEU 3.6 0.7 - - - +
262A VAL* 3.3 3.5 - - - +
263A LEU* 2.6 47.8 + - + +
264A THR 3.8 0.4 - - - +
265A LEU* 3.4 22.2 - - + +
577A SGV 3.7 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLN* 4.2 3.4 - - - +
199A GLU 4.0 0.3 - - - +
200A VAL* 3.5 2.7 - - - +
201A CYS* 2.7 43.3 + - - +
203A CYS* 3.9 19.3 - - + -
213A ALA* 1.3 74.8 - - - +
215A LYS* 1.3 59.1 + - - +
216A LYS* 3.4 25.8 + - - +
253A TYR* 3.8 15.0 - - - -
260A CYS* 3.7 30.5 - - - -
261A LEU 3.4 4.5 - - - -
262A VAL* 4.4 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLY* 5.9 5.8 - - - -
196A GLY 6.1 0.9 - - - +
197A PHE* 6.1 1.6 - - - -
199A GLU 4.0 3.1 - - - -
200A VAL* 3.8 20.8 - - + +
213A ALA* 4.0 1.4 - - - +
214A CYS* 1.3 70.0 - - - +
216A LYS* 1.3 60.9 + - - +
217A LEU* 3.9 27.4 - - + +
234A GLU* 2.8 41.9 + - - +
259A LEU 3.7 0.9 - - - +
260A CYS* 3.4 3.4 - - - -
261A LEU* 2.7 47.9 + - + +
263A LEU* 4.3 13.2 - - + +
329A ASP* 2.9 29.0 + - - +
331A GLY* 5.2 1.0 - - - +
577A SGV 3.6 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLN* 2.8 34.7 + - - +
198A GLY* 3.3 19.1 - - - -
199A GLU* 2.9 40.9 + - + +
201A CYS* 4.1 11.8 - - - -
214A CYS* 3.9 19.7 - - - +
215A LYS* 1.3 75.8 - - - +
217A LEU* 1.3 68.2 + - - +
218A GLU* 4.1 2.5 - - + -
253A TYR* 5.5 0.4 - - - -
255A THR* 6.2 1.9 - - - +
258A ALA* 4.5 13.9 - - + -
259A LEU 3.6 4.5 - - - -
260A CYS* 4.2 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLY* 6.4 0.7 - - - -
196A GLY 6.1 0.2 - - - +
197A PHE* 3.8 32.8 - - + +
198A GLY 4.9 0.2 - - - +
215A LYS* 3.9 31.6 - - + +
216A LYS* 1.3 84.2 - - - +
218A GLU* 1.3 64.0 + - - +
219A LYS 3.4 0.3 + - - -
222A ILE* 3.9 17.2 - - + +
231A ALA* 3.9 31.6 - - + -
234A GLU* 4.9 4.9 - - - +
258A ALA* 3.6 2.4 - - - +
259A LEU* 2.7 43.8 + - + +
261A LEU* 4.8 15.9 - - + -
502A PHE* 5.1 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 2.9 20.5 + - - +
198A GLY* 4.4 9.4 - - - -
199A GLU* 5.2 10.2 + - - +
216A LYS* 5.6 2.2 - - + -
217A LEU* 1.3 70.7 - - - +
219A LYS* 1.3 67.5 + - - +
220A LYS* 3.1 3.5 + - + +
221A ARG* 3.1 43.4 + - + +
222A ILE* 3.1 23.1 + - - +
257A ASP* 3.4 14.7 - - + +
258A ALA* 3.7 6.5 - - + -
485A THR* 5.1 9.3 - - - +
----------------------------------------------------------
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