Contacts of the strand formed by residues 209 - 217 (chain A) in PDB entry 3C7N
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 TYR 209 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A VAL* 3.7 25.0 - - + +
203A ASP 3.7 2.5 - - - -
204A ILE* 3.4 22.4 - - + +
208A SER* 1.3 76.1 - - - +
210A THR* 1.3 82.8 + - - +
211A CYS* 4.3 3.7 - - + +
228A CYS* 3.4 4.7 - - - +
229A ASP* 2.8 42.1 + - + +
232A PHE* 2.9 37.1 + + + +
316A ARG 4.2 0.9 - - - -
317A VAL* 2.8 38.9 + - + +
320A PRO* 3.2 34.0 - - + +
321A VAL* 3.5 20.1 + - - +
354A ILE* 5.6 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PRO* 5.4 0.5 - - - +
147A PRO* 3.7 38.2 - - + +
148A TRP* 5.1 0.9 - - - -
174A ASP* 4.8 1.7 + - - -
175A VAL* 3.8 23.3 - - + +
201A PHE 3.9 0.9 - - - +
202A VAL* 3.6 2.1 - - - -
203A ASP* 2.9 34.8 + - - -
208A SER* 4.8 7.4 - - - -
209A TYR* 1.3 85.7 + - - +
211A CYS* 1.3 67.4 + - - +
212A SER* 4.6 0.4 - - - +
226A THR* 4.1 15.3 - - + -
227A ALA 3.7 7.4 - - - +
228A CYS* 4.2 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ALA* 5.2 0.9 - - - -
201A PHE 3.4 6.3 - - - +
202A VAL* 4.2 11.2 - - + -
209A TYR* 4.3 13.7 - - + +
210A THR* 1.3 75.9 - - - +
212A SER* 1.3 65.8 + - - +
213A ILE* 4.9 2.0 - - - -
226A THR* 3.6 0.7 - - - -
227A ALA 3.0 32.9 + - - +
320A PRO 4.4 6.7 - - - +
321A VAL* 4.0 8.3 - - - -
324A ALA* 3.8 23.0 - - - +
358A PHE* 3.7 30.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL* 4.0 10.1 - - - +
176A THR* 5.0 1.6 + - - -
199A VAL 4.1 0.7 - - - +
201A PHE* 2.9 34.6 + - - +
210A THR* 4.3 3.7 - - - +
211A CYS* 1.3 74.4 - - - +
213A ILE* 1.3 62.4 + - - +
214A MET* 3.0 27.5 + - - +
223A VAL* 4.2 2.9 - - - +
225A GLY 3.0 6.1 - - - -
226A THR* 2.8 35.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 3.2 34.8 - - + -
199A VAL 3.7 7.6 - - - +
200A ALA* 3.8 17.3 - - + +
211A CYS* 4.9 1.3 - - - -
212A SER* 1.3 73.7 - - - +
214A MET* 1.3 64.0 + - - +
223A VAL* 3.8 0.5 - - - +
224A LEU* 2.8 29.2 + - + +
225A GLY 2.7 16.7 + - - +
324A ALA* 4.0 13.0 - - + +
325A LEU* 3.8 49.4 - - + +
328A ALA* 4.5 4.5 - - + -
330A LEU* 3.9 10.8 - - + -
335A VAL* 4.5 4.3 - - + -
358A PHE* 4.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL* 3.5 28.3 - - + +
176A THR* 4.0 7.6 - - - +
179A GLY* 4.0 20.9 - - - -
197A ARG 3.4 1.0 - - - +
198A ILE* 3.3 4.3 - - - +
199A VAL 2.8 37.9 + - - +
201A PHE* 4.1 18.6 - - + -
212A SER* 3.0 26.7 - - - +
213A ILE* 1.3 78.8 - - - +
215A ALA* 1.3 61.3 + - - +
216A PHE* 3.9 15.3 - - + -
221A LEU* 4.1 11.2 - - + -
222A LYS 3.4 9.6 - - - +
223A VAL* 3.6 26.9 - - + -
224A LEU* 3.9 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PRO* 3.8 17.0 - - + -
197A ARG 3.4 3.6 - - - -
198A ILE* 3.5 22.4 - - + -
214A MET* 1.3 70.9 - - - +
216A PHE* 1.3 62.5 + - - +
220A GLN* 3.8 1.7 - - - +
221A LEU* 3.2 4.8 - - - -
222A LYS* 2.9 39.6 + - + +
224A LEU* 3.7 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLY* 3.4 24.9 - - - -
182A TYR* 3.4 22.9 - + - -
183A GLY* 3.7 16.4 - - - -
189A LEU* 4.1 19.5 - - + -
190A PRO* 3.7 3.3 - - - +
196A PRO* 3.2 0.3 - - - +
197A ARG* 2.9 36.0 + - + +
199A VAL* 3.6 27.6 - - + -
201A PHE* 3.5 31.9 - + - -
214A MET* 3.9 13.9 - - + -
215A ALA* 1.3 74.1 - - - +
217A LYS* 1.3 70.0 + - - +
220A GLN 3.3 7.0 - - - -
221A LEU* 3.6 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 4.0 10.2 - - - +
190A PRO* 3.5 16.2 - - + +
191A GLU 3.9 9.0 - - - +
192A GLY* 3.2 24.0 + - - +
193A GLU 5.1 0.6 - - - -
194A GLU 2.7 29.7 + - - -
195A LYS* 4.6 0.6 - - - +
196A PRO* 3.5 28.9 - - + +
216A PHE* 1.3 83.9 - - - +
218A LYS* 1.3 68.4 + - - +
219A GLY 2.9 0.7 + - - -
220A GLN* 2.8 48.4 + - + +
392A PHE* 4.9 0.5 - - - -
----------------------------------------------------------
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