Contacts of the helix formed by residues 206 - 220 (chain A) in PDB entry 4YD1
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 GLY 206 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PHE* 1.3 72.5 - - - +
207A GLU* 1.3 65.5 + - - -
210A SER* 2.8 26.4 + - - -
2D C 2.9 34.3 + - - -
3D C 5.1 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLY* 1.3 71.6 - - - +
208A HIS* 1.3 64.3 + - - +
210A SER* 4.0 2.8 - - - -
211A ARG* 3.1 26.2 + - + +
2D C 3.3 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 4.5 0.4 - - - +
179A PHE* 3.9 23.3 - + - -
207A GLU* 1.3 79.7 - - - +
209A SER* 1.3 63.4 + - - +
211A ARG* 3.3 10.9 + - + +
212A VAL* 3.2 25.4 + - + +
224A GLU* 2.8 38.6 + - - -
1D G 2.8 41.6 + - - -
2D C 3.0 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 4.3 11.2 - - - +
178A THR* 4.7 1.4 - - - +
179A PHE* 3.6 23.8 - - - -
182A ALA* 3.9 11.9 - - - +
204A HIS 4.0 6.5 + - - -
205A PHE* 3.6 24.4 - - - -
208A HIS* 1.3 76.9 - - - +
210A SER* 1.3 62.8 + - - +
212A VAL* 3.4 4.6 + - - +
213A VAL* 3.2 26.3 + - - +
1D G 4.0 1.6 + - - -
2D C 2.9 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 3.7 13.8 - - - +
199A LEU* 3.8 26.6 - - - +
205A PHE* 3.9 14.6 + - - +
206A GLY 2.8 24.8 + - - -
207A GLU* 4.0 2.7 - - - -
209A SER* 1.3 73.4 - - - +
211A ARG* 1.3 61.5 + - - +
213A VAL* 3.3 1.7 + - - +
214A GLN* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLU* 3.1 21.5 + - + +
208A HIS* 3.3 11.2 + - - +
210A SER* 1.3 74.5 - - - +
212A VAL* 1.3 65.6 + - + +
214A GLN* 3.2 7.1 + - + +
215A GLU* 3.0 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ALA* 4.5 3.1 - - + -
160A LEU* 3.9 20.4 - - + -
163A LEU* 3.7 24.2 - - + -
208A HIS* 3.2 24.4 + - + +
209A SER* 3.6 7.9 - - - +
210A SER 3.3 0.2 - - - -
211A ARG* 1.3 80.1 - - + +
213A VAL* 1.3 60.9 + - + +
215A GLU* 3.3 2.3 + - - +
216A LEU* 3.1 38.5 + - + +
222A CYS* 4.0 27.3 - - + +
224A GLU* 4.4 2.9 - - - +
225A VAL* 4.3 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 4.0 26.5 - - + -
160A LEU* 4.5 8.1 - - + -
186A LEU* 4.4 15.9 - - + -
193A VAL* 4.4 6.7 - - + -
196A LEU* 5.4 0.2 - - + -
199A LEU* 3.9 18.6 - - + -
205A PHE* 3.8 20.6 - - + -
209A SER 3.2 13.9 + - - +
210A SER 3.8 6.3 - - - +
212A VAL* 1.3 74.0 - - + +
214A GLN* 1.3 60.6 + - - +
216A LEU* 3.3 2.9 + - + +
217A LEU* 2.9 48.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
196A LEU* 3.9 32.0 - - + +
210A SER 2.8 21.1 + - - +
211A ARG* 3.2 10.5 + - + +
213A VAL* 1.3 73.2 - - - +
215A GLU* 1.3 59.9 + - + +
217A LEU* 3.3 8.5 + - - +
218A GLU* 2.9 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ARG* 3.0 42.9 + - + +
212A VAL 3.8 3.6 - - - +
214A GLN* 1.3 74.9 - - + +
216A LEU* 1.3 61.6 + - - +
218A GLU* 4.7 1.1 - - - -
219A HIS* 2.8 43.9 + - + +
221A VAL 3.4 16.6 - - - +
222A CYS* 3.5 13.4 - - + -
223A GLU* 3.3 28.8 + - - +
224A GLU 4.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLY 4.7 2.2 - - - +
156A LEU* 3.6 35.9 - - + +
159A ALA* 3.5 31.9 - - + -
212A VAL* 3.1 25.7 + - + +
213A VAL* 3.7 2.9 - - + +
215A GLU* 1.3 76.5 - - - +
217A LEU* 1.3 58.2 + - - +
220A GLY* 2.9 35.6 + - - +
221A VAL* 3.7 9.9 - - - +
222A CYS* 3.6 25.1 - - + +
225A VAL* 6.0 0.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
156A LEU* 4.7 9.9 - - + -
193A VAL* 3.5 27.6 - - + +
194A THR* 3.9 11.7 - - - +
195A THR* 3.8 34.5 - - - +
196A LEU* 3.8 6.7 - - + +
213A VAL* 2.9 40.2 + - + +
214A GLN* 3.7 6.7 - - - +
215A GLU 3.2 0.2 - - - -
216A LEU* 1.3 77.4 - - - +
218A GLU* 1.3 60.4 + - - +
220A GLY 4.8 0.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
214A GLN* 2.9 28.1 + - + +
215A GLU* 5.5 0.2 - - - -
217A LEU* 1.3 78.6 - - + +
219A HIS* 1.3 95.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A GLU* 2.8 28.0 + - + +
218A GLU* 1.3 112.3 + - + +
220A GLY* 1.3 58.6 + - - +
221A VAL* 3.1 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU* 2.9 30.2 + - - +
217A LEU 4.6 0.4 - - - -
218A GLU 3.8 0.4 - - - -
219A HIS* 1.3 76.9 - - - +
221A VAL* 1.3 67.1 + - - +
----------------------------------------------------------
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