Contacts of the helix formed by residues 205 - 215 (chain A) in PDB entry 2YZ5
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 205 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ASP* 2.8 20.9 + - - +
159A LYS* 3.2 7.3 - - + +
170A LEU* 3.9 22.0 - - + -
201A GLU* 3.4 17.9 - - - +
202A VAL 3.9 0.2 - - - -
204A PRO* 1.3 75.0 - - - +
206A PRO* 1.3 74.8 - - + +
207A ALA* 3.1 4.7 - - + +
208A LEU* 2.9 15.2 + - + +
209A LEU* 3.0 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLU* 3.5 28.3 - - + +
202A VAL* 5.1 1.6 - - + +
204A PRO 3.6 2.0 - - - +
205A ALA* 1.3 83.1 - - + +
207A ALA* 1.3 61.6 + - - +
209A LEU* 3.1 11.8 + - + +
210A ARG* 2.9 32.5 + - - +
241A LEU* 4.4 24.9 - - + -
245A LEU* 4.0 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU* 4.2 28.3 - - + +
170A LEU* 5.1 10.5 - - + -
171A LEU* 3.6 29.3 - - + +
205A ALA* 3.1 2.5 + - + +
206A PRO* 1.3 79.5 - - - +
208A LEU* 1.3 63.1 + - - +
210A ARG* 3.3 21.3 + - - +
211A ARG 3.3 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PHE* 4.5 0.9 - - + -
155A LEU* 3.8 27.1 - - + -
156A ASP* 4.0 26.7 - - + +
170A LEU* 3.7 38.6 - - + +
171A LEU* 4.0 18.6 - - + -
174A ALA* 3.7 26.9 - - + -
178A LEU* 4.3 9.3 - - + +
204A PRO* 4.1 10.8 - - + -
205A ALA 2.9 8.5 + - - +
207A ALA* 1.3 77.0 - - - +
209A LEU* 1.3 58.8 + - - +
211A ARG* 3.2 5.6 + - - +
212A ALA* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 4.9 0.4 - - + -
190A VAL* 4.3 5.2 - - + -
202A VAL* 4.5 12.1 - - + -
204A PRO* 3.5 46.2 - - + +
205A ALA 3.0 7.4 + - - +
206A PRO* 3.1 11.4 + - + +
208A LEU* 1.3 74.0 - - - +
210A ARG* 1.3 58.2 + - - +
212A ALA* 3.1 4.5 + - + +
213A ARG 2.9 25.1 + - - -
219A LEU* 3.8 34.8 - - + -
241A LEU* 4.8 3.4 - - + -
242A LEU* 3.7 21.8 - - + -
245A LEU* 3.7 17.7 - - + -
247A PHE* 3.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PRO* 2.9 22.8 + - - +
207A ALA* 3.5 13.4 - - - +
209A LEU* 1.3 75.6 - - - +
211A ARG* 1.3 63.4 + - - +
213A ARG* 3.3 37.5 + - - +
214A GLU* 3.3 12.3 + - - +
244A GLY 5.3 2.8 + - - -
245A LEU* 3.3 43.6 + - + +
247A PHE* 5.3 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
171A LEU* 4.0 21.8 - - + -
175A GLU* 2.7 37.7 + - - +
178A LEU* 3.5 26.0 - - + -
179A ARG* 4.4 7.3 - - - +
207A ALA 3.3 1.8 + - - -
208A LEU 3.2 9.1 + - - +
209A LEU 3.2 0.2 - - - -
210A ARG* 1.3 78.2 - - - +
212A ALA* 1.3 63.9 + - - +
214A GLU* 3.4 22.6 + - - +
215A LEU* 3.1 52.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 4.6 4.2 - - + +
188A LEU* 3.7 29.2 - - + -
208A LEU 2.9 12.8 + - - +
209A LEU* 3.1 14.1 + - + +
211A ARG* 1.3 73.9 - - - +
213A ARG* 1.3 65.1 + - - +
215A LEU* 3.2 1.8 + - - -
216A GLY 3.1 4.9 + - - -
217A ILE* 3.0 43.8 + - + +
219A LEU* 4.9 0.7 - - + -
247A PHE* 4.4 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU 2.9 6.5 + - - +
210A ARG* 3.4 42.8 + - - +
211A ARG 3.2 0.2 - - - -
212A ALA* 1.3 77.0 - - - +
214A GLU* 1.3 82.5 + - - +
216A GLY* 3.0 19.8 + - - -
217A ILE 5.0 0.7 - - - -
245A LEU* 2.9 30.8 + - - +
246A GLY* 3.9 18.8 - - - +
247A PHE* 3.5 38.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ARG 3.3 8.7 + - - +
211A ARG* 3.8 25.7 + - - +
212A ALA 3.3 0.2 - - - -
213A ARG* 1.3 105.8 + - - +
215A LEU* 1.3 61.9 + - - +
216A GLY 3.2 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A GLU* 4.7 1.8 - - - +
178A LEU* 3.8 39.9 - - + +
179A ARG* 4.3 10.1 - - + +
182A ALA* 4.0 23.7 - - + +
211A ARG* 3.1 59.4 + - + +
212A ALA 3.8 4.0 - - - +
213A ARG 3.2 0.6 - - - -
214A GLU* 1.3 78.3 - - - +
216A GLY* 1.3 61.5 + - - +
217A ILE* 3.4 6.6 + - + -
----------------------------------------------------------
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