Contacts of the helix formed by residues 164 - 173 (chain D) in PDB entry 2AXZ
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 PRO 164 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D VAL 4.6 1.3 - - - +
163D LEU* 1.3 90.5 - - + +
165D TYR* 1.3 66.0 + - - +
166D GLU* 3.0 23.8 - - - +
167D GLU* 2.9 39.3 + - - +
168D VAL 3.5 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D LEU* 4.2 17.5 - - + -
163D LEU 3.4 3.1 + - - -
164D PRO* 1.3 71.8 - - - +
166D GLU* 1.3 70.0 + - + +
167D GLU 3.0 0.3 + - - -
168D VAL* 3.1 4.3 + - - +
169D SER* 2.7 54.4 + - - -
172D ILE* 4.3 6.5 - - + -
173D LYS* 3.6 9.0 + - - -
197D ALA* 4.9 2.9 - - + -
200D ILE* 4.0 33.3 - - + +
201D SER* 4.7 5.6 - - - -
204D ASN* 5.2 2.9 - - - +
206D ASN* 4.9 11.9 - - - +
209D GLU* 2.7 41.6 + - + -
213D TYR* 2.6 38.2 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D PRO* 3.0 25.4 - - - +
165D TYR* 1.3 90.5 + - + +
167D GLU* 1.3 60.3 + - + +
169D SER* 2.7 20.7 + - - -
170D SER* 4.8 0.7 + - - -
204D ASN* 5.6 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D ILE* 5.9 1.4 - - - +
135D THR* 5.0 7.1 + - - -
138D LEU* 5.2 5.2 - - + +
163D LEU* 3.3 27.7 - - + +
164D PRO* 2.9 46.4 + - + +
165D TYR 3.0 0.8 - - - -
166D GLU* 1.3 82.0 - - + +
168D VAL* 1.3 62.9 + - - +
169D SER 3.3 0.4 - - - -
170D SER* 4.3 7.8 + - - -
171D ILE* 4.4 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D LEU* 6.0 0.2 - - - -
156D VAL* 3.9 15.9 - - + -
159D LEU* 3.5 38.1 - - + +
160D LEU* 3.4 30.5 - - + -
163D LEU* 3.7 25.6 - - + +
164D PRO 3.9 7.6 - - - +
165D TYR 3.1 3.0 + - - +
167D GLU* 1.3 76.5 - - - +
169D SER* 1.3 67.6 + - - +
170D SER 3.3 0.4 - - - -
171D ILE* 2.9 21.1 + - + +
172D ILE* 3.3 14.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D TYR* 2.7 47.7 + - - -
166D GLU* 2.7 25.4 + - - -
168D VAL* 1.3 77.4 - - - +
170D SER* 1.3 69.4 + - - -
172D ILE* 3.2 13.6 + - - +
173D LYS* 3.5 23.2 + - - +
209D GLU* 4.9 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D GLU 5.6 0.4 - - - -
167D GLU 4.3 6.2 + - - -
168D VAL 3.3 1.0 - - - -
169D SER* 1.3 83.9 + - - +
171D ILE* 1.3 62.5 + - - +
173D LYS* 4.4 6.6 - - - +
174D PRO* 3.1 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D LEU* 5.1 20.4 - - + +
142D TYR* 4.2 47.1 - - + -
143D ASP* 6.0 1.8 - - - +
148D PHE* 4.8 2.6 - - + -
156D VAL* 5.1 7.9 - - + -
159D LEU* 5.4 7.4 - - + -
167D GLU 4.4 11.0 - - - +
168D VAL* 2.9 17.9 + - + +
170D SER* 1.3 83.4 - - - +
172D ILE* 1.3 62.3 + - - +
174D PRO* 3.6 7.2 - - - +
175D MSE 3.4 25.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D VAL* 3.6 21.3 - - + -
160D LEU* 3.9 33.9 - - + -
165D TYR* 4.3 7.0 - - + -
168D VAL* 3.5 14.6 - - + +
169D SER* 3.2 6.6 + - - +
171D ILE* 1.3 77.4 - - - +
173D LYS* 1.3 61.0 + - + +
174D PRO 3.3 0.4 - - - -
175D MSE 2.7 40.0 + - - +
176D TYR* 3.6 26.9 - - + -
193D VAL* 4.1 10.1 - - + -
197D ALA* 4.7 0.7 - - + -
212D TYR* 5.4 0.7 - - + -
213D TYR* 3.8 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D TYR* 3.6 18.2 + - - -
169D SER* 3.5 21.3 - - - +
170D SER* 4.4 4.9 - - - +
172D ILE* 1.3 75.4 - - + +
174D PRO* 1.3 65.1 - - + +
175D MSE 3.2 0.3 + - - -
176D TYR 3.0 24.8 + - - +
209D GLU* 3.4 23.5 + - - -
212D TYR* 3.1 53.6 + - + +
213D TYR* 3.8 3.2 + - - -
----------------------------------------------------------
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