Contacts of the strand formed by residues 163 - 169 (chain D) in PDB entry 2PZX
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 163 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D VAL* 5.5 0.5 - - - -
68D ARG* 2.9 58.1 + - + +
125D PRO* 3.9 4.2 - - - +
143D LEU* 3.6 15.2 - - + +
147D GLY* 2.9 33.6 + - - -
149D PHE* 3.2 38.4 - + + -
158D LEU* 4.1 11.7 - - + -
159D ARG 4.2 0.7 - - - -
160D LYS* 3.5 28.4 - - + +
161D ARG 3.6 1.6 + - - -
162D GLU* 1.3 80.4 - - - +
164D CYS* 1.3 85.2 + - - +
165D LEU* 4.2 16.8 - - + -
182D PRO* 5.3 0.7 - - + -
183D HIS 3.6 12.6 - - - +
184D ASN* 4.0 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ARG* 3.3 28.3 - - - +
69D PHE 3.7 0.4 - - - -
70D CYS* 2.0 53.3 - - - +
125D PRO* 3.6 25.8 - - - -
129D MET* 4.3 7.2 - - - -
163D TYR* 1.3 82.4 - - - +
165D LEU* 1.3 63.3 + - - +
183D HIS* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D VAL* 4.0 6.5 - - + -
68D ARG 2.6 17.8 + - - +
69D PHE* 3.3 12.4 - - + -
70D CYS* 3.0 20.3 + - - -
98D LEU* 3.3 29.8 - - + -
141D TYR* 5.0 3.8 - - - +
143D LEU* 3.2 34.1 - - + -
149D PHE* 4.8 2.5 - - + -
163D TYR* 4.2 13.7 - - + -
164D CYS* 1.3 75.2 - - - +
166D GLN* 1.3 68.1 + - - +
180D ILE* 3.5 10.8 - - + -
181D ALA 3.6 3.1 - - - -
182D PRO* 3.2 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D PHE* 3.6 11.6 - - - -
70D CYS* 3.3 12.5 - - - +
71D CYS* 3.0 53.6 + - - +
72D PRO 3.7 3.4 - - - +
75D HIS* 2.9 24.4 - - - +
77D MET* 3.4 36.3 - - + +
165D LEU* 1.3 85.0 + - - +
167D HIS* 1.3 66.5 + - - +
168D LEU* 3.3 2.4 + - - +
180D ILE* 3.4 7.2 - - - +
181D ALA* 3.0 27.9 + - - +
183D HIS* 4.6 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D PHE* 4.4 7.8 - + - -
73D HIS 3.2 28.5 + - - -
75D HIS 3.6 17.6 + - - +
76D ILE* 3.2 5.5 - - + +
77D MET* 2.5 35.0 + - - +
86D MET* 3.6 13.7 - - + +
94D LEU* 3.5 31.8 - - + +
95D ASP 4.9 2.8 + - - -
112D PHE* 3.7 29.1 - + - -
166D GLN* 1.3 76.0 - - - +
168D LEU* 1.3 55.4 + - - +
178D ILE* 4.1 12.3 - - + -
180D ILE* 3.5 31.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ILE* 4.3 0.2 - - - -
77D MET* 4.1 13.7 - - + +
79D ASN 5.5 2.9 - - - +
131D TYR* 3.4 37.2 - - + -
166D GLN 3.3 8.1 + - - +
167D HIS* 1.3 75.2 - - - +
169D THR* 1.3 84.8 + - - +
170D PHE* 2.8 49.5 - - + -
178D ILE* 3.5 6.2 - - - +
179D ARG 3.3 18.5 + - - +
181D ALA* 4.3 4.0 - - + -
183D HIS* 3.1 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ILE* 2.8 30.9 - - - +
77D MET 4.3 2.5 + - - -
90D GLU* 5.6 0.7 + - - -
168D LEU* 1.3 86.0 - - - +
170D PHE* 1.3 65.6 + - - +
176D THR* 3.5 24.0 - - - +
177D SER 3.9 4.0 - - - +
178D ILE* 3.7 11.8 - - + +
----------------------------------------------------------
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