Contacts of the strand formed by residues 132 - 138 (chain D) in PDB entry 1PZN
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 132 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D GLU* 3.9 25.7 - - + +
130D THR 3.0 8.7 - - - +
131D GLN* 1.3 81.9 - - - +
133D ILE* 1.3 70.5 - - - +
134D THR* 3.9 3.9 + - - +
269D HIS* 5.6 0.7 - - - -
272D ALA* 3.7 2.8 - - - +
278D ALA 3.9 0.2 - - - -
279D VAL* 2.9 28.1 + - - +
310D THR* 3.5 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ALA* 1.3 80.0 - - - +
134D THR* 1.3 61.0 + - - +
135D GLU 3.9 0.2 + - - -
265D LEU* 5.1 7.2 - - + +
268D LEU* 4.1 11.0 - - + -
269D HIS* 3.2 49.8 - - + +
272D ALA* 3.9 10.1 - - + -
279D VAL* 3.2 22.9 - - + +
281D VAL* 4.1 24.9 - - + -
306D ALA* 5.6 3.4 - - + -
309D ALA* 4.0 26.0 - - + -
310D THR* 2.9 26.8 + - - -
311D LEU 3.3 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D LEU* 5.6 0.2 - - + -
128D ILE* 3.7 35.0 - - + +
129D GLU* 4.5 9.0 + - - +
132D ALA* 4.8 3.3 + - - +
133D ILE* 1.3 75.3 + - - +
135D GLU* 1.3 62.4 + - - +
279D VAL 2.7 13.9 + - - -
280D PHE* 3.5 20.5 - - + -
281D VAL* 2.9 27.4 + - - +
311D LEU* 3.4 31.4 - - + +
313D VAL* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ILE 3.9 0.8 + - - -
134D THR* 1.3 75.9 - - - +
136D VAL* 1.3 63.7 + - - +
137D PHE* 3.8 5.8 - - + -
240D LEU* 5.7 0.4 - - + -
281D VAL* 3.3 22.4 - - + +
283D ASN* 3.2 28.5 - - + +
306D ALA* 3.4 25.5 + - + +
309D ALA* 4.5 8.5 - - + -
311D LEU 2.8 13.4 + - - +
312D ARG* 2.7 49.1 + - - +
313D VAL* 2.7 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D THR* 4.0 0.6 + - + -
135D GLU* 1.3 74.1 - - - +
137D PHE* 1.3 62.8 + - - +
144D LYS* 3.5 21.8 - - + +
147D LEU* 4.2 7.0 - - + -
280D PHE* 3.5 31.2 - - + -
281D VAL 2.9 13.4 + - - +
282D THR* 3.3 8.4 - - + -
283D ASN* 3.0 21.0 + - - +
313D VAL* 3.1 15.7 - - + +
315D LEU* 3.2 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLU* 3.8 8.5 - - + +
136D VAL* 1.3 75.1 - - - +
138D GLY* 1.3 59.3 + - - +
144D LYS* 4.1 4.5 - - - -
283D ASN* 3.0 30.7 - - + +
285D VAL* 3.9 19.3 - - + -
312D ARG* 3.1 48.5 - - + -
313D VAL 3.0 12.8 + - - -
314D TYR* 3.3 41.7 - + + -
315D LEU* 3.1 25.2 + - - -
328D ILE* 4.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D PHE* 1.3 79.5 - - - +
139D GLU* 1.3 68.5 + - - -
142D SER* 3.5 3.8 - - - -
144D LYS* 3.1 15.6 + - - +
283D ASN 3.4 2.2 + - - -
285D VAL* 3.1 28.7 + - - +
314D TYR* 4.3 4.5 - - - -
315D LEU 3.4 15.7 - - - -
----------------------------------------------------------
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