Contacts of the helix formed by residues 84 - 89 (chain D) in PDB entry 1ZQ1
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 ASP 84 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A TYR* 3.7 25.8 - - + +
431A THR 3.0 15.5 + - - +
29D LYS* 5.2 1.2 + - - -
32D SER* 2.6 27.6 + - - -
34D VAL* 3.8 10.2 - - + +
82D LEU 3.9 1.8 + - - +
83D THR* 1.3 76.7 - - - +
85D LEU* 1.3 64.9 + - - +
86D VAL* 3.0 21.5 + - - +
87D TYR* 3.0 31.9 + - - +
88D MET* 3.5 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A GLY* 5.7 0.2 - - - -
431A THR* 2.9 45.1 + - + +
432A ARG 4.3 1.1 - - - +
433A PHE* 4.2 10.3 - - - -
435A THR* 5.6 0.2 - - + -
258B HIS* 3.7 29.4 - - + +
261B ARG* 3.8 20.4 - - - +
84D ASP* 1.3 71.5 - - - +
86D VAL* 1.3 61.4 + - - +
88D MET* 3.0 33.2 + - + +
90D GLU* 2.8 42.2 + - + +
91D GLU* 3.6 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PHE 3.2 22.9 - - - +
32D SER* 3.8 12.8 - - - +
84D ASP* 3.0 20.3 + - - +
85D LEU* 1.3 78.2 - - - +
87D TYR* 1.3 69.0 + - + +
88D MET 3.4 2.3 + - - -
89D ASP* 3.5 8.8 + - - -
91D GLU* 3.4 38.9 - - + +
92D PRO 3.6 13.0 - - - +
93D PRO* 3.8 19.1 - - + -
94D ARG* 5.4 4.7 - - - +
133D SER* 4.9 1.0 + - - -
137D ARG* 4.3 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LYS* 3.8 28.0 - - + +
30D LEU 3.9 0.3 - - - -
31D PHE* 2.9 28.3 + - + +
32D SER* 3.7 22.2 - - - -
83D THR* 5.7 1.8 - - + -
84D ASP* 3.0 25.0 + - - +
86D VAL* 1.3 81.9 - - + +
88D MET* 1.3 58.1 + - - +
89D ASP 3.4 3.1 - - - -
132D VAL* 3.8 5.0 - - - +
137D ARG* 5.1 6.1 - - - -
163D GLU* 2.8 33.4 + - - -
180D LEU* 3.5 27.6 - - + +
183D LEU* 3.5 40.4 - - + +
184D GLY* 3.3 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A PHE* 3.2 48.0 - - + -
241B THR* 4.5 6.1 - - - -
44D PHE* 4.1 8.7 - - + -
46D PHE* 3.7 34.8 - - + -
48D ARG* 2.4 36.1 + - - +
83D THR* 4.0 11.0 - - + -
84D ASP 3.7 8.5 - - - +
85D LEU* 3.0 46.2 + - + +
87D TYR* 1.3 79.7 - - - +
89D ASP* 1.3 61.3 + - - +
90D GLU* 3.3 6.7 + - + -
132D VAL* 3.5 6.6 - - - +
180D LEU* 4.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ARG* 3.0 34.4 + - - +
210B ARG* 4.6 5.4 + - - -
212B SER* 2.7 30.3 + - - -
262B ARG* 2.6 29.7 + - - +
85D LEU 3.2 2.0 + - - -
86D VAL 3.5 8.7 + - - -
87D TYR 3.4 2.4 - - - -
88D MET* 1.3 82.8 - - - +
90D GLU* 1.3 55.9 + - - +
91D GLU 3.7 4.0 - - - +
132D VAL* 3.3 18.8 - - + +
133D SER* 2.9 24.2 + - - +
----------------------------------------------------------
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