Contacts of the helix formed by residues 133 - 146 (chain H) in PDB entry 2ZNZ
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 ASN 133 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H SER* 4.1 6.3 - - - +
87H MET* 4.2 7.4 - - - -
131H THR* 3.0 19.7 + - - -
132H LYS* 1.3 88.8 + - - +
134H SER* 1.3 62.8 + - - +
135H GLU* 3.0 15.8 + - + +
136H GLU* 2.8 41.5 + - - +
137H LEU 3.3 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 134 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H MET* 3.6 24.6 - - - +
133H ASN* 1.3 75.7 - - - +
135H GLU* 1.3 63.4 + - - +
136H GLU 3.5 0.2 - - - -
137H LEU* 3.5 8.4 + - - +
138H ASN* 3.1 23.2 + - - +
157H ILE* 5.8 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H ASN* 3.0 14.9 + - + +
134H SER* 1.3 79.5 + - - +
136H GLU* 1.3 76.9 + - - +
138H ASN* 3.4 7.7 + - - +
139H ASN* 3.2 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H THR* 4.2 13.5 - - + -
132H LYS* 4.7 12.8 - - + +
133H ASN* 2.8 31.8 + - - +
135H GLU* 1.3 82.0 - - - +
137H LEU* 1.3 61.3 + - - +
139H ASN* 3.1 27.0 + - - +
140H PHE* 3.0 40.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H MET* 4.1 14.8 - - + -
89H ALA* 4.2 7.0 - - + -
91H ILE* 4.4 11.0 - - + -
129H ILE* 3.8 33.9 - - + -
131H THR* 3.8 19.6 + - + +
133H ASN 3.3 7.3 + - - +
134H SER* 3.6 11.4 - - - +
135H GLU 3.3 0.4 - - - -
136H GLU* 1.3 74.2 - - - +
138H ASN* 1.3 60.5 + - - +
140H PHE* 3.1 5.1 + - - +
141H LEU* 2.8 43.4 + - + +
155H THR* 4.1 10.5 - - + -
157H ILE* 4.1 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 138 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H SER 3.1 11.1 + - - +
135H GLU* 3.6 10.1 - - - +
136H GLU 3.4 0.2 - - - -
137H LEU* 1.3 79.5 - - - +
139H ASN* 1.3 60.1 + - - +
141H LEU* 3.1 11.9 + - + +
142H ASP* 2.9 37.1 + - - -
172H LYS* 2.7 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 139 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135H GLU* 3.2 21.5 + - - +
136H GLU* 3.1 33.7 - - - +
137H LEU 3.3 0.2 - - - -
138H ASN* 1.3 80.9 - - - +
140H PHE* 1.3 62.4 + - + +
142H ASP* 3.3 14.5 + - - +
143H LEU* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H TYR* 4.3 27.8 - + + -
112H GLU* 3.2 50.0 - - + -
113H ILE* 5.2 2.7 - - + -
129H ILE* 3.7 27.4 - - + -
131H THR* 4.1 7.4 - - + -
136H GLU* 3.0 29.2 + - + -
137H LEU* 3.1 9.2 + - + +
139H ASN* 1.3 75.8 - - + +
141H LEU* 1.3 57.0 + - + +
143H LEU* 3.2 20.1 + - + +
144H ILE* 2.8 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H ILE* 3.7 28.3 - - + -
137H LEU* 2.8 41.6 + - + +
138H ASN* 3.1 10.5 + - - +
140H PHE* 1.3 73.0 - - - +
142H ASP* 1.3 58.9 + - - +
144H ILE* 3.9 4.5 - - + +
145H GLY* 2.8 26.5 + - - -
153H THR* 3.9 14.2 + - + +
155H THR* 3.2 32.1 - - - +
172H LYS* 3.7 41.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 142 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138H ASN* 2.9 24.7 + - - +
139H ASN* 3.4 16.4 + - - +
141H LEU* 1.3 73.0 - - - +
143H LEU* 1.3 65.3 - - - +
145H GLY* 3.5 2.5 + - - -
146H SER* 3.3 21.8 + - - -
172H LYS* 2.7 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H TYR* 4.0 40.4 - - + +
139H ASN 3.0 12.6 + - - +
140H PHE* 3.3 28.3 - - + +
142H ASP* 1.3 73.6 - - - +
144H ILE* 1.3 65.7 + - + +
146H SER* 2.8 29.4 + - - +
147H ILE* 3.5 12.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H ILE* 3.8 31.2 - - + -
93H VAL* 4.5 8.1 - - + -
107H LEU* 3.7 32.1 - - + -
110H TYR* 6.0 2.7 - - + -
113H ILE* 4.4 13.9 - - + -
127H VAL* 5.4 1.1 - - + -
129H ILE* 5.0 0.4 - - + -
140H PHE* 2.8 35.4 + - + +
141H LEU* 3.9 7.2 - - + +
143H LEU* 1.3 72.8 - - + +
145H GLY* 1.3 62.5 + - - +
147H ILE* 3.1 27.5 + - + +
150H VAL* 3.5 16.2 - - + +
153H THR* 3.6 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H LEU 2.8 18.1 + - - -
142H ASP* 3.8 3.4 - - - -
144H ILE* 1.3 77.4 - - - +
146H SER* 1.3 57.4 + - - +
147H ILE 3.4 1.3 + - - +
150H VAL* 4.1 23.6 - - - +
152H GLY* 6.2 1.1 - - - -
153H THR* 5.0 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 146 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142H ASP 3.3 10.2 + - - -
143H LEU* 2.8 29.7 + - - +
145H GLY* 1.3 74.2 - - - +
147H ILE* 1.3 66.2 + - - +
148H PRO* 3.4 7.3 - - - +
----------------------------------------------------------
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