Contacts of the helix formed by residues 133 - 147 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B SER* 4.2 5.6 - - - +
87B MET* 4.0 8.7 - - - -
131B THR* 2.9 20.0 + - - -
132B LYS* 1.3 88.8 - - - +
134B SER* 1.3 61.6 + - - +
135B GLU* 2.8 34.3 + - - +
136B GLU* 2.8 21.3 + - - +
137B LEU* 3.3 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B MET* 3.5 24.7 - - - +
133B ASN* 1.3 73.5 - - - +
135B GLU* 1.3 61.1 + - - +
136B GLU 3.4 0.2 - - - -
137B LEU* 3.6 8.0 - - - +
138B ASN* 3.1 27.2 + - - +
157B ILE* 6.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASN* 2.8 20.9 + - - +
134B SER* 1.3 74.8 + - - +
136B GLU* 1.3 64.2 + - - +
138B ASN* 3.4 7.5 + - - +
139B ASN* 3.1 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B THR* 4.2 13.7 - - - -
132B LYS* 4.7 10.3 - - + +
133B ASN* 2.8 25.5 + - - +
135B GLU* 1.3 77.0 - - - +
137B LEU* 1.3 61.1 + - - +
139B ASN* 3.1 26.4 + - - +
140B PHE* 3.0 47.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B MET* 4.1 15.3 - - + -
89B ALA* 4.2 5.8 - - + -
91B ILE* 4.3 12.3 - - + -
129B ILE* 3.9 31.9 - - + -
131B THR* 3.8 20.5 + - + +
133B ASN 3.3 8.3 + - - +
134B SER* 3.6 10.8 - - - +
135B GLU 3.3 0.2 - - - -
136B GLU* 1.3 76.5 - - - +
138B ASN* 1.3 51.6 + - - +
140B PHE* 3.2 5.7 + - - +
141B LEU* 2.8 49.4 + - + +
155B THR* 4.2 9.9 - - + -
157B ILE* 4.1 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B SER 3.1 14.4 + - - +
135B GLU* 3.7 6.5 - - - +
136B GLU 3.3 0.2 - - - -
137B LEU* 1.3 76.3 - - - +
139B ASN* 1.3 64.0 + - - +
141B LEU* 3.1 12.4 + - + +
142B ASP* 2.9 37.2 + - - -
172B LYS* 2.9 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLU* 3.1 25.6 + - - +
136B GLU* 3.1 33.8 - - - +
137B LEU 3.3 0.2 - - - -
138B ASN* 1.3 79.8 - - - +
140B PHE* 1.3 59.7 + - + +
142B ASP* 3.3 16.0 + - - +
143B LEU* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 4.2 23.6 - + + -
112B GLU* 3.1 46.4 - - + -
113B ILE* 5.1 4.0 - - + -
129B ILE* 3.7 28.0 - - + -
131B THR* 4.2 7.9 - - + -
136B GLU* 3.0 33.5 + - + -
137B LEU* 3.2 9.2 + - + +
139B ASN* 1.3 73.9 - - + +
141B LEU* 1.3 59.0 + - - +
143B LEU* 3.2 26.0 + - + +
144B ILE* 2.8 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 3.6 33.4 - - + -
137B LEU* 2.8 36.0 + - + +
138B ASN* 3.1 15.2 + - + +
140B PHE* 1.3 72.7 - - - +
142B ASP* 1.3 58.3 + - - +
144B ILE* 3.9 4.4 - - + +
145B GLY* 2.9 26.5 + - - -
153B THR* 4.1 11.0 + - - +
155B THR* 3.2 32.5 - - + +
172B LYS* 3.7 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ASN* 2.9 24.5 + - - +
139B ASN* 3.4 18.3 + - - +
140B PHE 3.2 0.2 - - - -
141B LEU* 1.3 75.3 - - - +
143B LEU* 1.3 62.2 + - - +
145B GLY* 3.5 2.4 + - - -
146B SER* 3.3 21.1 + - - -
172B LYS* 2.6 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 4.0 41.1 - - + +
139B ASN 3.0 12.4 + - - +
140B PHE* 3.4 28.7 - - + +
142B ASP* 1.3 77.1 - - - +
144B ILE* 1.3 63.5 + - + +
146B SER* 2.7 31.1 + - - +
147B ILE* 3.4 10.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 3.8 31.0 - - + -
93B VAL* 4.5 10.8 - - + -
107B LEU* 3.8 31.4 - - + -
110B TYR* 6.1 1.8 - - + -
113B ILE* 4.5 13.5 - - + -
127B VAL* 5.4 1.3 - - + -
129B ILE* 4.9 0.2 - - + -
140B PHE* 2.8 36.8 + - + +
141B LEU* 3.9 7.2 - - + +
143B LEU* 1.3 73.8 - - + +
145B GLY* 1.3 61.9 + - - +
146B SER 3.1 1.0 + - - -
147B ILE* 3.2 19.3 + - + +
150B VAL* 3.4 21.0 - - + +
153B THR* 3.6 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU 2.9 16.3 + - - -
142B ASP* 3.5 3.6 + - - -
143B LEU 3.3 0.2 - - - -
144B ILE* 1.3 77.0 - - - +
146B SER* 1.3 58.3 + - - +
147B ILE 3.5 2.0 - - - +
150B VAL* 4.1 23.7 - - - +
152B GLY* 6.1 1.1 - - - -
153B THR* 5.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ASP 3.3 10.3 + - - -
143B LEU* 2.7 29.5 + - - +
145B GLY* 1.3 75.0 - - - +
147B ILE* 1.3 66.9 + - - +
148B PRO* 3.3 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B VAL* 4.2 14.1 - - + -
106B ASN* 3.4 30.7 - - + +
107B LEU* 3.7 33.4 - - + +
110B TYR* 4.9 9.0 - - + +
143B LEU* 3.7 10.5 - - + +
144B ILE* 3.2 22.8 + - + +
145B GLY 4.2 0.9 - - - +
146B SER* 1.3 79.3 + - - +
148B PRO* 1.4 83.8 - - + +
149B GLY 3.3 0.3 + - - -
150B VAL* 3.2 33.3 + - + +
----------------------------------------------------------
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