Contacts of the helix formed by residues 142 - 157 (chain C) in PDB entry 1Z83
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 142 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C LEU* 5.2 0.7 - - - -
139C VAL 3.8 15.8 - - - +
140C ASP 3.4 0.6 - - - -
141C ASP* 1.3 78.0 - - - +
143C GLU* 1.3 66.9 + - - +
144C GLU* 2.8 28.9 + - - +
145C THR* 3.0 41.6 + - - +
146C ILE* 2.9 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C THR* 5.8 4.5 - - + -
130C LEU* 4.2 32.5 - - + +
141C ASP 4.1 0.4 + - - -
142C ASN* 1.3 73.5 - - - +
144C GLU* 1.3 71.5 + - - +
146C ILE* 3.4 5.7 + - + +
147C LYS* 3.2 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C ASN* 2.8 20.7 + - - +
143C GLU* 1.3 84.5 + - - +
145C THR* 1.3 60.6 + - - +
147C LYS* 3.5 18.5 + - - +
148C LYS* 3.3 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C GLU 3.1 27.5 + - - +
63C LYS* 4.2 0.7 - - - -
64C GLY 3.7 17.5 - - - +
139C VAL 5.3 0.2 + - - -
140C ASP* 3.5 31.2 - - + +
142C ASN* 3.0 25.5 + - - +
144C GLU* 1.3 76.1 - - - +
146C ILE* 1.3 60.7 + - - +
148C LYS* 3.3 7.5 + - - +
149C ARG* 2.9 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C MET 5.4 0.2 - - - -
126C THR* 3.9 28.7 - - + +
129C LEU* 3.6 45.1 - - + -
130C LEU* 3.6 27.1 - - + -
140C ASP 4.1 1.8 + - - +
141C ASP* 3.3 31.2 - - - +
142C ASN 2.9 13.8 + - - +
143C GLU* 3.6 8.3 - - + +
144C GLU 3.4 0.2 - - - -
145C THR* 1.3 75.9 - - - +
147C LYS* 1.3 57.0 + - + +
149C ARG* 3.3 9.6 + - - +
150C LEU* 3.0 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C GLU* 3.2 36.1 + - + +
144C GLU* 3.7 23.0 - - - +
145C THR 3.2 0.4 - - - -
146C ILE* 1.3 78.9 - - + +
148C LYS* 1.3 62.3 + - + +
150C LEU* 3.3 12.4 + - + +
151C GLU* 3.1 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LYS* 3.2 40.1 + - - +
64C GLY* 4.2 2.0 - - - -
65C GLN* 6.0 1.8 - - - +
144C GLU* 3.3 21.0 + - - +
145C THR* 3.3 11.5 + - - +
147C LYS* 1.3 76.5 - - + +
149C ARG* 1.3 61.9 + - - +
151C GLU* 3.3 14.9 + - - +
152C THR* 3.1 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PRO* 3.8 22.1 - - + +
61C MET 5.4 0.2 - - - -
64C GLY* 3.7 23.8 - - - +
97C ARG* 4.8 2.3 + - - -
129C LEU* 4.0 19.3 - - - +
132C ARG* 4.1 0.2 - - - +
138C ARG* 3.4 7.3 - - - +
140C ASP* 3.0 43.7 + - - -
141C ASP* 3.1 20.4 + - - +
145C THR* 2.9 28.0 + - - +
146C ILE* 3.6 7.0 - - - +
147C LYS 3.3 0.2 - - - -
148C LYS* 1.3 74.9 - - - +
150C LEU* 1.3 65.3 + - - +
152C THR* 3.6 2.5 + - - -
153C TYR* 3.1 23.0 + - - +
633C AP5 3.1 56.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PRO* 3.6 22.9 - - + +
122C PRO* 4.5 13.2 - - + +
125C MET* 3.9 34.5 - - + -
126C THR* 3.5 24.2 - - - +
146C ILE* 3.0 27.6 + - + +
147C LYS* 3.3 10.7 + - + +
149C ARG* 1.3 77.1 - - - +
151C GLU* 1.3 62.9 + - + +
153C TYR* 3.1 3.5 + - + +
154C TYR* 3.0 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C LYS* 3.1 23.9 + - - +
148C LYS* 3.3 13.8 + - - +
150C LEU* 1.3 77.4 - - + +
152C THR* 1.3 60.9 + - - +
154C TYR* 3.4 5.4 + - - +
155C LYS* 3.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLY 3.0 27.4 + - - +
65C GLN* 4.5 4.4 - - - +
66C LEU* 3.8 39.7 - - + +
97C ARG* 4.1 7.0 - - - +
148C LYS* 3.1 11.0 + - - +
149C ARG* 3.8 4.7 - - - -
151C GLU* 1.3 72.4 - - - +
153C TYR* 1.3 66.2 + - - +
155C LYS* 4.7 4.5 - - - -
156C ALA* 3.0 26.5 + - + +
157C THR* 3.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 4.8 3.3 - - + +
15C GLY* 3.4 28.1 + - - -
16C GLY* 3.5 29.6 + - - -
17C PRO* 3.8 12.6 - - + -
97C ARG* 3.5 15.3 - - - +
117C TYR* 3.8 20.6 + - - -
125C MET* 5.3 2.9 - - + -
149C ARG 3.1 18.4 + - - +
150C LEU 3.1 3.6 + - - +
152C THR* 1.3 76.1 - - - +
154C TYR* 1.3 91.4 + + - +
157C THR* 3.0 54.0 + - + -
158C GLU* 3.0 30.8 + - + +
161C ILE* 5.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ALA 4.7 1.2 + - - -
122C PRO* 3.6 27.3 - - + +
125C MET* 3.5 23.6 - - + +
150C LEU* 3.0 46.9 + - + +
151C GLU* 4.2 5.2 - - - +
153C TYR* 1.3 92.9 - + - +
155C LYS* 1.3 60.4 + - - +
158C GLU* 3.5 48.1 - - - +
159C PRO* 4.0 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C GLU 3.0 19.5 + - - +
152C THR* 4.2 2.9 - - - +
154C TYR* 1.3 78.1 - - - +
156C ALA* 1.3 60.0 + - + +
159C PRO* 3.6 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 4.3 17.7 - - + -
97C ARG 3.3 17.5 - - - +
98C GLU* 3.6 20.6 - - + +
99C VAL* 4.6 1.4 + - - +
152C THR* 3.0 16.8 + - + +
155C LYS* 1.3 78.8 - - + +
157C THR* 1.3 64.4 + - - +
159C PRO* 3.6 12.4 - - - +
160C VAL* 4.2 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 4.1 17.7 - - + +
15C GLY 5.6 0.2 - - - +
96C PRO 4.1 4.9 - - - +
97C ARG* 2.8 61.7 + - - +
152C THR 4.0 1.2 + - - -
153C TYR* 3.0 33.1 + - + -
156C ALA* 1.3 75.2 - - - +
158C GLU* 1.3 68.4 + - - +
159C PRO* 3.2 2.0 - - - -
160C VAL* 2.8 23.7 + - + +
161C ILE* 3.9 3.1 + - - +
----------------------------------------------------------
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