Contacts of the helix formed by residues 121 - 135 (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 GLY 121 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ALA* 1.3 75.3 - - - +
122C PRO* 1.3 74.8 - - - +
123C GLU* 3.4 4.3 - - - -
124C THR* 3.3 5.4 + - - -
125C MET* 3.1 21.6 + - - +
176C GLU* 2.7 21.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ALA 4.6 0.2 - - - +
121C GLY* 1.3 81.6 - - - +
123C GLU* 1.3 66.9 + - + +
125C MET* 3.3 12.7 + - + +
126C THR* 2.9 29.1 + - - -
150C LEU* 4.5 14.7 - - + +
154C TYR* 3.6 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C GLY* 5.4 1.8 - - - -
122C PRO* 1.3 81.6 - - + +
124C THR* 1.3 66.3 + - - +
126C THR* 3.5 5.9 + - - -
127C GLN* 2.9 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ALA* 4.8 2.9 - - + -
121C GLY* 3.3 5.6 + - - -
122C PRO 3.2 0.2 - - - -
123C GLU* 1.3 86.1 - - - +
125C MET* 1.3 60.3 + - - +
127C GLN* 3.4 6.2 + - - +
128C ARG* 3.1 65.1 + - + +
176C GLU* 3.0 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLY* 3.5 29.2 - - - +
17C PRO* 3.0 30.1 - - - +
18C GLY 3.9 8.3 - - - -
19C SER* 3.9 15.7 - - - +
120C ALA* 3.4 31.6 - - + +
121C GLY 3.1 18.1 + - - +
122C PRO* 3.8 6.3 - - + +
124C THR* 1.3 74.0 - - - +
126C THR* 1.3 67.2 + - - +
128C ARG* 3.3 2.6 + - - +
129C LEU* 3.1 28.9 + - - +
150C LEU* 3.9 13.2 - - + -
153C TYR* 5.3 2.5 - - + -
154C TYR* 3.5 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C PRO* 2.9 17.8 + - - +
123C GLU* 3.7 6.9 - - - -
125C MET* 1.3 77.5 - - - +
127C GLN* 1.3 62.6 + - + +
129C LEU* 3.4 1.7 + - - +
130C LEU* 3.0 42.4 + - + +
143C GLU* 5.8 4.7 - - + -
146C ILE* 3.9 20.5 - - + +
150C LEU* 3.5 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C GLU* 2.9 26.7 + - + +
124C THR* 3.8 6.1 - - - +
125C MET 3.3 0.4 - - - -
126C THR* 1.3 76.5 - - + +
128C ARG* 1.3 64.0 + - + +
130C LEU* 3.4 8.6 + - + +
131C LYS* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLY 3.3 20.2 + - - +
19C SER* 3.1 29.1 + - - +
120C ALA* 4.5 1.8 - - - +
124C THR* 3.1 40.6 + - + +
125C MET 3.7 4.0 - - - +
127C GLN* 1.3 76.6 - - + +
129C LEU* 1.3 62.9 + - + +
131C LYS* 3.5 7.5 + - - +
132C ARG* 3.1 22.0 + - - +
175C ALA 3.0 23.4 + - - -
176C GLU* 4.2 3.2 - - - +
177C GLY 3.9 5.5 + - - +
633C AP5 3.4 77.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PRO* 3.5 26.9 - - + +
18C GLY* 3.7 20.6 - - - -
125C MET* 3.1 19.5 + - + +
126C THR 3.9 0.7 - - - +
128C ARG* 1.3 73.7 - - - +
130C LEU* 1.3 60.6 + - - +
132C ARG* 3.4 36.8 + - - +
133C GLY* 2.9 25.3 + - - -
141C ASP* 3.8 12.9 - - - +
146C ILE* 3.6 41.1 - - + -
149C ARG* 4.0 11.7 - - - +
150C LEU* 6.1 0.2 - - + -
633C AP5 3.8 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C THR* 3.0 36.9 + - + +
127C GLN* 3.9 8.3 - - + +
129C LEU* 1.3 76.6 - - - +
131C LYS* 1.3 62.2 + - - +
133C GLY* 3.2 9.6 + - - +
134C GLU* 3.4 16.0 + - - +
141C ASP 4.3 4.5 - - - +
142C ASN* 5.2 0.2 - - - -
143C GLU* 4.2 35.9 - - + +
146C ILE* 3.6 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C GLN 3.1 13.8 + - - +
128C ARG* 3.6 10.5 - - - +
130C LEU* 1.3 75.3 - - - +
132C ARG* 1.3 63.1 + - - +
134C GLU* 3.0 24.9 + - + +
135C THR* 3.7 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ARG 3.1 13.3 + - - +
129C LEU* 3.4 15.4 + - - +
131C LYS* 1.3 78.6 - - - +
133C GLY* 1.3 57.8 + - - +
134C GLU 3.1 0.7 + - - -
135C THR* 3.1 20.7 + - - +
136C SER* 2.6 29.7 + - - +
138C ARG* 3.3 26.9 - - - +
141C ASP* 2.9 37.4 + - - +
633C AP5 2.8 79.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LEU 2.9 14.8 + - - -
130C LEU 3.2 6.3 + - - -
131C LYS 3.2 0.6 - - - -
132C ARG* 1.3 75.8 - - - +
134C GLU* 1.3 62.1 + - - +
135C THR 3.6 0.2 + - - -
136C SER* 3.8 12.6 + - - -
138C ARG 5.7 0.2 - - - -
141C ASP* 3.9 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C LEU 3.7 13.9 - - - +
131C LYS* 3.0 13.4 + - - +
133C GLY* 1.3 80.5 - - - +
135C THR* 1.3 64.6 + - + +
136C SER 3.7 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LYS* 3.7 10.7 + - - +
132C ARG* 3.1 14.4 + - - +
134C GLU* 1.3 81.9 - - + +
136C SER* 1.3 59.8 + - - +
----------------------------------------------------------
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