Contacts of the helix formed by residues 118 - 141 (chain C) in PDB entry 1ZOY
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 THR 118 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B THR* 5.4 2.0 - - - -
230B ASN* 4.4 6.3 - - - +
116C GLY 3.2 1.2 + - - -
117C LEU* 1.3 80.9 - - - +
119C ILE* 1.3 67.6 + - - +
120C PRO* 3.3 13.4 - - + +
121C GLN* 2.9 46.5 + - - +
122C LEU* 2.7 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B MET 4.6 1.8 - - - +
222B THR* 3.8 20.3 - - + +
223B GLY* 3.4 37.9 - - - +
118C THR* 1.3 71.5 - - - +
120C PRO* 1.3 75.9 - - + +
122C LEU* 3.0 31.3 + - + +
123C THR* 3.2 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C THR* 3.3 15.3 - - - +
119C ILE* 1.3 97.1 - - + +
121C GLN* 1.3 68.9 + - + +
122C LEU 3.1 0.2 + - - -
123C THR* 3.3 12.5 + - - +
124C GLN* 3.4 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLY* 3.5 38.1 + - - +
117C LEU 4.0 0.2 + - - -
118C THR* 2.9 40.5 + - - +
120C PRO* 1.3 81.0 - - + +
122C LEU* 1.3 61.9 + - - +
124C GLN* 3.5 16.6 + - - +
125C SER* 3.1 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B MET* 3.6 39.7 - - + -
38C PRO* 4.5 23.6 - - + +
107C ARG* 3.4 8.4 + - - +
111C TRP* 3.4 43.1 - - + +
116C GLY 3.9 8.3 - - - +
117C LEU* 5.1 2.0 - - - -
118C THR 2.7 26.1 + - - +
119C ILE* 3.2 18.6 - - + +
121C GLN* 1.3 74.8 - - - +
123C THR* 1.3 62.2 + - - +
125C SER* 2.7 18.2 + - - +
126C GLY* 3.0 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 4.6 20.8 - - + +
38C PRO* 5.5 8.5 - - + +
119C ILE* 3.2 18.6 + - - +
120C PRO* 4.0 5.6 - - - +
122C LEU* 1.3 74.3 - - - +
124C GLN* 1.3 67.8 + - - +
126C GLY* 3.2 2.3 + - - +
127C VAL* 3.0 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C PRO* 3.4 11.6 + - - +
121C GLN* 3.6 24.1 + - - +
122C LEU 3.3 0.2 - - - -
123C THR* 1.3 80.1 - - - +
125C SER* 1.3 64.2 + - - +
127C VAL* 3.0 7.2 + - - +
128C VAL* 2.9 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ARG* 3.0 31.1 + - - +
111C TRP* 4.8 2.7 + - - -
116C GLY 5.4 0.5 + - - -
121C GLN 3.1 10.6 + - - -
122C LEU* 2.7 25.8 + - - +
124C GLN* 1.3 77.9 - - - +
126C GLY* 1.3 51.9 + - - +
128C VAL* 3.4 9.7 - - - +
129C VAL* 2.7 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 4.5 5.8 - - - -
41C MET* 3.4 26.8 - - - +
107C ARG* 3.5 14.8 - - - -
122C LEU 3.0 12.9 + - - -
123C THR* 3.7 3.1 - - - -
124C GLN 3.2 0.4 - - - -
125C SER* 1.3 77.6 + - - +
127C VAL* 1.3 61.2 + - - +
130C LEU* 2.9 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 4.5 11.2 - - + +
123C THR* 3.0 22.8 + - + +
124C GLN* 3.4 7.6 - - - +
126C GLY* 1.3 73.9 - - - +
128C VAL* 1.3 65.7 + - + +
130C LEU* 3.0 12.3 + - + +
131C ILE* 2.9 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C GLN* 2.9 24.2 + - + +
125C SER* 3.4 10.8 - - - +
127C VAL* 1.3 77.1 - - + +
129C VAL* 1.3 66.9 + - + +
131C ILE* 2.8 20.2 + - - +
132C LEU* 2.8 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C MET* 3.7 17.9 - - + -
100C TYR* 4.5 4.5 - - + +
103C TRP* 3.9 22.7 - - + +
104C ASN* 3.7 27.1 - - + +
107C ARG* 3.6 24.7 - - + +
125C SER* 2.7 23.9 + - - +
126C GLY 3.7 3.6 - - - +
128C VAL* 1.3 76.8 - - + +
130C LEU* 1.3 56.2 + - - +
132C LEU* 3.6 9.1 + - + +
133C THR* 2.6 38.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
37C LEU* 4.5 24.0 - - + -
41C MET* 3.6 26.5 - - + -
100C TYR* 3.9 19.7 - - + -
126C GLY 2.9 11.6 + - - +
127C VAL* 3.0 13.2 + - + +
129C VAL* 1.3 78.9 - - - +
131C ILE* 1.3 63.8 + - + +
133C THR* 3.3 18.1 - - - -
134C VAL* 3.3 16.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C VAL* 2.9 29.7 + - + +
128C VAL* 2.8 13.5 + - + +
130C LEU* 1.3 71.1 - - + +
132C LEU* 1.3 69.2 + - + +
133C THR 3.2 0.3 + - - -
134C VAL* 3.3 10.3 + - + +
135C LEU* 3.0 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C TRP* 3.8 48.0 - - + +
128C VAL* 2.8 37.7 + - + +
129C VAL* 3.9 7.6 - - + +
131C ILE* 1.3 79.3 - - + +
133C THR* 1.3 63.0 + - - +
135C LEU* 3.8 14.7 - - + +
136C SER* 2.9 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C PHE* 3.6 30.5 - - + -
99C MET* 4.6 0.2 - - - -
100C TYR* 3.5 49.8 - - + +
103C TRP* 3.8 8.0 - - - -
129C VAL* 2.6 22.4 + - - +
130C LEU* 3.3 12.7 - - + -
131C ILE 3.1 0.2 - - - -
132C LEU* 1.3 74.8 - - - +
134C VAL* 1.3 65.2 + - + +
136C SER* 2.9 8.2 + - - -
137C SER* 2.8 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C PHE* 5.5 3.1 - - + -
96C PHE* 4.6 15.7 - - + -
130C LEU* 3.3 14.2 + - + +
131C ILE* 3.7 11.2 - - + +
133C THR* 1.3 78.6 - - + +
135C LEU* 1.3 69.0 + - + +
137C SER* 3.2 6.4 + - - -
138C VAL* 3.0 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ILE* 3.0 36.9 + - + +
132C LEU* 3.8 15.7 - - + +
134C VAL* 1.3 79.9 - - + +
136C SER* 1.3 58.2 + - - +
138C VAL* 4.0 3.0 - - - +
139C GLY* 2.8 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C MET* 3.2 26.1 - - - +
103C TRP* 3.1 23.5 + - - -
132C LEU* 2.9 25.8 + - - -
133C THR 2.9 7.1 + - - -
135C LEU* 1.3 73.6 - - - +
137C SER* 1.3 57.1 + - - +
139C GLY* 3.8 2.2 - - - -
140C LEU* 2.9 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C PHE* 3.3 28.1 - - - -
95C VAL* 3.8 14.3 - - - +
96C PHE* 3.3 28.6 - - - -
99C MET* 3.9 7.3 - - - +
133C THR 2.8 22.7 + - - -
134C VAL 3.5 3.1 - - - -
136C SER* 1.3 74.0 - - - +
138C VAL* 1.3 68.3 + - - +
139C GLY 3.0 1.1 - - - -
140C LEU* 3.2 2.9 + - - +
141C ALA* 2.8 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C TYR* 3.4 22.5 + - + +
92C PHE* 3.7 17.9 - - + -
134C VAL* 3.0 26.3 + - + +
135C LEU* 4.1 2.9 - - - +
137C SER* 1.3 79.9 - - - +
139C GLY* 1.3 65.2 + - - +
141C ALA* 3.3 8.0 + - - +
142C ALA* 3.6 12.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C LEU 2.8 18.4 + - - -
136C SER* 3.9 2.2 - - - -
138C VAL* 1.3 80.9 - - - +
140C LEU* 1.3 61.2 + - - +
142C ALA* 3.2 19.3 + - - +
143C MET* 3.9 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C VAL* 3.5 31.4 - - + -
98C LEU* 6.0 0.2 - - + -
99C MET* 3.7 24.9 - - + -
136C SER* 2.9 21.7 + - - +
139C GLY* 1.3 70.1 - - - +
141C ALA* 1.3 58.4 + - - +
142C ALA 2.8 11.0 + - - -
143C MET* 3.1 29.7 + - + +
134D TRP* 3.0 28.7 + - + -
1306D EPH 4.1 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C TYR* 3.2 47.6 - - + +
91C LYS* 4.0 25.6 - - + -
92C PHE* 4.1 25.1 - - + +
95C VAL* 4.6 1.9 - - + +
137C SER 2.8 19.9 + - - +
138C VAL 3.8 0.7 - - - +
139C GLY 3.3 0.8 - - - -
140C LEU* 1.3 71.3 - - - +
142C ALA* 1.3 57.3 + - - +
143C MET 3.7 0.7 - - - -
----------------------------------------------------------
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