Contacts of the helix formed by residues 128 - 142 (chain C) in PDB entry 5BZZ
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 LYS 128 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C CYS* 3.4 6.5 - - - -
126C ALA* 4.1 19.1 - - + +
127C GLY* 1.3 77.2 - - - +
129C GLY* 1.3 56.7 + - - +
130C ARG 3.5 0.7 - - - -
132C GLY* 2.8 31.6 + - - -
155C TYR* 2.9 12.4 + - - -
159C ARG* 5.4 0.7 - - + -
160C THR* 5.1 7.4 - - + -
164C LYS* 3.4 19.5 + - - +
165C GLY* 2.8 29.4 - - - +
167C THR* 3.2 27.5 + - - +
401C TLA 4.3 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C LYS* 1.3 80.1 - - - +
130C ARG* 1.3 57.5 + - - +
132C GLY* 3.3 1.4 + - - -
133C VAL* 2.9 33.1 + - - +
165C GLY 4.1 9.9 - - - -
166C VAL* 3.8 6.7 - - - +
171C GLN* 3.4 23.6 - - - -
401C TLA 3.5 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LEU* 3.4 18.4 + - + -
71C CYS* 3.8 3.4 - - - +
73C GLU* 2.9 37.7 + - - -
90C PHE* 2.7 60.3 + - + -
91C GLU 3.6 14.8 - - - +
92C ASP* 3.4 19.2 + - - +
124C CYS* 3.9 15.8 - - + +
125C LYS* 4.3 7.3 - - - +
129C GLY* 1.3 71.4 - - - +
131C THR* 1.3 67.5 + - - +
133C VAL* 3.3 4.4 + - - +
134C MET* 3.2 27.5 + - - +
171C GLN* 3.9 13.9 - - - +
401C TLA 3.1 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ALA* 3.7 13.2 - - + -
70C LEU* 3.7 9.1 - - - +
122C ILE* 3.5 24.7 - - + +
123C HIS* 3.6 3.3 - - - -
124C CYS* 3.0 38.1 + - - -
127C GLY* 3.5 7.7 - - - -
129C GLY 3.4 0.2 - - - -
130C ARG* 1.3 78.0 - - - +
132C GLY* 1.3 57.1 + - - +
134C MET* 3.4 1.4 + - - +
135C ILE* 2.9 57.0 + - + +
155C TYR* 3.9 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C LYS 2.8 20.0 + - - -
129C GLY 3.5 1.3 - - - -
130C ARG 3.2 0.2 - - - -
131C THR* 1.3 74.8 - - - +
133C VAL* 1.3 58.4 + - - +
135C ILE 4.6 0.2 - - - -
136C CYS* 2.9 36.6 + - - +
155C TYR* 3.4 26.4 + - - -
166C VAL* 3.8 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C PHE* 4.8 0.4 - - + -
96C PRO* 3.7 32.8 - - + -
101C ILE* 5.0 5.4 - - + -
129C GLY 2.9 24.1 + - - +
130C ARG* 3.3 9.4 + - - +
132C GLY* 1.3 71.5 - - - +
134C MET* 1.3 63.0 + - + +
136C CYS* 3.8 1.0 - - - +
137C ALA* 2.8 33.1 + - + +
166C VAL* 3.9 4.2 - - + +
171C GLN* 3.6 42.0 - - + +
174C TYR* 4.7 4.9 - - + -
175C VAL* 3.9 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LEU* 3.6 17.9 - - + -
88C TYR* 4.4 4.5 - - + -
90C PHE* 3.8 17.7 - - + -
96C PRO* 4.4 14.6 - - - -
100C LEU* 4.0 30.1 - - + +
101C ILE* 4.4 11.0 - - - -
104C PHE* 3.5 64.9 - - + -
122C ILE* 4.9 0.9 - - + -
130C ARG 3.2 14.9 + - - +
131C THR 3.8 5.8 - - - +
133C VAL* 1.3 76.3 - - - +
135C ILE* 1.3 60.5 + - - +
137C ALA* 3.5 3.9 + - - +
138C TYR* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ILE* 4.1 16.4 - - + -
32C ILE* 4.1 28.9 - - + -
34C ALA* 3.7 20.0 - - + -
104C PHE* 5.3 1.1 - - + -
108C LEU* 5.8 0.9 - - + -
122C ILE* 4.4 16.4 - - + -
131C THR* 2.9 42.3 + - + +
132C GLY 4.3 1.8 - - - +
134C MET* 1.3 72.8 - - - +
136C CYS* 1.3 55.8 + - - +
138C TYR* 3.2 7.1 + - + +
139C LEU* 2.8 54.2 + - + +
155C TYR* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C GLY 2.9 24.7 + - - +
133C VAL 3.8 2.9 - - - +
135C ILE* 1.3 73.8 - - - +
137C ALA* 1.3 65.9 + - - +
139C LEU* 3.4 6.6 + - - +
140C LEU* 2.9 32.3 + - - +
151C ALA* 3.3 39.6 - - + +
152C LEU* 3.8 12.8 - - - -
155C TYR* 3.6 19.3 - - - -
175C VAL* 4.0 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ILE* 3.7 31.9 - - + -
104C PHE* 6.0 0.2 - - + -
105C CYS* 3.9 4.0 - - - -
133C VAL* 2.8 24.9 + - + +
134C MET* 3.6 7.4 - - - +
136C CYS* 1.3 74.0 - - - +
138C TYR* 1.3 51.0 + - - +
140C LEU* 3.2 8.6 + - - +
141C HIS* 2.6 35.7 + - - +
175C VAL* 4.5 5.3 - - + +
178C TYR* 3.8 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ILE* 3.9 28.5 - - + -
104C PHE* 4.6 1.3 - - + -
105C CYS* 3.6 40.1 - - - -
108C LEU* 3.3 24.2 - - + -
109C ASP* 2.7 36.5 + - + -
112C LEU* 3.8 21.7 - - + +
134C MET 2.9 17.9 + - - +
135C ILE* 3.5 5.2 - - - +
137C ALA* 1.3 77.2 - - - +
139C LEU* 1.3 58.9 + - + +
141C HIS* 3.1 7.2 - + - +
142C ARG* 2.7 59.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ILE* 3.9 9.2 - - + -
29C TYR* 3.6 35.4 - - + -
32C ILE* 3.7 19.1 - - + -
135C ILE* 2.8 43.7 + - + +
136C CYS* 3.4 8.3 + - - +
138C TYR* 1.3 76.3 - - + +
140C LEU* 1.3 58.3 + - - +
142C ARG* 3.7 4.8 + - + +
143C GLY 3.5 1.2 + - - -
144C LYS* 2.9 39.3 + - + +
145C PHE* 3.3 35.5 + - + -
151C ALA 5.9 0.2 - - - +
154C PHE* 5.0 1.6 - - + -
155C TYR* 6.4 1.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
136C CYS 2.9 24.2 + - - +
137C ALA* 3.4 6.3 - - - +
139C LEU* 1.3 76.1 - - - +
141C HIS* 1.3 65.9 + - - +
143C GLY* 3.0 14.6 + - - -
145C PHE* 3.6 27.9 - - + +
146C LEU 4.4 2.2 - - - -
147C LYS* 3.7 28.3 - - - +
148C ALA* 4.0 6.5 - - - +
151C ALA* 4.1 6.1 - - + -
175C VAL* 3.5 30.3 - - + +
178C TYR* 5.6 0.4 - - + -
179C SER* 4.0 22.4 - - - +
182C LEU* 3.7 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LYS* 5.4 3.6 - - + -
105C CYS* 3.6 27.5 - - + +
106C GLU* 4.1 21.1 - - + +
109C ASP* 4.0 18.4 + - - -
137C ALA 2.6 17.9 + - - +
138C TYR* 3.1 28.9 - + - +
140C LEU* 1.3 74.0 - - - +
142C ARG* 1.3 62.4 + - + +
143C GLY 3.4 0.9 + - - -
178C TYR* 3.0 24.3 + - + -
182C LEU* 3.7 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ASP* 3.1 28.2 + - - -
113C SER* 5.8 5.1 - - - -
138C TYR* 2.7 50.2 + - + +
139C LEU* 4.1 9.4 - - + +
140C LEU 3.2 0.4 - - - -
141C HIS* 1.3 75.2 - - + +
143C GLY* 1.3 58.6 + - - +
144C LYS* 3.1 16.8 + - + +
----------------------------------------------------------
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