Contacts of the helix formed by residues 152 - 165 (chain C) in PDB entry 4ZZ7
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 VAL 152 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ILE* 4.1 12.1 - - + -
86C ILE* 3.6 28.7 - - + -
100C GLU* 2.8 11.7 + - - +
101C LEU* 3.9 27.8 - - + -
151C PRO* 1.3 81.2 - - - +
153C MET* 1.3 65.9 + - - +
154C VAL 3.4 1.1 - - - -
155C PRO* 3.5 4.8 - - - +
156C LEU* 3.2 42.6 + - + +
180C SER* 4.1 18.4 - - - +
184C ILE* 4.1 13.7 - - + +
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Residues in contact with MET 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C GLU* 3.1 32.1 + - + +
103C ARG* 3.3 53.6 - - + +
104C GLY* 4.0 11.9 - - - +
107C ASN* 4.4 0.2 - - - +
150C PHE* 3.7 34.1 - - + -
152C VAL* 1.3 81.7 - - - +
154C VAL* 1.3 60.7 + - + +
156C LEU* 3.0 8.9 + - - +
157C TRP* 2.9 68.7 + - + +
280C CYS* 6.3 0.2 - - - -
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Residues in contact with VAL 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C THR* 3.8 9.0 - - + -
147C PRO* 3.6 29.4 - - + -
150C PHE* 3.4 34.6 + - + +
153C MET* 1.3 78.0 - - + +
155C PRO* 1.4 68.9 - - + +
157C TRP* 3.1 44.8 - - + +
158C MET* 3.7 7.3 - - + +
223C VAL* 3.8 28.0 - - + -
501C NAD 4.9 1.3 - - + -
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Residues in contact with PRO 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C THR* 3.9 28.5 - - + +
150C PHE 3.4 15.0 - - - +
151C PRO 3.2 19.3 - - - +
152C VAL 3.5 8.7 - - - +
154C VAL* 1.4 91.1 - - + +
156C LEU* 1.3 53.0 + - - +
158C MET* 2.8 26.1 + - + +
159C PHE* 3.1 37.0 + - + -
171C LEU* 4.0 16.6 - - + -
181C THR* 4.2 5.6 - - + +
184C ILE* 4.8 3.8 - - + -
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Residues in contact with LEU 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PHE* 3.6 32.8 - - + -
75C LEU* 4.4 11.4 - - + -
101C LEU* 4.9 2.2 - - + -
104C GLY* 3.5 39.5 - - - +
105C ILE 4.3 0.7 - - - +
107C ASN* 3.1 19.7 - - - +
108C VAL* 3.9 4.9 - - + -
152C VAL* 3.2 31.4 + - + +
153C MET 3.0 9.0 + - - +
155C PRO* 1.3 74.1 - - - +
157C TRP* 1.3 63.2 + - - +
158C MET 3.2 0.2 - - - -
159C PHE* 3.8 12.1 - - + -
160C PRO* 3.3 27.5 - - + +
184C ILE* 4.1 7.4 - - + -
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Residues in contact with TRP 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ARG* 5.4 1.6 - - - -
107C ASN* 3.3 17.3 + - - -
153C MET* 2.9 60.1 + - + +
154C VAL* 3.1 20.9 - - + +
155C PRO 3.1 0.2 - - - -
156C LEU* 1.3 77.7 - - - +
158C MET* 1.3 63.6 + - + +
161C MET* 4.5 9.0 - - - +
223C VAL* 4.0 25.6 - - + -
246C LEU* 4.2 2.5 - - + -
280C CYS* 5.1 1.1 - - - -
442C VAL* 5.7 0.9 - - + -
449C PHE* 3.7 40.6 - + - -
462C ALA* 4.0 15.9 - - + -
463C TYR* 3.4 57.9 + + + +
471C TYR* 4.8 2.3 - - - -
501C NAD 3.9 25.1 - + - -
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Residues in contact with MET 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C GLY* 3.8 24.7 - - - -
145C ILE 3.7 14.8 - - - +
146C THR* 3.8 19.3 - - + -
154C VAL* 3.7 11.2 - - + +
155C PRO* 2.8 7.4 + - + +
157C TRP* 1.3 82.7 - - + +
159C PHE* 1.3 60.3 + - - +
160C PRO* 3.5 1.1 - - - -
161C MET 3.4 3.3 + - - -
162C ALA* 3.0 25.8 + - - +
169C PHE* 3.6 14.1 - - + -
171C LEU* 5.0 0.2 - - - -
221C SER* 3.7 29.4 - - - +
222C PHE 4.2 0.2 - - - +
223C VAL* 3.8 26.5 - - + -
244C GLN* 5.7 0.4 - - - +
471C TYR* 3.4 25.5 - - - +
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Residues in contact with PHE 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C MET* 5.5 0.2 - - + -
71C PHE* 4.0 19.1 - + - -
155C PRO* 3.1 43.7 + - + -
156C LEU* 3.8 15.7 - - + -
158C MET* 1.3 73.1 - - - +
160C PRO* 1.3 77.8 - - + +
163C ILE* 2.7 47.5 + - + +
169C PHE* 3.7 35.0 - + + -
171C LEU* 4.5 4.5 - - + -
181C THR* 6.1 0.2 - - + -
184C ILE* 4.0 17.3 - - + -
185C ALA* 5.0 4.0 - - + -
188C LEU* 3.6 22.7 - - + -
198C MET* 3.3 34.3 - - + -
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Residues in contact with PRO 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C MET* 3.4 33.0 - - + +
107C ASN 4.5 2.0 - - - +
108C VAL* 4.1 9.9 - - + -
111C ALA* 4.1 13.6 - - + +
156C LEU* 3.3 52.5 - - + +
158C MET 3.5 1.3 - - - -
159C PHE* 1.3 104.0 - - + +
161C MET* 1.3 62.8 + - - +
163C ILE* 3.9 1.4 - - + +
164C VAL* 3.0 23.2 + - - +
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Residues in contact with MET 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ASN 5.5 0.9 - - - +
110C TYR* 3.4 40.2 - - + -
111C ALA* 4.2 12.4 - - + +
114C ALA* 5.9 0.4 - - - -
117C LEU* 3.8 12.8 - - + -
157C TRP 4.5 7.0 + - - +
158C MET 3.4 8.0 + - - +
159C PHE 3.4 0.2 - - - -
160C PRO* 1.3 80.1 - - - +
162C ALA* 1.3 63.2 + - - +
164C VAL* 3.4 12.9 + - - +
165C CYS* 3.0 33.1 + - - -
463C TYR* 5.7 0.9 - - + -
464C GLY 4.0 6.7 - - - +
467C ALA* 3.8 26.5 - - + -
468C VAL* 3.5 20.6 - - + -
471C TYR* 4.0 11.9 - - + -
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Residues in contact with ALA 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C VAL* 4.6 2.2 - - + -
158C MET 3.0 17.3 + - - +
159C PHE 3.8 0.4 - - - +
161C MET* 1.3 76.7 - - - +
163C ILE* 1.3 62.8 + - + +
165C CYS 3.3 4.9 + - - -
167C ASN* 2.8 36.5 + - + +
169C PHE* 3.6 28.7 - - + -
471C TYR* 3.6 30.1 - - + -
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Residues in contact with ILE 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C TRP* 2.8 42.7 + - + +
64C ARG* 3.7 1.5 - - - +
67C VAL* 5.9 0.2 - - + -
68C MET* 4.8 11.9 - - - -
159C PHE* 2.7 48.2 + - + +
160C PRO* 3.9 3.4 - - + +
162C ALA* 1.3 73.5 - - - +
164C VAL* 1.3 58.0 + - - +
166C GLY 2.8 17.0 + - - -
167C ASN 3.7 8.1 - - - +
169C PHE* 4.3 7.6 - - + -
188C LEU* 4.4 2.9 - - + -
193C LEU* 3.8 21.1 - - + -
197C VAL* 4.0 15.3 - - + +
198C MET* 3.9 26.2 - - + -
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Residues in contact with VAL 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C PRO* 5.0 0.3 - - - +
64C ARG* 2.8 33.5 + - + +
65C ALA* 3.6 27.1 - - - +
68C MET* 4.1 8.7 - - + -
111C ALA* 3.6 29.8 - - + +
114C ALA* 3.5 25.1 - - + +
118C LEU* 3.9 6.8 - - - +
160C PRO 3.0 17.0 + - - +
161C MET* 3.5 20.4 - - - +
163C ILE* 1.3 78.6 - - - +
165C CYS* 1.3 60.1 + - - +
166C GLY 3.1 1.1 - - - -
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Residues in contact with CYS 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ARG* 3.5 9.5 + - - +
118C LEU* 4.1 23.6 - - - +
136C PHE 5.5 0.7 - - - +
138C PRO* 3.5 23.0 - - - +
161C MET* 3.0 46.7 + - - +
162C ALA 3.6 5.6 - - - +
163C ILE 3.1 0.2 - - - -
164C VAL* 1.3 79.1 - - - +
166C GLY* 1.3 56.0 + - - +
167C ASN* 3.4 10.8 + - - +
468C VAL* 4.1 17.0 - - - -
471C TYR* 4.1 4.7 - - + +
472C THR* 4.0 16.6 - - + +
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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) + - + + + + + -
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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