Contacts of the helix formed by residues 152 - 165 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ILE* 3.9 10.3 - - + -
86A ILE* 3.6 24.0 - - + -
100A GLU* 2.8 9.5 + - - +
101A LEU* 4.1 30.1 - - + -
151A PRO* 1.3 80.0 - - - +
153A MET* 1.3 65.6 + - - +
154A VAL 3.4 1.1 - - - -
155A PRO* 3.3 4.7 - - - +
156A LEU* 3.1 44.6 + - + +
180A SER* 3.8 22.0 - - - -
184A ILE* 4.0 19.5 - - + +
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Residues in contact with MET 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLU* 3.1 26.3 + - + +
103A ARG* 3.5 50.9 - - + +
104A GLY* 3.8 22.4 - - - +
150A PHE* 3.7 33.7 - - + -
152A VAL* 1.3 81.7 - - - +
154A VAL* 1.3 61.6 + - + +
156A LEU* 3.0 5.2 + - - +
157A TRP* 2.9 68.0 + - + +
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A THR* 4.0 8.3 - - + -
147A PRO* 3.5 27.4 - - + -
150A PHE* 3.3 31.8 + - + +
153A MET* 1.3 79.5 - - + +
155A PRO* 1.3 70.7 - - + +
157A TRP* 2.9 54.7 + - + +
158A MET* 3.7 6.0 + - + +
223A VAL* 3.7 29.6 - - + -
501A NAD 5.0 1.3 - - + -
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Residues in contact with PRO 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A THR* 3.7 28.7 - - + +
150A PHE 3.2 15.9 - - - +
151A PRO 3.2 19.1 - - - +
152A VAL 3.3 9.6 - - - +
154A VAL* 1.3 92.0 - - + +
156A LEU* 1.3 55.3 + - - +
158A MET* 3.0 17.8 + - + +
159A PHE* 3.0 37.5 + - + -
171A LEU* 4.0 13.9 - - + -
181A THR* 4.0 10.3 - - + -
184A ILE* 4.9 2.0 - - + -
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A PHE* 3.7 26.2 - - + -
75A LEU* 4.5 10.3 - - + -
101A LEU* 5.0 2.2 - - + +
104A GLY* 3.5 38.8 - - - +
105A ILE 4.2 1.8 - - - +
107A ASN* 3.3 15.0 - - - +
108A VAL* 3.9 4.7 - - + -
152A VAL* 3.1 31.3 + - + +
153A MET 3.0 9.9 + - - +
155A PRO* 1.3 71.4 - - - +
157A TRP* 1.3 64.2 + - - +
158A MET 3.1 1.6 - - - -
159A PHE* 3.8 12.8 - - + -
160A PRO* 3.3 36.7 - - + +
161A MET* 5.1 0.3 + - - +
184A ILE* 4.3 7.2 - - + -
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Residues in contact with TRP 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG* 5.4 2.0 - - - -
107A ASN* 3.1 20.9 + - - -
153A MET* 2.9 54.3 + - + +
154A VAL* 2.9 36.2 + - + +
156A LEU* 1.3 79.5 - - - +
158A MET* 1.3 62.4 + - + +
161A MET* 4.7 6.5 - - - +
223A VAL* 4.0 15.9 - - + -
280A CYS* 5.1 1.8 - - - -
442A VAL* 5.8 0.4 - - + -
449A PHE* 3.8 40.4 - + - -
462A ALA* 3.9 17.5 - - + -
463A TYR* 3.3 59.5 + + + +
471A TYR* 4.6 5.5 + - - -
501A NAD 3.9 22.9 - + - -
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Residues in contact with MET 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLY* 3.7 15.3 - - - -
145A ILE 3.6 11.9 - - - +
146A THR* 3.8 19.7 - - + -
154A VAL* 3.9 10.8 - - + +
155A PRO 3.0 8.2 + - - +
156A LEU 3.1 0.4 - - - -
157A TRP* 1.3 84.5 - - + +
159A PHE* 1.3 61.6 + - - +
160A PRO 3.6 1.1 - - - -
161A MET 3.5 2.5 + - - -
162A ALA* 3.0 28.1 + - - +
169A PHE* 3.7 13.0 - - + -
171A LEU* 4.9 0.9 - - + -
221A SER* 3.4 38.8 - - - +
223A VAL* 3.5 31.0 - - + -
244A GLN* 5.7 0.2 - - - +
471A TYR* 3.3 24.5 - - - +
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Residues in contact with PHE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A MET* 5.7 0.4 - - + -
71A PHE* 4.2 16.2 - + - -
155A PRO* 3.0 43.4 + - + -
156A LEU* 3.8 16.2 - - + -
158A MET* 1.3 74.2 - - - +
160A PRO* 1.3 81.4 - - + +
162A ALA* 4.1 0.2 - - - -
163A ILE* 2.9 37.3 + - + +
169A PHE* 3.6 35.4 - + + -
171A LEU* 4.4 6.7 - - + -
184A ILE* 4.4 15.7 - - + -
185A ALA* 5.1 4.0 - - + -
188A LEU* 3.7 21.8 - - + -
198A MET* 3.3 29.2 - - + -
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Residues in contact with PRO 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A MET* 3.6 30.1 - - + +
107A ASN 4.4 6.7 - - - +
108A VAL* 4.1 9.0 - - + -
111A ALA* 4.1 13.2 - - + -
156A LEU* 3.3 51.6 - - + +
158A MET 3.7 0.4 - - - -
159A PHE* 1.3 106.2 - - + +
161A MET* 1.3 60.1 + - - +
163A ILE* 3.8 1.2 - - - +
164A VAL* 3.0 23.4 + - - +
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Residues in contact with MET 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASN 5.4 2.5 - - - +
110A TYR* 3.6 33.4 - - + -
111A ALA* 4.2 14.1 - - + +
114A ALA* 5.9 0.7 - - - -
117A LEU* 3.6 17.0 - - + -
156A LEU 5.1 0.8 + - - +
157A TRP 4.7 6.5 - - - +
158A MET 3.5 6.7 + - - +
159A PHE 3.3 0.2 - - - -
160A PRO* 1.3 76.9 - - - +
162A ALA* 1.3 66.8 + - - +
164A VAL* 3.4 13.2 - - - +
165A CYS* 3.0 39.8 + - - -
463A TYR* 5.9 0.9 - - - -
464A GLY 4.0 5.6 - - - +
467A ALA* 3.8 28.0 - - + -
468A VAL* 3.5 20.2 - - + -
471A TYR* 4.0 9.2 - - + -
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A VAL* 4.6 2.5 - - + -
158A MET 3.0 19.5 + - - +
159A PHE 4.1 0.2 - - - +
160A PRO 3.3 0.2 - - - -
161A MET* 1.3 77.4 - - - +
163A ILE* 1.3 61.6 + - - +
165A CYS 3.3 5.2 + - - -
167A ASN* 2.9 33.8 + - + +
169A PHE* 3.7 26.0 - - + -
471A TYR* 3.5 32.6 - - + -
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Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A TRP* 3.0 43.7 + - + +
64A ARG 5.9 0.2 - - - +
67A VAL* 6.1 0.4 - - + -
68A MET* 5.0 9.6 - - - -
159A PHE* 2.9 40.5 + - + +
160A PRO* 3.8 2.7 - - + +
162A ALA* 1.3 73.9 - - - +
164A VAL* 1.3 61.6 + - - +
166A GLY* 2.8 19.6 + - - -
167A ASN 3.7 9.4 - - - +
169A PHE* 4.3 12.8 - - + -
188A LEU* 4.2 3.1 - - + -
193A LEU* 3.8 20.9 - - + -
197A VAL* 3.9 10.1 - - + +
198A MET* 4.0 28.9 - - + -
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PRO* 4.9 0.2 - - - +
64A ARG* 2.6 38.2 + - + +
65A ALA* 3.6 31.2 - - - +
68A MET* 4.1 9.6 - - + -
111A ALA* 3.5 29.4 - - + +
114A ALA* 3.6 18.2 - - + +
118A LEU* 4.2 4.9 - - - +
160A PRO 3.0 15.3 + - - +
161A MET* 3.4 26.7 - - - +
163A ILE* 1.3 79.5 - - - +
165A CYS* 1.3 57.6 + - - +
166A GLY 3.2 0.4 - - - -
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Residues in contact with CYS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 3.5 8.8 + - - +
114A ALA* 5.9 0.4 - - - -
118A LEU* 4.0 25.1 - - - +
136A PHE 5.1 0.7 - - - +
138A PRO* 3.3 23.7 - - - +
161A MET* 3.0 47.8 + - - +
162A ALA 3.5 6.5 - - - +
163A ILE 3.1 0.8 - - - -
164A VAL* 1.3 78.3 - - - +
166A GLY* 1.3 55.9 + - - +
167A ASN* 3.6 10.5 - - - +
468A VAL* 4.3 11.0 - - - -
471A TYR* 4.2 4.3 - - + +
472A THR* 4.0 19.9 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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