Contacts of the helix formed by residues 152 - 165 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82J ILE* 3.8 10.3 - - + -
86J ILE* 3.5 24.5 - - + -
100J GLU* 2.7 16.9 + - - +
101J LEU* 3.9 29.4 - - + -
151J PRO* 1.3 73.9 - - - +
153J MET* 1.3 62.9 + - - +
154J VAL 3.5 0.7 - - - -
155J PRO* 3.6 4.4 - - - +
156J LEU* 3.2 46.5 + - + +
180J SER* 3.7 27.8 - - - +
184J ILE* 4.1 14.3 - - + +
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Residues in contact with MET 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100J GLU* 2.9 40.4 + - + +
103J ARG* 3.1 52.5 - - + +
104J GLY* 4.0 11.7 - - - +
107J ASN* 4.4 0.2 - - - +
150J PHE* 3.7 34.5 - - + -
152J VAL* 1.3 73.1 - - - +
154J VAL* 1.3 60.1 + - + +
156J LEU* 3.0 9.3 + - - +
157J TRP* 2.9 67.2 + - + +
280J CYS* 6.2 0.4 - - - -
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Residues in contact with VAL 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J THR* 3.8 8.1 - - + -
147J PRO* 3.5 29.6 - - + -
150J PHE* 3.2 38.0 + - + +
153J MET* 1.3 76.3 - - + +
155J PRO* 1.3 65.8 - - + +
157J TRP* 3.2 45.4 - - + +
158J MET* 3.6 9.7 - - + +
223J VAL* 3.7 28.5 - - + -
280J CYS* 5.9 1.1 - - - -
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Residues in contact with PRO 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J THR* 3.7 28.7 - - + +
150J PHE 3.3 14.8 - - - +
151J PRO 3.5 17.0 - - - +
152J VAL 3.6 10.5 - - - +
154J VAL* 1.3 93.3 - - + +
156J LEU* 1.3 56.0 + - - +
158J MET* 3.1 6.4 + - + +
159J PHE* 3.0 43.6 + - + -
171J LEU* 3.7 21.8 - - + -
181J THR* 3.9 11.7 - - + -
184J ILE* 4.8 1.6 - - + -
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Residues in contact with LEU 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71J PHE* 3.5 34.3 - - + -
75J LEU* 4.4 11.7 - - + -
101J LEU* 5.0 1.8 - - + -
104J GLY* 3.5 37.5 - - - +
105J ILE 4.4 0.7 - - - +
107J ASN* 3.3 15.9 - - - +
108J VAL* 3.9 5.2 - - + -
152J VAL* 3.2 32.9 + - + +
153J MET 3.0 9.3 + - - +
155J PRO* 1.3 72.9 - - - +
157J TRP* 1.3 64.7 + - - +
158J MET 3.2 0.4 - - - -
159J PHE* 3.7 11.7 - - + -
160J PRO* 3.2 29.4 - - + +
161J MET* 5.1 0.3 + - - +
184J ILE* 4.2 6.5 - - + -
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Residues in contact with TRP 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J ASN* 3.4 16.4 + - - -
153J MET* 2.9 54.1 + - + +
154J VAL* 3.2 24.2 - - + +
155J PRO 3.2 0.4 - - - -
156J LEU* 1.3 77.2 - - - +
158J MET* 1.3 66.1 + - + +
161J MET* 4.5 9.0 - - - +
223J VAL* 4.0 33.2 - - + -
246J LEU* 4.1 6.1 - - + -
280J CYS* 4.8 8.5 - - - -
442J VAL* 5.5 2.7 - - + +
449J PHE* 3.6 46.0 - + - -
462J ALA* 3.9 14.1 - - + -
463J TYR* 3.4 59.4 + + + +
471J TYR* 4.7 2.3 + - - -
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Residues in contact with MET 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144J GLY* 3.8 15.3 - - - -
145J ILE 3.8 11.7 - - - +
146J THR* 3.9 20.0 - - + -
154J VAL* 3.6 10.8 - - + +
155J PRO* 3.1 7.2 + - + +
157J TRP* 1.3 82.7 - - + +
159J PHE* 1.3 60.1 + - - +
160J PRO* 3.5 1.6 - - - -
161J MET 3.4 2.9 + - - -
162J ALA* 2.9 28.9 + - - +
169J PHE* 3.6 12.6 - - + -
171J LEU* 5.1 0.4 - - - -
221J SER* 3.6 38.4 - - - +
223J VAL* 3.7 30.3 - - + -
244J GLN* 5.6 0.2 - - - +
471J TYR* 3.3 24.9 - - - +
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Residues in contact with PHE 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68J MET* 5.6 0.4 - - + -
71J PHE* 4.1 22.4 - + - -
155J PRO* 3.0 47.7 + - + -
156J LEU* 3.7 17.5 - - + -
158J MET* 1.3 72.4 - - - +
160J PRO* 1.3 73.4 - - + +
163J ILE* 2.8 44.1 + - + +
169J PHE* 3.7 35.9 - + + -
171J LEU* 4.3 4.3 - - + -
184J ILE* 4.1 15.9 - - + -
185J ALA* 5.0 5.8 - - + -
188J LEU* 4.1 13.5 - - + -
198J MET* 3.5 33.9 - - + -
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Residues in contact with PRO 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J MET* 3.5 30.1 - - + +
107J ASN 4.7 2.0 - - - +
108J VAL* 4.1 12.8 - - + -
111J ALA* 4.2 11.7 - - + -
155J PRO 3.5 4.5 - - - +
156J LEU* 3.2 47.8 - - + +
158J MET 3.5 1.8 - - - -
159J PHE* 1.3 107.8 - - + +
161J MET* 1.3 60.1 + - - +
163J ILE* 3.8 1.4 - - - +
164J VAL* 3.0 22.9 + - - +
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Residues in contact with MET 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J ASN 5.5 2.0 - - - +
110J TYR* 3.4 39.7 - - + -
111J ALA* 4.3 12.0 - - + +
114J ALA* 5.9 0.7 - - - -
117J LEU* 3.7 14.6 - - + -
157J TRP 4.5 7.4 + - - +
158J MET 3.4 6.5 + - - +
159J PHE 3.4 0.4 - - - -
160J PRO* 1.3 80.1 - - - +
162J ALA* 1.3 59.0 + - - +
164J VAL* 3.5 13.6 + - - -
165J CYS* 3.1 37.4 + - - -
463J TYR* 5.6 1.6 - - + -
464J GLY 4.1 5.2 - - - +
467J ALA* 3.8 31.6 - - + -
468J VAL* 3.8 17.7 - - + +
471J TYR* 4.1 4.5 - - + -
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Residues in contact with ALA 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J VAL* 4.6 2.2 - - + -
158J MET 2.9 19.1 + - - +
161J MET* 1.3 76.9 - - - +
163J ILE* 1.3 60.0 + - - +
165J CYS 3.5 3.6 + - - -
167J ASN* 3.0 37.2 + - + +
169J PHE* 3.7 24.2 - - + -
471J TYR* 3.5 35.6 - - + -
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Residues in contact with ILE 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J TRP* 2.9 47.4 + - + -
64J ARG* 4.0 0.4 - - - +
67J VAL* 6.3 0.2 - - + -
68J MET* 5.1 9.9 - - - -
159J PHE* 2.8 45.4 + - + +
160J PRO* 3.9 3.6 - - + +
162J ALA* 1.3 79.0 - - - +
164J VAL* 1.3 56.5 + - - +
166J GLY* 3.0 9.2 + - - -
167J ASN 3.5 12.6 - - - +
169J PHE* 4.2 9.4 - - + -
188J LEU* 4.0 13.7 - - + -
193J LEU* 3.8 10.3 - - + -
197J VAL* 3.7 20.2 - - + +
198J MET* 3.9 22.7 - - + -
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Residues in contact with VAL 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61J PRO* 4.9 0.3 - - - +
64J ARG* 2.9 32.6 + - + +
65J ALA* 3.5 33.7 - - - +
68J MET* 4.2 8.7 - - + -
111J ALA* 3.7 25.4 - - + +
114J ALA* 3.5 24.0 - - + +
118J LEU* 3.8 7.3 - - - +
160J PRO 3.0 16.1 + - - +
161J MET* 3.6 20.6 - - - +
163J ILE* 1.3 73.5 - - - +
165J CYS* 1.3 59.5 + - - +
166J GLY 3.1 4.5 - - - -
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Residues in contact with CYS 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64J ARG* 3.5 8.0 + - - +
118J LEU* 3.8 25.1 - - - +
136J PHE 5.5 0.2 - - - +
138J PRO* 3.3 24.6 - - - +
161J MET* 3.1 41.9 + - - +
162J ALA 3.8 6.1 - - - +
163J ILE 3.2 0.6 - - - -
164J VAL* 1.3 76.2 - - - +
166J GLY* 1.3 57.3 + - - +
167J ASN* 3.4 8.6 + - - +
468J VAL* 4.1 15.5 - - - -
471J TYR* 4.0 4.9 - - + +
472J THR* 3.9 21.8 - - + +
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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