Contacts of the helix formed by residues 152 - 165 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ILE* 3.8 12.8 - - + -
86B ILE* 3.5 29.2 - - + -
100B GLU* 2.6 19.0 + - - +
101B LEU* 4.0 28.9 - - + -
151B PRO* 1.3 76.8 - - - +
153B MET* 1.3 65.4 + - - +
154B VAL 3.5 0.4 - - - -
155B PRO* 3.6 5.2 - - - +
156B LEU* 3.1 45.8 + - + +
180B SER* 4.0 16.6 - - - +
184B ILE* 4.1 13.3 - - + +
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Residues in contact with MET 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B GLU* 3.0 36.1 + - + +
103B ARG* 3.3 49.1 - - + +
104B GLY* 3.9 11.4 - - - +
150B PHE* 3.7 33.0 - - + -
152B VAL* 1.3 76.6 - - - +
154B VAL* 1.3 64.3 + - + +
156B LEU* 2.8 22.0 + - - +
157B TRP* 2.8 57.6 + - + +
280B CYS* 6.2 0.4 - - - -
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B THR* 3.9 7.9 - - + -
147B PRO* 3.6 30.3 - - + -
150B PHE* 3.3 29.7 + - + +
153B MET* 1.3 85.9 - - + +
155B PRO* 1.3 72.5 - - + +
157B TRP* 3.2 38.8 - - + +
158B MET* 3.7 8.4 + - + +
223B VAL* 3.7 27.4 - - + -
280B CYS* 5.9 1.3 - - - -
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Residues in contact with PRO 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B THR* 3.7 27.4 - - + +
150B PHE 3.2 16.4 - - - +
151B PRO 3.3 18.8 - - - +
152B VAL 3.6 9.9 - - - +
154B VAL* 1.3 91.4 - - + +
156B LEU* 1.3 56.7 + - - +
157B TRP 3.1 0.2 - - - -
158B MET* 2.9 17.9 + - + +
159B PHE* 3.2 36.1 + - + -
171B LEU* 4.0 13.7 - - + -
181B THR* 3.8 13.5 - - + -
184B ILE* 5.0 1.3 - - + -
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PHE* 3.7 19.3 - - + -
75B LEU* 4.5 10.3 - - + -
101B LEU* 4.9 2.9 - - + +
104B GLY* 3.6 37.0 - - - +
105B ILE 4.3 1.1 - - - +
107B ASN* 3.2 19.4 - - - +
108B VAL* 3.9 4.9 - - + -
152B VAL* 3.1 35.1 + - + +
153B MET 2.8 12.9 + - - +
155B PRO* 1.3 69.5 - - - +
157B TRP* 1.3 63.1 + - - +
158B MET 3.2 0.2 - - - -
159B PHE* 3.6 19.5 - - + -
160B PRO* 3.2 33.4 - - + +
161B MET 5.2 0.2 + - - -
184B ILE* 4.2 8.7 - - + -
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Residues in contact with TRP 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ARG* 5.4 1.5 - - - +
107B ASN* 3.4 16.4 + - - -
153B MET* 2.8 58.5 + - + +
154B VAL* 3.2 34.1 - - + +
155B PRO 3.1 0.2 - - - -
156B LEU* 1.3 78.0 - - - +
158B MET* 1.3 61.9 + - + +
160B PRO* 4.7 0.2 - - - -
161B MET* 4.5 8.9 - - - +
223B VAL* 4.2 22.0 - - + -
246B LEU* 4.3 1.6 - - + -
280B CYS* 4.8 8.1 - - - -
442B VAL* 5.6 0.9 - - + -
449B PHE* 3.6 46.4 - + - -
462B ALA* 3.9 18.8 - - + -
463B TYR* 3.3 59.6 + + + +
471B TYR* 4.5 3.1 + - - -
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Residues in contact with MET 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B GLY* 3.7 26.5 - - - -
145B ILE 3.7 13.0 - - - +
146B THR* 4.0 18.2 - - + -
154B VAL* 3.7 10.5 - - + +
155B PRO* 2.9 7.2 + - + +
156B LEU 3.2 0.2 - - - -
157B TRP* 1.3 81.4 - - + +
159B PHE* 1.3 61.6 + - - +
160B PRO 3.5 1.6 - - - -
161B MET 3.5 2.6 + - - -
162B ALA* 3.0 22.5 + - - +
169B PHE* 3.6 12.6 - - + -
171B LEU* 5.0 0.7 - - - -
221B SER* 3.6 28.3 - - - +
223B VAL* 3.7 30.5 - - + -
244B GLN* 5.5 0.7 - - - +
471B TYR* 3.1 28.5 - - - +
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Residues in contact with PHE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B MET* 5.7 0.2 - - + -
71B PHE* 3.9 19.3 - + - -
155B PRO* 3.2 45.9 + - + -
156B LEU* 3.6 18.4 - - + -
158B MET* 1.3 73.9 - - - +
160B PRO* 1.3 77.1 - - + +
163B ILE* 2.8 38.1 + - + +
169B PHE* 3.6 36.8 - + + -
171B LEU* 4.3 6.3 - - + -
181B THR 5.9 0.2 - - - -
184B ILE* 4.2 16.6 - - + -
185B ALA* 5.0 4.5 - - + -
188B LEU* 3.8 19.3 - - + -
198B MET* 3.3 33.4 - - + -
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Residues in contact with PRO 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B MET* 3.5 29.8 - - + +
107B ASN 4.7 1.3 - - - +
108B VAL* 4.0 13.7 - - + +
111B ALA* 4.1 12.1 - - + +
156B LEU* 3.2 53.2 - - + +
158B MET 3.6 1.6 - - - -
159B PHE* 1.3 104.2 - - + +
161B MET* 1.3 61.1 + - - +
163B ILE* 4.0 1.4 - - + +
164B VAL* 3.1 22.2 + - - +
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Residues in contact with MET 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASN 5.4 1.5 + - - +
110B TYR* 3.4 38.8 - - + -
111B ALA* 4.3 12.2 - - + +
114B ALA* 5.9 0.2 - - - -
117B LEU* 3.7 11.9 - - + -
156B LEU 5.2 0.2 + - - -
157B TRP 4.5 6.9 + - - +
158B MET 3.5 7.6 + - - +
159B PHE 3.4 0.2 - - - -
160B PRO* 1.3 79.0 - - - +
162B ALA* 1.3 63.4 + - - +
164B VAL* 3.4 13.7 - - - +
165B CYS* 3.1 32.9 + - - -
463B TYR* 5.7 1.6 - - + -
464B GLY 4.1 9.4 - - - +
467B ALA* 3.8 28.5 - - + +
468B VAL* 3.9 15.3 - - + -
471B TYR* 4.0 9.4 - - + -
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Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B VAL* 4.7 2.2 - - + -
158B MET 3.0 18.4 + - - +
159B PHE 4.0 0.4 - - - +
161B MET* 1.3 75.6 - - - +
163B ILE* 1.3 62.7 + - - +
165B CYS 3.3 4.9 + - - -
167B ASN* 3.0 34.0 + - + +
169B PHE* 3.7 26.0 - - + -
471B TYR* 3.5 33.4 - - + -
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Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TRP* 2.9 46.5 + - + -
64B ARG* 3.8 1.1 - - - +
67B VAL* 6.0 0.7 - - + -
68B MET* 5.1 10.5 - - - -
159B PHE* 2.8 41.7 + - + +
160B PRO* 4.0 2.9 - - + +
162B ALA* 1.3 77.3 - - - +
164B VAL* 1.3 57.6 + - - +
166B GLY 3.0 10.2 + - - -
167B ASN 3.5 9.6 - - - +
169B PHE* 4.4 11.9 - - + -
188B LEU* 4.1 8.7 - - + -
193B LEU* 3.7 15.7 - - + -
197B VAL* 3.7 13.0 - - + -
198B MET* 3.9 28.5 - - + -
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B PRO* 5.0 0.5 - - - +
64B ARG* 2.8 35.4 + - + +
65B ALA* 3.7 28.7 - - - +
68B MET* 4.3 10.1 - - + -
111B ALA* 3.6 17.5 - - + +
114B ALA* 3.5 31.4 - - + +
118B LEU* 3.9 6.1 - - - +
160B PRO 3.1 16.3 + - - +
161B MET* 3.4 26.2 - - - +
163B ILE* 1.3 78.2 - - - +
165B CYS* 1.3 58.1 + - - +
166B GLY 3.1 0.7 - - - -
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Residues in contact with CYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ARG* 3.5 10.0 + - - +
114B ALA* 6.2 0.2 - - - -
118B LEU* 4.1 10.8 - - - +
136B PHE 5.3 0.5 - - - +
137B GLN 4.8 0.2 - - - -
138B PRO* 3.4 23.0 - - - +
161B MET* 3.1 42.7 + - - +
162B ALA 3.6 7.4 - - - +
163B ILE 3.2 0.4 - - - -
164B VAL* 1.3 76.4 - - - +
166B GLY* 1.3 55.4 + - - +
167B ASN* 3.6 8.1 - - - +
468B VAL* 4.0 24.2 - - - -
471B TYR* 3.9 4.9 - - + +
472B THR* 3.8 28.1 - - + +
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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