Contacts of the helix formed by residues 145 - 160 (chain B) in PDB entry 4PHZ
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 SER 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 3.3 4.4 - - - +
143B SER* 3.0 13.1 + - - -
144B GLY* 1.3 78.3 - - - +
146B TYR* 1.3 54.3 + - - +
147B VAL* 3.2 10.0 + - - +
148B ILE* 3.4 21.7 + - - +
149B THR* 2.7 33.3 + - - -
252J ILE* 3.2 40.1 + - - +
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Residues in contact with TYR 146 (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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140B LEU* 4.0 3.4 - - - +
144B GLY 4.3 0.6 + - - -
145B SER* 1.3 70.8 - - - +
147B VAL* 1.3 73.9 + - + +
149B THR* 4.0 6.3 - - - -
150B ALA* 2.7 36.7 + - - +
233B TYR* 3.6 4.9 - + + +
234B PHE* 4.2 10.7 - + - -
237B TRP* 3.6 63.7 - + + -
238B PHE* 3.2 39.7 - + - -
241B ARG* 6.3 0.9 - - - -
249J ILE* 5.2 5.5 - - - +
251J THR 4.5 5.8 + - - -
252J ILE* 2.9 48.6 + - - +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B SER* 3.2 9.5 + - - +
146B TYR* 1.3 104.9 - - + +
148B ILE* 1.3 70.8 + - + +
150B ALA* 3.3 7.0 - - - +
151B VAL* 3.0 25.2 + - + +
234B PHE* 3.8 15.3 - - + -
252J ILE* 4.5 18.8 - - + +
184K LEU* 5.8 6.3 - - + -
188K ILE* 3.8 36.3 - - + -
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ILE* 4.1 4.0 - - + -
143B SER* 3.7 28.7 - - - +
145B SER* 3.4 22.0 + - - +
146B TYR 3.4 0.2 - - - -
147B VAL* 1.3 85.4 - - + +
149B THR* 1.3 56.5 + - - +
151B VAL* 3.1 4.8 + - - +
152B VAL* 2.7 55.8 + - + -
153B GLY 3.4 1.4 + - - -
252J ILE* 4.8 6.7 - - + -
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Residues in contact with THR 149 (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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81B GLN* 3.7 6.1 - - - +
136B LEU* 3.5 35.7 - - + +
139B ILE* 3.5 10.1 - - + +
140B LEU* 3.2 22.6 + - + +
145B SER 2.7 23.5 + - - -
146B TYR* 3.6 1.8 - - - -
147B VAL 3.2 0.6 - - - -
148B ILE* 1.3 74.0 - - - +
150B ALA* 1.3 64.2 + - - +
153B GLY* 2.6 25.7 + - - -
154B SER 2.8 9.9 + - - -
233B TYR* 3.4 28.0 - - + +
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B TYR 2.7 22.2 + - - +
147B VAL 3.3 5.8 - - - +
149B THR* 1.3 71.0 - - - +
151B VAL* 1.3 57.6 + - + +
154B SER* 2.3 26.7 + - - -
230B MET* 3.4 13.9 - - + +
233B TYR* 3.4 30.0 - - + -
234B PHE* 3.5 31.6 - - + -
192K MET* 6.3 0.2 - - - -
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B VAL* 3.0 19.3 + - + +
148B ILE* 3.1 6.7 + - - +
149B THR 3.0 1.2 + - - -
150B ALA* 1.3 78.4 - - + +
152B VAL* 1.3 73.9 + - + +
155B LEU* 3.2 31.1 + - + +
230B MET* 3.7 24.6 - - + +
234B PHE* 5.8 1.6 - - + -
188K ILE* 5.2 11.2 - - + -
191K PHE* 4.1 38.4 - - + -
192K MET* 5.5 6.3 - - - -
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TRP* 2.8 32.3 + - + -
139B ILE* 3.8 33.4 - - + -
148B ILE* 2.7 25.5 + - + +
151B VAL* 1.3 84.5 - - + +
153B GLY* 1.3 59.0 + - - +
155B LEU* 4.0 11.3 - - + +
156B GLY 3.3 9.0 + - - -
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Residues in contact with GLY 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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135B TRP* 3.0 30.8 + - - -
136B LEU* 3.2 18.3 - - - +
139B ILE* 3.9 13.0 - - - -
148B ILE 3.4 1.4 + - - -
149B THR* 2.6 22.0 + - - +
152B VAL* 1.3 75.9 - - - +
154B SER* 1.3 59.5 + - - -
157B TRP 3.1 7.6 + - - -
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Residues in contact with SER 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 4.4 5.2 - - - -
136B LEU* 3.5 10.5 - - - +
149B THR 2.8 10.0 + - - -
150B ALA* 2.3 30.2 + - - -
151B VAL 3.7 0.2 + - - -
153B GLY* 1.3 73.4 - - - +
155B LEU* 1.3 56.5 + - - +
157B TRP* 3.2 7.5 - - - +
158B GLY* 3.0 25.1 + - - -
226B GLY* 4.0 7.2 - - - +
229B SER* 3.9 23.6 - - - -
230B MET* 3.2 15.1 + - - +
233B TYR* 4.2 11.4 - - - -
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Residues in contact with LEU 155 (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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151B VAL* 3.2 20.4 + - + +
152B VAL* 4.2 10.8 - - + +
154B SER* 1.3 75.5 + - - +
156B GLY* 1.3 58.5 + - - +
158B GLY* 3.4 1.4 + - - -
159B LEU* 3.0 48.3 + - + +
223B PHE* 4.6 13.0 - - + +
226B GLY* 4.0 21.4 + - - -
227B PHE* 4.2 24.2 - - + +
230B MET* 3.8 14.4 - - + -
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Residues in contact with GLY 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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135B TRP* 3.5 26.7 - - - -
152B VAL 3.3 5.1 + - - -
153B GLY 3.3 4.2 + - - -
155B LEU* 1.3 74.1 - - - +
157B TRP* 1.3 58.6 + - - +
159B LEU* 3.2 7.9 + - - -
160B LEU* 2.8 47.7 + - - +
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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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42B TYR* 4.5 2.2 - - - -
70B PRO* 2.9 30.2 + - + +
73B GLY* 3.3 9.9 - - - -
74B VAL* 3.1 37.6 - - + +
77B CYS* 3.9 25.4 - - - -
98B ALA* 5.2 0.7 - - + -
129B LEU* 4.3 24.2 - - + -
132B PRO* 3.3 60.2 - - + +
133B ALA* 3.6 22.9 - - + -
135B TRP* 3.9 2.6 - - - -
136B LEU* 4.3 11.2 - - + -
153B GLY 3.1 12.9 + - - +
154B SER* 3.2 15.3 - - - +
156B GLY* 1.3 75.2 - - - +
158B GLY* 1.3 68.3 + - - +
161B PHE* 3.7 10.8 + + - +
229B SER* 3.8 16.4 - - - -
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Residues in contact with GLY 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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70B PRO* 4.4 3.8 - - - -
154B SER 3.0 15.1 + - - -
155B LEU 3.4 3.1 + - - -
157B TRP* 1.3 81.3 - - - +
159B LEU* 1.3 63.3 + - - +
161B PHE* 2.9 21.7 + - - +
162B TYR 4.7 0.2 + - - -
222B ALA* 3.9 6.0 - - - +
225B SER* 3.4 25.5 + - - -
226B GLY 4.0 7.6 - - - -
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Residues in contact with LEU 159 (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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155B LEU* 3.0 34.7 + - + +
156B GLY* 3.8 7.0 - - - +
158B GLY* 1.3 72.6 - - - +
160B LEU* 1.3 62.4 + - + +
161B PHE 3.4 0.5 + - - -
162B TYR 4.4 0.2 + - - -
163B PRO* 3.3 19.4 - - - +
222B ALA* 4.0 17.6 + - + +
223B PHE* 3.5 63.3 - - + +
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Residues in contact with LEU 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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240A ILE* 5.1 13.9 - - + -
243A THR* 4.3 23.6 - - + -
131B VAL* 4.5 16.6 - - + -
132B PRO* 4.3 14.8 - - + -
135B TRP* 3.9 35.4 - - + -
156B GLY* 2.8 31.7 + - - +
157B TRP 4.3 0.7 - - - -
159B LEU* 1.3 75.1 - - + +
161B PHE* 1.3 63.6 + - - +
162B TYR 3.5 0.7 - - - -
163B PRO* 3.7 9.3 - - + +
164B ASN* 3.0 26.9 + - - +
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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