Contacts of the helix formed by residues 149 - 169 (chain B) in PDB entry 5W0P
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 GLY 149 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PRO* 3.9 7.5 - - - +
146B PHE 5.2 1.1 - - - -
147B ARG 3.0 9.7 + - - -
148B PHE* 1.3 76.6 - - - +
150B GLU* 1.3 65.7 + - - -
151B ASN* 3.1 4.3 - - - -
152B HIS* 3.0 18.3 + - - -
153B ALA* 3.0 12.3 + - - +
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Residues in contact with GLU 150 (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 PRO* 4.0 14.6 - - + +
74B TYR* 3.5 32.1 + - + +
149B GLY* 1.3 72.1 - - - -
151B ASN* 1.3 58.4 + - - +
153B ALA* 3.3 4.5 + - - +
154B ILE* 2.8 49.6 + - + +
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Residues in contact with ASN 151 (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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149B GLY* 3.1 1.3 - - - -
150B GLU* 1.3 81.7 - - - +
152B HIS* 1.3 65.8 + - + +
154B ILE* 3.9 10.0 - - - +
155B MET* 3.0 41.3 + - - +
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Residues in contact with HIS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLU* 4.5 1.2 - - - +
147B ARG* 3.2 30.5 + - + +
148B PHE* 4.0 23.8 - + + -
149B GLY* 3.0 16.9 + - - +
151B ASN* 1.3 85.1 - - + +
153B ALA* 1.3 62.5 + - - +
155B MET* 3.8 14.4 + - - +
156B GLY* 3.4 15.8 + - - -
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PRO* 3.1 41.3 - - + +
74B TYR* 3.6 19.3 - - + -
134B GLU* 4.4 4.3 - - - +
148B PHE* 4.0 10.9 - - + -
149B GLY 3.0 4.8 + - - -
150B GLU 3.7 4.7 - - - +
152B HIS* 1.3 75.4 - - - +
154B ILE* 1.3 64.8 + - - +
156B GLY* 3.1 4.3 + - - -
157B VAL* 3.0 27.1 + - - +
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Residues in contact with ILE 154 (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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74B TYR* 5.1 9.6 - - + -
150B GLU* 2.8 36.9 + - + +
151B ASN* 3.9 8.7 - - - +
153B ALA* 1.3 71.6 - - - +
155B MET* 1.3 55.7 + - + +
157B VAL* 3.2 7.7 + - + +
158B ALA* 2.7 40.6 + - + +
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Residues in contact with MET 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 ASN* 3.0 28.4 + - + +
152B HIS* 3.8 15.0 - - - +
153B ALA 3.3 0.2 - - - -
154B ILE* 1.3 78.3 - - + +
156B GLY* 1.3 57.2 + - - +
158B ALA* 4.1 5.5 - - - +
159B PHE* 3.0 29.6 + - - +
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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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75B ILE* 4.1 5.8 - - - -
130B VAL* 3.7 27.6 - - - +
134B GLU* 4.5 1.8 - - - -
152B HIS 3.4 7.4 + - - -
153B ALA 3.1 8.4 + - - -
155B MET* 1.3 78.2 - - - +
157B VAL* 1.3 53.2 + - - +
159B PHE* 3.7 2.5 + - - +
160B THR* 2.7 32.2 + - - -
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Residues in contact with VAL 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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74B TYR* 3.7 36.3 - - + +
75B ILE* 4.1 11.9 - - + +
78B ASN* 3.7 23.6 - - + +
153B ALA 3.0 14.3 + - - +
154B ILE* 3.2 8.3 + - - +
156B GLY* 1.3 74.3 - - - +
158B ALA* 1.3 64.5 + - - +
160B THR* 3.3 18.9 - - - -
161B TRP* 3.3 17.8 + - + +
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Residues in contact with ALA 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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154B ILE* 2.7 29.7 + - + +
155B MET* 4.1 6.1 - - - +
157B VAL* 1.3 71.5 - - - +
159B PHE* 1.3 65.7 + - - +
161B TRP* 3.1 8.8 + - - +
162B VAL* 2.9 29.3 + - + +
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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
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126B TRP* 4.1 25.4 - + - -
129B VAL* 5.9 1.1 - - + -
130B VAL* 4.2 19.3 - - + -
133B ILE* 6.4 1.6 - - + -
155B MET 3.0 20.8 + - - +
156B GLY* 3.8 4.9 - - - +
157B VAL 3.4 0.2 - - - -
158B ALA* 1.3 75.7 - - - +
160B THR* 1.3 59.7 + - - +
162B VAL* 3.3 11.8 + - + +
163B MET* 3.0 64.0 + - + +
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Residues in contact with THR 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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75B ILE* 3.7 13.3 - - - +
78B ASN* 3.4 15.9 - - - +
123B ILE* 3.1 37.5 - - + +
126B TRP* 3.7 14.2 + - + -
127B SER* 3.6 9.2 - - - +
130B VAL* 3.9 7.1 - - - +
156B GLY 2.7 20.9 + - - -
157B VAL 3.3 10.0 + - - -
158B ALA 3.1 0.4 - - - -
159B PHE* 1.3 79.8 - - - +
161B TRP* 1.3 58.0 + - - +
163B MET* 3.5 2.3 + - - +
164B ALA* 2.9 28.4 + - - +
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Residues in contact with TRP 161 (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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78B ASN* 2.9 28.5 + - - -
81B VAL* 4.7 17.5 - - + -
85B PHE* 4.9 11.0 - + - -
119B LEU* 5.0 0.8 - - + +
123B ILE* 3.7 31.2 - - + +
157B VAL* 3.3 20.4 + - + +
158B ALA* 3.1 10.3 + - - +
160B THR* 1.3 77.1 - - - +
162B VAL* 1.3 60.4 + - + +
164B ALA* 3.6 5.5 - - - +
165B LEU* 3.0 41.8 + - + +
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ALA* 2.9 22.4 + - + +
159B PHE* 3.6 14.6 - - + +
161B TRP* 1.3 77.2 - - + +
163B MET* 1.3 66.5 + - + +
165B LEU* 3.4 8.3 + - + +
166B ALA* 3.0 26.1 + - + +
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Residues in contact with MET 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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122B GLU* 4.1 0.9 - - - +
126B TRP* 3.4 46.2 - - + +
159B PHE* 3.0 55.3 + - + +
160B THR 4.0 0.2 - - - +
162B VAL* 1.3 79.7 - - + +
164B ALA* 1.3 64.7 + - - +
166B ALA* 3.3 12.9 + - + -
167B CYS 3.4 1.4 + - - -
206B TYR* 5.4 0.9 - - - +
210B VAL* 3.9 22.2 - - + -
211B HIS* 3.2 32.2 + - + -
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Residues in contact with ALA 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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119B LEU* 3.8 9.6 - - + -
122B GLU* 3.8 15.7 - - + +
123B ILE* 3.4 38.1 - - + +
126B TRP* 4.4 0.4 - - - -
160B THR 2.9 19.3 + - - +
161B TRP 3.6 5.2 - - - +
162B VAL 3.2 0.2 - - - -
163B MET* 1.3 77.2 - - - +
165B LEU* 1.3 56.4 + - - +
167B CYS* 3.2 5.9 + - - +
168B ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 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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115B PHE* 3.9 23.3 - - + -
119B LEU* 3.7 22.7 - - + -
161B TRP* 3.0 31.3 + - + +
162B VAL* 3.8 7.0 - - - +
164B ALA* 1.3 73.2 - - - +
166B ALA* 1.3 62.1 + - - +
167B CYS 3.2 0.2 - - - -
168B ALA* 3.7 2.9 - - - +
169B ALA* 3.0 38.2 + - + +
170B PRO* 3.5 0.7 - - - +
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Residues in contact with ALA 166 (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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162B VAL* 3.0 14.9 + - + +
163B MET* 3.4 21.5 - - - +
164B ALA 3.2 0.2 - - - -
165B LEU* 1.3 78.3 - - - +
167B CYS* 1.3 55.9 + - - +
170B PRO* 3.2 23.5 - - - +
175B TRP* 5.2 0.2 - - - -
206B TYR* 3.4 32.0 + - - +
211B HIS* 4.3 2.7 - - + +
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Residues in contact with CYS 167 (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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118B THR* 3.5 22.5 - - - +
122B GLU* 3.6 31.6 - - + +
163B MET 3.4 1.6 + - - -
164B ALA 3.2 3.6 + - - +
165B LEU 3.2 0.2 - - - -
166B ALA* 1.3 79.5 - - - +
168B ALA* 1.3 57.6 + - - +
169B ALA 3.6 0.2 - - - -
170B PRO* 3.7 0.6 - - - +
171B PRO* 3.2 23.2 - - - +
189B ILE* 5.2 2.6 - - - +
203B PHE* 3.6 15.2 - - - -
206B TYR* 4.9 1.3 - - - -
207B MET* 3.5 31.6 - - - -
211B HIS* 4.1 11.8 - - + +
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PHE* 3.6 30.5 - - + -
118B THR* 4.2 3.6 - - + -
119B LEU* 4.0 27.6 - - + +
164B ALA 2.9 18.2 + - - +
165B LEU* 4.3 1.6 - - - -
167B CYS* 1.3 76.5 - - - +
169B ALA* 1.3 63.5 + - - +
170B PRO 3.7 0.2 - - - -
171B PRO* 3.5 4.5 - - - +
172B LEU* 4.3 0.5 - - - +
178B TYR* 2.9 29.7 + - - +
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PHE* 4.2 10.5 - - + -
165B LEU* 3.0 28.5 + - + +
168B ALA* 1.3 77.2 - - - +
170B PRO* 1.4 65.4 - - + +
172B LEU* 3.0 19.7 + - - +
173B ALA* 3.0 11.9 + - - +
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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
------------------------------------------------------------
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