Contacts of the helix formed by residues 144 - 160 (chain B) in PDB entry 2W93
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 THR 144 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ASP* 3.2 28.3 + - - +
143B ALA* 1.3 80.7 - - + +
145B ALA* 1.3 66.7 + - - +
146B PRO* 3.4 2.9 - - - -
147B ALA* 3.2 11.9 + - + +
148B GLU* 3.0 30.9 + - - +
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Residues in contact with ALA 145 (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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6B LEU* 3.6 32.3 - - + -
139B ILE* 3.8 23.7 - - + +
141B ASP 3.0 15.3 + - - +
142B ILE* 3.3 9.4 + - - +
144B THR* 1.3 77.4 - - - +
146B PRO* 1.4 70.8 - - + +
148B GLU* 3.1 2.4 + - - +
149B ILE* 2.9 25.8 + - - +
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Residues in contact with PRO 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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6B LEU* 4.2 4.5 - - + -
9B TYR* 3.5 32.9 + - + +
142B ILE 3.4 14.1 - - - +
143B ALA 4.4 4.9 - - - +
144B THR 3.6 3.1 - - - -
145B ALA* 1.4 91.0 - - + +
147B ALA* 1.3 56.2 + - - +
149B ILE* 3.4 1.4 + - - +
150B ASP* 3.0 34.7 + - - +
176B VAL* 4.0 22.4 - - + -
180B LEU* 3.8 25.8 - - + -
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Residues in contact with ALA 147 (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 THR* 3.2 14.0 + - - +
146B PRO* 1.3 79.8 - - - +
148B GLU* 1.3 61.6 + - + +
150B ASP* 3.3 10.1 + - - +
151B ARG* 2.8 29.0 + - - +
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Residues in contact with GLU 148 (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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137B ALA* 3.6 11.3 - - + +
138B MET 6.1 0.2 - - - -
139B ILE* 3.5 27.9 - - + +
144B THR* 3.0 24.8 + - - +
145B ALA 3.1 3.1 + - - +
147B ALA* 1.3 76.4 - - + +
149B ILE* 1.3 64.8 + - - +
151B ARG* 2.8 48.6 + - - +
152B CYS* 2.9 29.4 + - - -
165B LEU* 5.0 0.2 - - - -
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Residues in contact with ILE 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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6B LEU* 3.6 42.0 - - + +
9B TYR* 4.0 23.6 - - + -
10B LEU* 3.8 24.2 - - + -
13B ARG* 4.7 0.7 - - + -
139B ILE* 4.9 1.5 - - + +
145B ALA* 2.9 14.4 + - + +
146B PRO 3.7 5.6 - - - +
148B GLU* 1.3 74.2 - - - +
150B ASP* 1.3 64.6 + - - +
152B CYS* 3.2 3.3 + - - +
153B ILE* 2.9 44.5 + - + +
165B LEU* 4.0 24.7 - - + -
167B LEU* 4.7 12.1 - - + -
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Residues in contact with ASP 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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9B TYR* 2.8 23.5 + - - -
13B ARG* 2.8 41.8 + - - +
146B PRO 3.0 13.3 + - - +
147B ALA* 3.4 11.9 - - - +
149B ILE* 1.3 74.8 - - - +
151B ARG* 1.3 58.6 + - - +
153B ILE* 3.3 1.7 + - - +
154B ARG* 2.8 31.9 + - - +
185B ILE* 4.1 19.8 - - + +
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Residues in contact with ARG 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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135B THR* 3.0 35.7 + - - +
136B THR 3.0 23.2 + - - -
137B ALA* 3.7 6.8 - - - +
147B ALA 2.8 17.1 + - - +
148B GLU* 2.8 43.4 + - - +
150B ASP* 1.3 75.7 - - - +
152B CYS* 1.3 62.3 + - - +
154B ARG* 3.4 6.0 + - - +
155B THR* 2.9 41.4 + - - +
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Residues in contact with CYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 3.9 12.6 - - + -
135B THR* 5.1 0.9 - - - -
136B THR 4.8 0.2 - - - -
137B ALA* 3.7 28.9 - - - -
148B GLU 2.9 20.5 + - - +
149B ILE 3.6 4.0 - - - +
151B ARG* 1.3 86.1 - - - +
153B ILE* 1.3 53.3 + - - +
155B THR* 3.5 1.9 + - - -
156B THR* 2.7 37.9 + - - -
163B VAL* 3.7 29.1 - - + +
164B TYR 4.4 1.1 - - - -
165B LEU* 3.8 18.2 - - + -
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Residues in contact with ILE 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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10B LEU* 4.5 3.8 - - + -
13B ARG* 3.6 31.2 - - + -
14B LEU* 4.3 15.7 - - + -
17B VAL* 3.8 28.7 - - + -
67B MET* 4.0 9.5 - - + +
96B LEU* 4.0 19.5 - - + -
149B ILE* 2.9 32.4 + - + +
150B ASP 3.9 3.1 - - - +
152B CYS* 1.3 72.5 - - - +
154B ARG* 1.3 67.9 + - - +
156B THR* 3.3 6.7 + - - -
157B TYR* 3.1 21.8 + - - +
185B ILE* 3.8 18.6 - - + -
187B MET* 4.1 1.8 - - + -
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Residues in contact with ARG 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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150B ASP 2.8 18.1 + - - +
151B ARG* 3.7 6.3 - - - +
153B ILE* 1.3 77.2 - - - +
155B THR* 1.3 59.3 + - - +
157B TYR* 3.2 1.7 + - - -
158B VAL* 2.8 52.9 + - + +
185B ILE* 3.7 9.8 - - + +
186B ASP* 2.3 46.5 + - - +
187B MET* 3.4 18.3 - - - +
188B SER 2.9 29.9 + - - -
189B LEU* 4.5 5.5 - - - +
190B LYS* 4.7 5.1 - - - +
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Residues in contact with THR 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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134B GLU* 3.6 29.8 - - + -
135B THR* 3.8 24.2 - - + +
151B ARG* 2.9 27.3 + - - +
152B CYS 3.9 3.1 - - - -
153B ILE 3.3 0.2 - - - -
154B ARG* 1.3 78.3 - - - +
156B THR* 1.3 59.3 + - - +
158B VAL* 4.3 6.5 - - - -
159B THR* 2.6 41.2 + - + +
163B VAL* 4.0 3.8 - - + -
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Residues in contact with THR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B MET* 3.9 16.8 - - + -
94B GLY* 3.2 37.2 - - - +
95B VAL 3.5 13.7 - - - +
96B LEU* 3.7 10.2 - - - +
152B CYS 2.7 23.6 + - - -
153B ILE 3.6 4.7 - - - -
155B THR* 1.3 74.3 - - - +
157B TYR* 1.3 59.6 + - - +
160B GLN* 3.0 29.5 + - - -
161B ARG 3.6 10.5 + - - +
163B VAL* 3.2 17.9 - - - +
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Residues in contact with TYR 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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17B VAL* 6.0 2.2 - - + -
66B GLY* 3.8 28.3 - - - -
67B MET* 3.9 18.6 - - + -
153B ILE 3.1 13.5 + - - +
154B ARG 3.9 1.8 - - - +
156B THR* 1.3 82.5 - - - +
158B VAL* 1.3 69.8 + - + +
159B THR 3.6 0.2 + - - -
160B GLN* 3.0 34.5 + - - +
187B MET* 3.9 43.1 - - + -
226B ASP* 6.1 1.0 - - - +
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Residues in contact with VAL 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 ARG* 2.8 57.1 + - + +
155B THR* 4.2 2.5 - - - +
157B TYR* 1.3 80.8 - - + +
159B THR* 1.3 75.6 + - + +
160B GLN* 4.9 0.7 - - - +
187B MET* 3.4 35.9 - - - +
189B LEU* 4.3 23.4 - - + +
225B HIS* 4.6 8.0 + - - -
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Residues in contact with THR 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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134B GLU* 3.5 33.4 - - + +
155B THR* 2.6 38.3 + - + +
158B VAL* 1.3 87.4 - - + +
160B GLN* 1.3 66.6 + - - +
161B ARG* 3.4 18.5 + - - +
225B HIS* 3.0 22.2 - - - -
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Residues in contact with GLN 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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62B ALA 5.0 1.2 - - - +
66B GLY 2.8 28.1 + - - +
92B HIS* 2.8 37.7 - - - +
93B VAL* 4.8 0.9 - - - +
94B GLY* 3.0 29.1 + - - +
156B THR 3.0 11.4 + - - -
157B TYR* 3.0 35.3 + - - +
158B VAL 4.9 0.7 - - - +
159B THR* 1.3 82.3 - - - +
161B ARG* 1.3 57.1 + - - +
224B ARG* 3.2 33.9 + - - +
225B HIS* 3.8 13.7 - - + +
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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