Contacts of the helix formed by residues 144 - 160 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D ASP* 3.1 33.5 + - - +
143D ALA* 1.3 82.2 - - + +
145D ALA* 1.3 60.9 + - - +
146D PRO* 3.4 2.7 - - - -
147D ALA* 3.2 13.2 + - - +
148D GLU* 2.9 36.7 + - - +
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Residues in contact with ALA 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 3.4 26.2 - - + -
139D ILE* 3.6 30.7 - - + +
141D ASP 3.1 9.7 + - - +
142D ILE* 3.4 9.2 + - - +
144D THR* 1.3 77.5 - - - +
146D PRO* 1.3 65.6 - - + +
148D GLU* 3.1 6.4 + - - +
149D ILE* 2.8 32.9 + - - +
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Residues in contact with PRO 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 4.1 2.2 - - + -
9D TYR* 3.5 31.6 - - + +
142D ILE 3.5 11.9 - - - +
143D ALA 4.4 4.9 - - - +
144D THR 3.6 3.1 - - - -
145D ALA* 1.3 93.8 - - + +
147D ALA* 1.3 55.7 + - - +
149D ILE* 3.3 1.2 + - - +
150D ASP* 2.9 35.8 + - - +
176D VAL* 3.8 27.8 - - + -
177D PRO* 5.0 1.6 - - + -
180D LEU* 3.7 27.8 - - + -
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D THR* 3.2 16.2 + - - +
146D PRO* 1.3 78.5 - - - +
148D GLU* 1.3 60.6 + - + +
150D ASP* 3.4 9.7 + - - +
151D ARG* 2.8 28.2 + - - +
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Residues in contact with GLU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ALA* 3.7 10.2 - - + +
139D ILE* 3.5 28.0 - - + +
144D THR* 2.9 25.3 + - - +
145D ALA 3.6 3.6 - - - +
147D ALA* 1.3 76.2 - - + +
149D ILE* 1.3 65.2 + - - +
151D ARG* 2.7 52.6 + - - +
152D CYS* 3.0 29.6 + - - -
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Residues in contact with ILE 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 3.6 36.3 - - + +
9D TYR* 4.0 24.5 - - + -
10D LEU* 3.9 37.9 - - + -
13D ARG* 4.7 0.4 - - + -
139D ILE* 5.1 2.7 - - + -
145D ALA 2.8 18.7 + - - +
146D PRO 3.7 3.4 - - - +
148D GLU* 1.3 71.6 - - - +
150D ASP* 1.3 65.0 - - - +
152D CYS* 3.2 7.1 + - - +
153D ILE* 3.0 35.0 + - + +
165D LEU* 4.1 22.2 - - + -
167D LEU* 4.7 10.3 - - + -
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Residues in contact with ASP 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D TYR* 2.8 24.0 + - - -
13D ARG* 2.9 39.4 + - - +
146D PRO 2.9 19.3 + - - +
147D ALA* 3.5 9.1 - - - +
149D ILE* 1.3 76.4 - - - +
151D ARG* 1.3 62.4 + - - +
153D ILE* 3.4 0.3 + - - -
154D ARG* 3.0 26.9 + - - +
185D ILE* 3.7 23.9 - - + +
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Residues in contact with ARG 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D THR* 3.1 35.1 + - - +
136D THR 3.1 23.8 + - - -
137D ALA* 3.6 7.9 - - - +
147D ALA 2.8 17.5 + - - +
148D GLU* 2.7 43.9 + - - +
150D ASP* 1.3 76.8 - - - +
152D CYS* 1.3 61.0 + - - +
154D ARG* 3.8 5.5 - - - +
155D THR* 2.8 40.6 + - - +
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Residues in contact with CYS 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D LEU* 3.9 12.6 - - + -
135D THR* 5.1 1.3 - - - -
136D THR 4.9 0.2 - - - -
137D ALA* 3.7 27.6 - - - -
148D GLU 3.0 17.4 + - - -
149D ILE* 3.2 9.2 + - - +
151D ARG* 1.3 81.9 - - - +
153D ILE* 1.3 56.5 + - - +
155D THR* 3.4 3.2 + - - -
156D THR* 2.7 38.8 + - - -
163D VAL* 3.7 26.8 - - + +
164D TYR 4.4 1.3 - - - -
165D LEU* 4.1 16.4 - - + -
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Residues in contact with ILE 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 4.4 5.2 - - + -
13D ARG* 3.6 31.2 - - + -
14D LEU* 4.2 18.4 - - + -
17D VAL* 4.1 14.8 - - + -
67D MET* 4.0 5.8 - - + +
96D LEU* 3.9 20.4 - - + -
149D ILE* 3.0 31.7 + - + +
150D ASP 3.9 0.2 - - - +
152D CYS* 1.3 73.0 - - - +
154D ARG* 1.3 68.4 + - - +
156D THR* 3.4 7.2 + - - -
157D TYR* 3.2 20.8 + - - +
185D ILE* 3.7 20.6 - - + -
187D MET* 4.0 17.7 - - + -
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Residues in contact with ARG 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ASP 3.0 18.7 + - - +
151D ARG* 3.8 6.1 - - - +
153D ILE* 1.3 77.7 - - - +
155D THR* 1.3 59.7 + - - +
157D TYR* 3.2 2.4 + - - +
158D VAL* 3.0 47.7 + - + +
185D ILE* 3.8 5.6 - - + +
186D ASP* 2.7 65.7 + - - +
187D MET* 3.8 12.0 - - - -
188D SER 2.7 34.7 + - - +
189D LEU* 4.4 5.3 - - - +
190D LYS* 4.4 14.6 - - - +
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Residues in contact with THR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D GLU* 3.7 28.7 - - + -
135D THR* 3.8 21.1 - - + +
151D ARG* 2.8 32.0 + - - +
152D CYS 3.9 3.1 - - - -
154D ARG* 1.3 75.2 - - - +
156D THR* 1.3 63.3 + - - +
158D VAL* 4.1 7.6 - - - -
159D THR* 2.7 39.6 + - + +
163D VAL* 3.9 5.4 - - + -
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Residues in contact with THR 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D MET* 3.8 16.2 - - + -
94D GLY* 3.2 37.8 - - - +
95D VAL 3.5 14.1 - - - +
96D LEU* 3.7 10.6 - - - +
152D CYS 2.7 23.2 + - - -
153D ILE 3.6 5.8 - - - -
154D ARG 3.3 0.2 - - - -
155D THR* 1.3 74.7 - - - +
157D TYR* 1.3 58.1 + - - +
160D GLN* 3.0 28.4 + - - -
161D ARG 3.6 12.2 + - - +
163D VAL* 3.2 18.5 - - - +
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Residues in contact with TYR 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D GLY* 3.8 30.4 - - - -
67D MET* 3.9 14.6 - - + -
153D ILE 3.2 3.5 + - - +
154D ARG 3.2 2.8 + - - +
155D THR 3.2 0.6 - - - -
156D THR* 1.3 80.0 - - - +
158D VAL* 1.3 66.5 + - + +
159D THR 3.6 0.3 + - - -
160D GLN* 3.0 35.1 + - - +
187D MET* 3.2 61.0 - - + -
189D LEU* 6.2 1.8 - - + -
226D ASP* 4.5 16.2 + - + +
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Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ARG* 3.0 51.2 + - + +
155D THR* 4.1 5.6 - - - +
157D TYR* 1.3 80.1 - - + +
159D THR* 1.3 74.1 + - + +
160D GLN* 5.1 0.5 - - - +
187D MET* 3.5 32.1 - - - +
188D SER 4.2 0.7 - - - +
189D LEU* 3.9 33.7 - - + +
225D HIS* 4.7 7.6 + - - -
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Residues in contact with THR 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D GLU* 3.6 41.5 - - + +
155D THR* 2.7 28.2 + - + +
158D VAL* 1.3 88.2 - - + +
160D GLN* 1.3 70.0 + - - +
161D ARG* 3.3 18.3 + - - +
225D HIS* 3.2 16.8 - - - -
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Residues in contact with GLN 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ALA 5.0 0.3 - - - +
66D GLY 2.9 27.5 + - - +
92D HIS* 2.7 38.5 - - - +
93D VAL* 4.8 0.9 - - - +
94D GLY* 2.9 29.5 + - - +
156D THR 3.0 11.6 + - - -
157D TYR* 3.0 38.7 + - - +
158D VAL 3.4 0.9 - - - +
159D THR* 1.3 80.5 - - - +
161D ARG* 1.3 56.6 + - - +
224D ARG* 3.2 35.1 + - - +
225D HIS* 3.9 14.4 - - + +
226D ASP* 6.5 0.4 - - + -
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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