Contacts of the helix formed by residues 149 - 164 (chain B) in PDB entry 1D8D
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 HIS 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A TYR* 3.4 40.3 - + + +
167A GLN* 4.8 2.8 + - - -
140B PHE 3.0 6.6 + - - +
147B TYR 3.7 0.2 + - - -
148B PRO* 1.3 75.6 - - - +
150B LEU* 1.3 61.4 + - - +
151B ALA* 3.1 29.9 + - + -
152B PRO* 3.3 11.0 - - + +
153B THR* 2.7 28.8 + - - -
180B TYR* 3.2 6.4 + - - -
193B MET* 3.5 36.8 - - + +
194B HIS* 3.3 31.3 - + - -
198B GLU* 4.5 6.1 + - - -
202B ARG* 4.7 2.0 - - - -
11P MET* 3.8 18.9 + - + +
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Residues in contact with LEU 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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149B HIS* 1.3 72.3 + - - +
151B ALA* 1.3 56.8 + - - +
153B THR* 3.6 10.8 - - + -
154B TYR 3.0 23.2 + - - -
180B TYR* 3.9 9.8 + - + -
181B LEU* 3.6 28.3 - - + -
184B LEU* 3.7 16.8 - - + -
191B PHE* 4.4 5.8 - - + -
192B LEU 3.5 21.8 - - - +
193B MET* 2.7 23.0 + - + +
203B SER* 3.6 28.7 - - - +
206B CYS* 3.4 20.3 - - + +
207B ALA* 4.3 17.0 - - + +
210B VAL* 5.1 0.4 - - + -
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Residues in contact with ALA 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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102B TRP* 3.4 30.8 + - + +
149B HIS* 3.1 18.5 + - + +
150B LEU* 1.3 75.8 - - - +
152B PRO* 1.4 72.2 - - + +
154B TYR* 3.2 5.4 + - - +
155B ALA 3.1 17.8 + - - -
193B MET* 3.7 10.5 - - + +
202B ARG* 5.0 1.1 - - - +
206B CYS* 4.0 10.5 - - - -
1000B FII 5.0 2.5 - - + -
11P MET* 3.8 13.7 - - + -
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Residues in contact with PRO 152 (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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131A TYR* 4.1 0.9 - - - +
98B ALA 5.0 1.1 - - - +
101B PRO* 3.5 16.7 - - + +
102B TRP* 4.0 11.4 - - + +
140B PHE* 3.7 8.4 - - - +
141B GLY 3.6 26.9 - - - +
142B GLY* 4.0 5.6 - - - +
149B HIS* 3.3 33.2 - - + +
151B ALA* 1.4 96.1 - - + +
153B THR* 1.3 54.5 + - - -
155B ALA* 3.8 2.5 - - + -
156B ALA* 2.8 31.2 + - - +
11P MET* 3.7 15.0 - - + -
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Residues in contact with THR 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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139B GLY* 3.6 5.3 - - - -
140B PHE* 2.9 38.2 + - + -
149B HIS 2.7 25.3 + - - -
150B LEU* 3.6 15.4 - - + -
151B ALA 3.1 0.2 - - - -
152B PRO* 1.3 73.6 - - - +
154B TYR* 1.3 66.0 + - - +
156B ALA* 3.4 0.7 + - - +
157B VAL* 3.0 31.7 + - + +
177B LEU* 3.8 28.3 - - + -
180B TYR* 4.2 2.7 - - + -
210B VAL* 4.2 13.5 - - + -
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Residues in contact with TYR 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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102B TRP* 3.5 36.3 - + - -
105B TYR* 4.3 9.7 + + - -
150B LEU 3.0 17.2 + - - +
151B ALA 3.5 2.7 - - - +
153B THR* 1.3 77.1 - - - +
155B ALA* 1.3 61.4 + - - +
157B VAL* 3.9 2.3 - - - +
158B ASN* 3.0 56.1 + - - +
205B TYR* 2.9 44.9 + + - -
206B CYS* 3.8 19.3 - - + -
209B SER* 3.3 31.4 - - - -
210B VAL* 3.6 11.4 - - + +
253B PHE* 5.4 0.7 - - - -
302B PHE* 6.1 0.3 - - - -
303B TRP* 5.7 2.6 - - - -
365B TYR* 4.9 3.2 + - - -
401B TYR 3.3 6.5 + - - -
402B ASN* 4.6 2.8 - - - +
1000B FII 4.6 3.8 - - + +
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PRO 3.6 21.5 - - - +
102B TRP* 3.6 37.7 - - + +
105B TYR* 3.6 13.6 - - + +
151B ALA 3.1 6.9 + - - +
152B PRO* 3.8 3.4 - - + +
154B TYR* 1.3 85.9 - - - +
156B ALA* 1.3 56.8 + - - +
158B ASN* 3.3 1.5 + - - +
159B ALA* 2.9 31.0 + - - +
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Residues in contact with ALA 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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101B PRO* 4.1 13.4 - - + +
130B LEU* 3.8 14.3 - - + +
140B PHE* 3.5 38.6 - - + -
152B PRO 2.8 22.2 + - - +
155B ALA* 1.3 73.2 - - - +
157B VAL* 1.3 63.2 + - - +
159B ALA* 3.3 2.7 + - - +
160B LEU* 2.9 30.7 + - - +
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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
----------------------------------------------------------
140B PHE* 4.2 14.4 - - + -
153B THR* 3.0 20.3 + - + +
154B TYR 3.9 0.7 - - - +
156B ALA* 1.3 74.5 - - - +
158B ASN* 1.3 63.2 + - - +
160B LEU* 3.2 3.8 + - - +
161B CYS* 3.0 27.7 + - - -
172B ILE* 4.1 28.9 - - + -
177B LEU* 4.9 7.0 - - + -
210B VAL* 3.6 30.7 - - + -
213B LEU* 4.0 23.8 - - + -
214B THR* 4.4 8.1 - - + -
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Residues in contact with ASN 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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105B TYR* 3.6 28.3 - - + -
154B TYR* 3.0 41.4 + - - +
155B ALA 3.7 1.1 - - - +
156B ALA 3.3 0.2 - - - -
157B VAL* 1.3 75.9 - - - +
159B ALA* 1.3 63.2 + - - +
161B CYS* 3.2 6.3 + - - +
162B ILE* 2.9 28.9 + - - +
209B SER* 4.3 4.5 + - - -
213B LEU* 3.6 21.7 - - - +
401B TYR* 2.9 27.5 + - - +
403B ILE* 3.6 14.1 - - + +
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Residues in contact with ALA 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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101B PRO 4.9 0.2 - - - +
104B CYS* 4.4 3.6 - - + -
105B TYR* 4.1 18.1 - - - +
108B LEU* 4.0 22.6 - - + +
130B LEU* 4.1 14.8 - - + -
155B ALA 2.9 17.2 + - - +
156B ALA* 3.6 4.3 - - - +
158B ASN* 1.3 76.8 - - - +
160B LEU* 1.3 61.2 + - - +
162B ILE* 3.2 12.2 + - - +
163B ILE* 3.2 26.5 + - - +
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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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127B CYS* 4.2 22.0 - - - +
130B LEU* 3.7 22.0 - - + -
140B PHE* 4.3 9.9 - - + -
156B ALA 2.9 22.3 + - - +
157B VAL* 3.7 3.8 - - - +
159B ALA* 1.3 76.3 - - - +
161B CYS* 1.3 57.7 + - - +
163B ILE* 3.4 4.9 + - + -
164B GLY* 2.9 22.5 + - - -
168B ALA* 3.1 45.6 - - - +
169B TYR* 4.6 2.6 - - + -
171B VAL* 3.9 18.2 - - + -
172B ILE* 3.6 33.7 - - + -
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Residues in contact with CYS 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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157B VAL* 3.0 33.2 + - - +
158B ASN* 3.6 5.4 - - - +
160B LEU* 1.3 74.7 - - - +
162B ILE* 1.3 65.8 + - - +
163B ILE 3.2 0.4 - - - -
164B GLY* 3.2 11.5 + - - +
169B TYR* 4.3 13.8 + - - -
172B ILE* 5.4 2.0 - - - -
213B LEU* 4.3 13.2 - - - -
403B ILE* 3.8 17.9 - - + -
407B LYS* 3.4 20.6 - - - +
411B ALA* 3.6 28.3 - - + -
415B PHE* 4.8 5.6 - - - -
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Residues in contact with ILE 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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105B TYR* 4.0 9.4 - - + -
108B LEU* 4.2 24.9 - - + +
109B HIS* 3.7 28.9 - - + +
112B GLU* 3.7 35.0 - - + +
118B ILE* 5.1 12.0 - - + +
158B ASN 2.9 20.0 + - - +
159B ALA* 3.2 8.5 + - - +
161B CYS* 1.3 72.5 - - - +
163B ILE* 1.3 65.7 + - + +
403B ILE* 3.7 22.4 - - + -
407B LYS* 2.9 35.4 + - - +
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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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108B LEU* 4.2 12.1 - - + -
118B ILE* 4.7 11.9 - - + -
120B GLN* 6.1 0.2 - - - +
123B ALA* 3.7 35.7 - - + +
126B VAL* 3.6 37.5 - - + -
127B CYS* 4.5 8.1 - - - -
159B ALA 3.2 15.2 + - - +
160B LEU* 3.5 9.6 - - + +
162B ILE* 1.3 80.6 - - + +
164B GLY* 1.3 61.5 + - - +
165B THR* 3.3 31.0 + - + +
168B ALA* 3.7 5.4 - - + -
407B LYS* 4.8 3.8 + - - -
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Residues in contact with GLY 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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160B LEU 2.9 13.8 + - - -
161B CYS 3.2 14.8 + - - -
163B ILE* 1.3 76.1 - - - +
165B THR* 1.3 62.9 + - - +
169B TYR* 3.5 25.6 - - - -
407B LYS* 4.9 2.5 - - - -
410B GLN* 3.1 22.1 - - - +
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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