Contacts of the helix formed by residues 147 - 157 (chain B) in PDB entry 1W1J
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 147 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ILE* 4.0 19.1 - - + -
104B ARG* 3.7 12.6 - - - +
145B GLY 4.4 0.2 - - - +
146B VAL* 1.3 91.7 - - - +
148B TYR* 1.3 64.9 + - - +
149B HIS* 3.6 5.4 + - - +
150B ASP* 2.8 45.4 + - - +
151B LEU 3.2 6.6 + - - -
172B GLY 3.7 6.5 - - - -
173B GLY* 3.2 27.4 - - - +
174B GLY 3.3 6.3 - - - -
176B VAL* 3.7 4.5 - - - +
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Residues in contact with TYR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B THR* 1.3 73.4 - - - +
149B HIS* 1.3 56.3 - - - +
151B LEU* 3.4 0.9 + - - +
152B HIS* 3.0 24.2 + - - +
166B LEU* 3.5 18.1 - - + +
167B ASP 3.1 25.6 - - - -
168B VAL* 4.0 20.6 - - + -
169B PRO* 3.4 29.4 - - + -
171B LEU 4.5 1.8 - - - -
172B GLY* 3.3 13.2 + - - +
174B GLY* 2.9 36.3 + - - -
175B SER 3.4 19.5 - - - -
176B VAL* 3.8 29.7 + - + -
179B ASN* 3.0 16.0 + - + +
193B HIS* 3.0 25.4 + + - -
406B PRO* 4.8 2.6 - - - +
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Residues in contact with HIS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B THR* 3.2 4.5 - - - +
148B TYR* 1.3 72.9 - - - +
150B ASP* 1.3 66.3 + - - +
151B LEU 3.2 0.2 - - - -
152B HIS* 3.1 7.5 + - - -
153B ASN* 2.9 48.2 + - - -
172B GLY 3.1 9.1 + - - +
406B PRO* 3.9 28.3 + - + +
408B TYR* 2.7 45.2 + + - +
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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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128B ASN* 5.0 5.1 + - - -
130B VAL* 5.2 2.2 - - + +
145B GLY 3.2 13.8 - - - +
146B VAL* 3.8 9.9 - - + -
147B THR* 2.8 49.2 + - - +
149B HIS* 1.3 75.3 - - - +
151B LEU* 1.3 57.2 + - - +
153B ASN* 3.3 8.0 + - - +
154B TYR* 3.0 25.3 + - - +
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Residues in contact with LEU 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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130B VAL* 3.8 29.4 - - + -
133B VAL* 4.6 11.0 - - + -
140B CYS* 3.9 27.1 - - + -
142B VAL* 5.0 3.4 - - + -
146B VAL* 3.9 8.1 - - + -
147B THR 3.2 9.8 + - - +
148B TYR 3.7 7.6 - - - +
149B HIS 3.2 0.4 - - - -
150B ASP* 1.3 76.2 - - - +
152B HIS* 1.3 68.3 + - - +
154B TYR* 3.0 9.8 + - + +
155B LEU* 2.9 27.8 + - + +
166B LEU* 3.3 33.7 - - + -
176B VAL* 4.4 16.6 - - + -
269B LEU* 4.7 2.2 - - + -
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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
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148B TYR 3.0 14.9 + - - +
149B HIS* 3.1 15.9 + - - +
151B LEU* 1.3 74.5 - - - +
153B ASN* 1.3 63.4 + - - +
155B LEU* 2.9 27.5 + - + +
156B GLU* 3.0 42.4 + - + +
161B ARG* 5.7 3.7 - - + +
166B LEU* 3.9 10.9 - - + +
404B GLY 4.2 9.6 - - - -
405B ILE* 4.2 29.4 - - + +
406B PRO* 3.7 29.6 - - + +
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Residues in contact with ASN 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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149B HIS* 2.9 47.5 + - - +
150B ASP* 3.7 6.9 + - - +
152B HIS* 1.3 80.3 + - - +
154B TYR* 1.3 61.6 + - - +
156B GLU* 4.1 9.0 - - - +
157B ALA* 3.1 28.1 + - - +
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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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130B VAL* 3.7 39.8 + - + +
132B GLU* 5.5 1.2 - - - -
133B VAL* 3.5 35.9 + - + +
150B ASP 3.0 12.6 + - - +
151B LEU* 3.0 16.4 + - + +
153B ASN* 1.3 78.5 - - - +
155B LEU* 1.3 67.7 + - + +
157B ALA* 4.0 2.8 - - - +
158B ASN* 3.4 40.0 + - - +
160B LEU* 4.3 7.4 - - + -
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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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133B VAL* 4.1 18.2 - - + -
151B LEU* 2.9 18.1 + - + +
152B HIS* 2.9 13.2 + - + +
154B TYR* 1.3 81.9 - - + +
156B GLU* 1.3 61.4 + - + +
158B ASN 3.4 1.0 + - - -
159B ASN 3.3 2.3 + - - -
160B LEU* 2.8 61.8 + - + +
161B ARG* 3.6 12.2 + - + +
164B LEU* 4.0 25.4 - - + +
165B TRP 5.0 0.2 - - - -
166B LEU* 3.8 34.1 - - + +
269B LEU* 5.0 7.2 - - + -
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Residues in contact with GLU 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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152B HIS* 3.0 45.6 + - + +
153B ASN* 4.1 8.5 - - - +
155B LEU* 1.3 71.3 - - - +
157B ALA* 1.3 53.4 + - - +
158B ASN 2.8 15.3 + - - -
159B ASN* 2.9 17.9 + - - +
161B ARG* 2.9 59.2 + - + +
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Residues in contact with ALA 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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153B ASN* 3.1 17.1 + - + +
154B TYR* 4.0 3.8 - - - +
156B GLU* 1.3 75.1 - - - +
158B ASN* 1.3 64.2 + - - +
159B ASN* 3.8 3.0 + - - -
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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