Contacts of the helix formed by residues 147 - 157 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 4.2 14.6 - - + -
104A ARG* 3.6 14.4 - - - +
145A GLY 3.1 4.2 + - - +
146A VAL* 1.3 79.2 - - - +
148A TYR* 1.3 65.8 + - - +
149A HIS* 3.0 8.5 + - - +
150A ASP* 2.8 39.2 + - - +
151A LEU* 2.9 17.8 + - - +
172A GLY 3.8 4.0 - - - -
173A GLY* 3.0 26.2 - - - +
174A GLY 3.1 9.2 - - - -
175A SER* 4.3 0.9 - - - +
176A VAL* 3.8 1.1 - - - -
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Residues in contact with TYR 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A THR* 1.3 74.6 - - - +
149A HIS* 1.3 50.7 + - - +
151A LEU* 3.1 2.8 + - - -
152A HIS* 2.7 35.8 + - - +
166A LEU* 3.6 11.3 - - + +
167A ASP 3.4 20.2 - - - -
168A VAL* 3.7 23.6 - - + -
169A PRO* 3.3 28.5 - - + -
171A LEU 4.5 1.6 - - - -
172A GLY* 3.2 15.7 - - - +
174A GLY* 3.0 34.6 + - - -
175A SER 3.8 14.8 - - - -
176A VAL* 4.1 27.5 + - + -
179A ASN* 3.3 16.2 - - + +
193A HIS* 2.7 29.8 + + - -
406A PRO* 4.8 2.5 - - + -
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Residues in contact with HIS 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A THR* 3.0 5.1 + - - +
148A TYR* 1.3 70.6 - - - +
150A ASP* 1.3 57.2 + - - +
152A HIS* 2.9 15.5 + - - +
153A ASN* 2.6 65.6 + - - +
172A GLY 3.0 8.5 + - - +
406A PRO* 3.5 35.1 - - + +
408A TYR* 2.7 46.6 + + - +
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Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASN 5.9 2.2 - - - +
130A VAL* 5.1 2.4 - - + +
145A GLY 3.7 6.7 - - - +
146A VAL* 4.2 9.4 - - + -
147A THR* 2.8 50.8 + - - +
149A HIS* 1.3 73.3 - - - +
151A LEU* 1.3 58.6 + - - +
153A ASN* 3.2 11.2 + - - +
154A TYR* 2.9 27.1 + - - +
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A VAL* 4.2 26.2 - - + -
133A VAL* 4.6 9.2 - - + -
140A CYS* 4.1 28.9 - - - -
142A VAL* 4.5 3.1 - - + -
146A VAL* 3.6 15.7 - - + -
147A THR 2.9 12.3 + - - +
148A TYR* 3.7 3.1 - - + +
150A ASP* 1.3 73.2 - - - +
152A HIS* 1.3 70.9 + - - +
154A TYR* 3.0 15.9 + - + +
155A LEU* 3.1 16.4 + - + +
166A LEU* 4.0 27.1 - - + -
176A VAL* 3.8 23.8 - - + -
269A LEU* 4.7 2.9 - - + -
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Residues in contact with HIS 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A TYR 2.7 17.1 + - - +
149A HIS* 3.2 20.2 - - - +
151A LEU* 1.3 76.2 - - - +
153A ASN* 1.3 70.2 + - - +
155A LEU* 3.0 18.3 + - + +
156A GLU* 3.4 41.9 + - + +
161A ARG* 5.0 7.2 + - + -
166A LEU* 3.8 15.6 - - + +
404A GLY 4.5 5.8 - - - -
405A ILE* 4.7 15.4 - - + +
406A PRO* 3.4 39.8 - - + +
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Residues in contact with ASN 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A HIS* 2.6 51.9 + - - +
150A ASP* 3.6 10.5 + - - +
152A HIS* 1.3 80.7 + - - +
154A TYR* 1.3 63.6 + - - +
156A GLU* 3.3 8.6 + - - +
157A ALA* 3.2 23.9 + - - +
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Residues in contact with TYR 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A VAL* 4.0 41.4 + - + -
131A LEU 6.1 0.2 - - - -
132A GLU* 5.3 1.2 - - - -
133A VAL* 3.5 41.6 + - + +
150A ASP 2.9 14.1 + - - +
151A LEU* 3.0 10.2 + - + +
153A ASN* 1.3 76.6 - - - +
155A LEU* 1.3 65.6 + - + +
157A ALA* 3.8 4.5 + - + +
158A ASN* 3.0 42.2 + - - +
160A LEU* 4.2 10.3 - - + -
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A VAL* 4.1 25.1 - - + -
151A LEU* 3.1 14.8 + - + +
152A HIS* 3.0 11.6 + - + +
154A TYR* 1.3 77.1 - - + +
156A GLU* 1.3 64.7 + - + +
158A ASN 3.2 2.4 + - - -
159A ASN 3.2 2.8 + - - -
160A LEU* 3.0 53.5 + - + +
161A ARG* 3.6 15.9 + - + +
164A LEU* 3.4 30.1 - - + +
166A LEU* 3.6 30.1 - - + +
269A LEU* 4.4 8.7 - - + -
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Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A HIS* 3.6 38.7 + - + +
153A ASN* 3.3 9.1 + - - +
155A LEU* 1.3 74.4 - - + +
157A ALA* 1.3 59.2 + - - +
158A ASN 2.9 9.8 + - - -
159A ASN* 3.0 19.6 + - - +
161A ARG* 2.8 66.9 + - + +
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Residues in contact with ALA 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ASN 3.2 12.8 + - - +
154A TYR* 4.1 3.8 - - + +
155A LEU 3.4 0.4 - - - -
156A GLU* 1.3 78.0 - - - +
158A ASN* 1.3 71.3 + - - +
159A ASN* 5.0 2.9 + - - -
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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
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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