Contacts of the helix formed by residues 149 - 166 (chain A) in PDB entry 3CCY
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 ASN 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A MSE 3.4 11.5 + - - +
147A ALA 3.2 2.1 - - - -
148A ALA* 1.3 77.2 - - + +
150A ARG* 1.3 57.4 + - - +
151A THR* 3.2 12.6 + - - -
152A LEU* 3.1 47.0 + - + +
153A ALA* 3.0 27.4 + - - +
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Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A ARG* 3.5 40.4 + - - +
147A ALA* 4.0 14.8 + - - +
148A ALA 3.6 4.8 + - - +
149A ASN* 1.3 70.5 + - - +
151A THR* 1.3 64.1 + - - +
153A ALA* 3.7 6.1 - - - +
154A HIS* 3.1 23.6 + - - +
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Residues in contact with THR 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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149A ASN* 3.2 9.6 + - - -
150A ARG* 1.3 78.9 - - - +
152A LEU* 1.3 68.4 + - + +
154A HIS* 3.4 6.7 + - - +
155A VAL* 3.1 30.2 + - + +
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Residues in contact with LEU 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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149A ASN* 3.1 32.7 + - + +
151A THR* 1.3 85.3 - - + +
153A ALA* 1.3 59.5 + - - +
155A VAL* 3.6 18.3 - - + +
156A ASP* 2.8 44.5 + - - +
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Residues in contact with ALA 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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136A ARG* 4.1 24.2 - - + +
140A LEU* 4.1 25.8 - - + -
146A MSE 4.7 1.8 + - - +
147A ALA 5.5 0.4 - - - +
149A ASN 3.0 19.6 + - - +
150A ARG* 3.7 6.5 - - - +
151A THR 3.3 0.4 - - - -
152A LEU* 1.3 76.2 - - - +
154A HIS* 1.3 53.7 + - - +
156A ASP* 3.4 7.3 + - - +
157A THR* 2.7 38.1 + - - -
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Residues in contact with HIS 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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132A ILE* 5.3 6.8 - - + +
136A ARG* 5.0 6.3 - - - +
150A ARG 3.1 13.1 + - - +
151A THR* 3.6 10.3 - - - +
153A ALA* 1.3 72.8 - - - +
155A VAL* 1.3 71.2 + - + +
157A THR* 3.4 5.0 + - - -
158A MSE 3.0 63.5 + - + +
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Residues in contact with VAL 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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151A THR* 3.1 20.8 + - + +
152A LEU* 3.3 23.8 + - + +
154A HIS* 1.3 79.9 - - + +
156A ASP* 1.3 68.2 + - - +
158A MSE 3.3 4.2 + - - +
159A LEU* 3.0 44.6 + - + +
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Residues in contact with ASP 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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139A LEU* 4.7 4.5 - - + -
146A MSE 4.4 20.3 - - - +
152A LEU* 2.8 31.5 + - - +
153A ALA* 3.9 6.6 - - - +
154A HIS 3.3 0.4 - - - -
155A VAL* 1.3 80.7 - - - +
157A THR* 1.3 63.4 + - - +
159A LEU* 3.4 11.2 + - - +
160A PHE* 3.0 23.0 + - - +
190A PHE* 3.6 19.6 - - + -
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Residues in contact with THR 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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132A ILE* 3.9 11.4 - - + +
135A VAL* 4.1 5.4 - - + -
136A ARG* 3.3 46.7 + - + +
139A LEU* 4.1 13.2 - - - +
153A ALA 2.7 22.2 + - - -
154A HIS* 3.7 6.1 - - - -
156A ASP* 1.3 78.5 - - - +
158A MSE 1.3 57.6 + - - +
160A PHE* 3.3 4.5 + - - +
161A PHE* 2.9 47.2 + - + -
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Residues in contact with MSE 158 (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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132A ILE* 3.9 44.4 - - + -
154A HIS* 3.0 50.2 + - + +
155A VAL* 4.0 3.8 - - - +
157A THR* 1.3 73.5 - - - +
159A LEU* 1.3 65.7 + - - +
161A PHE* 3.8 17.0 - - + +
162A GLY* 3.1 19.6 + - - -
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Residues in contact with LEU 159 (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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155A VAL* 3.0 40.7 + - + +
156A ASP* 3.7 12.1 - - - +
158A MSE 1.3 73.6 - - - +
160A PHE* 1.3 67.9 + - - +
162A GLY* 3.4 3.3 + - - -
163A MSE 3.3 23.0 + - + +
190A PHE* 5.0 5.6 - - + -
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Residues in contact with PHE 160 (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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88A PHE* 3.7 23.1 - + - -
91A ILE* 6.0 0.9 - - + -
92A VAL* 3.4 27.6 - - + -
95A PHE* 5.4 0.7 - + - -
135A VAL* 3.8 30.7 - - + -
139A LEU* 4.7 1.3 - - + -
156A ASP 3.0 14.4 + - - +
157A THR* 3.4 10.1 - - - +
159A LEU* 1.3 77.2 - - - +
161A PHE* 1.3 71.5 + + - +
163A MSE 3.1 32.3 + - + +
164A ILE* 3.4 36.5 + - + +
186A THR* 4.0 19.1 - - + -
187A VAL* 5.4 0.4 - - + -
190A PHE* 3.9 27.2 - + + -
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Residues in contact with PHE 161 (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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95A PHE* 3.8 21.5 - + - -
131A LEU* 4.2 11.4 - - + -
132A ILE* 3.6 43.1 - - + -
135A VAL* 3.3 36.1 - - + -
157A THR* 2.9 35.7 + - + +
158A MSE 3.8 19.3 - - + +
159A LEU 3.4 0.4 - - - -
160A PHE* 1.3 76.1 - + - +
162A GLY* 1.3 53.3 + - - +
164A ILE* 3.3 12.7 + - + +
165A ASN* 2.6 68.0 + - - +
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Residues in contact with GLY 162 (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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158A MSE 3.1 14.1 + - - -
159A LEU* 3.4 5.1 + - - -
160A PHE 3.2 0.2 - - - -
161A PHE* 1.3 76.5 - - - +
163A MSE 1.3 61.1 + - - +
165A ASN* 4.8 3.4 - - - -
166A TRP* 3.0 30.8 + - - +
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Residues in contact with MSE 163 (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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159A LEU* 3.3 9.6 + - + +
160A PHE* 3.1 17.5 + - + +
162A GLY* 1.3 76.6 - - - +
164A ILE* 1.3 62.0 + - - +
166A TRP* 4.1 4.8 + - - +
167A THR* 3.5 15.9 + - - +
170A TRP* 4.9 4.0 + - - -
186A THR* 3.9 30.5 - - + +
189A LEU* 5.4 6.7 - - - -
190A PHE* 2.7 56.5 - - + -
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Residues in contact with ILE 164 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A VAL* 4.0 12.8 - - + -
95A PHE* 3.5 40.2 - - + -
96A LEU* 4.5 18.5 - - + +
106A HIS* 5.3 3.5 - - - -
160A PHE* 3.7 33.2 - - + +
161A PHE* 3.5 18.2 - - + +
163A MSE 1.3 81.4 - - - +
165A ASN* 1.3 67.1 + - - +
166A TRP 3.3 0.7 - - - -
167A THR* 2.5 32.5 + - + +
186A THR* 3.9 28.0 - - + +
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Residues in contact with ASN 165 (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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106A HIS* 5.0 5.2 - - - -
110A LEU* 3.5 39.6 - - + +
161A PHE* 2.6 48.8 + - - +
162A GLY* 4.6 2.7 - - - +
164A ILE* 1.3 82.0 - - - +
166A TRP* 1.3 57.2 + - - +
167A THR* 3.2 3.3 + - - -
168A TYR* 3.0 28.6 + - - -
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Residues in contact with TRP 166 (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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162A GLY* 3.0 20.5 + - - +
163A MSE 4.4 3.8 - - - +
164A ILE 3.3 0.2 - - - -
165A ASN* 1.3 73.5 - - - +
167A THR* 1.3 60.9 + - - +
168A TYR* 3.2 16.6 - + - -
169A THR* 2.8 70.8 + - + -
170A TRP* 3.4 16.6 - + - +
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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