Contacts of the helix formed by residues 133 - 155 (chain A) in PDB entry 3CX5
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 SER 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLU* 4.7 3.3 + - - -
129A ALA 3.7 10.8 + - - -
130A ASN 3.7 13.1 + - - -
131A LEU 3.2 1.8 - - - -
132A LEU* 1.3 81.0 - - - +
134A SER* 1.3 66.1 + - - +
135A SER* 4.0 4.3 + - - -
136A ASN* 3.3 23.7 + - - +
137A PHE* 2.9 23.1 + - - +
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Residues in contact with SER 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU 3.9 0.6 + - - -
133A SER* 1.3 72.3 - - - +
135A SER* 1.3 61.6 + - - +
137A PHE* 4.9 2.5 - - - -
138A GLU* 3.1 37.2 + - - +
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Residues in contact with SER 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU* 6.0 0.9 - - - -
133A SER* 3.3 5.1 + - - -
134A SER* 1.3 76.4 - - - +
136A ASN* 1.3 61.4 + - - +
138A GLU* 4.4 2.1 - - - +
139A ALA* 3.1 29.6 + - - +
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Residues in contact with ASN 136 (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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76A ILE* 4.4 5.9 + - - +
79A SER* 2.6 35.8 + - - -
81A GLU* 3.5 29.0 + - - +
131A LEU* 2.8 33.6 + - - +
133A SER* 3.3 19.1 + - - +
135A SER* 1.3 76.3 - - - +
137A PHE* 1.3 61.7 + - - +
139A ALA* 3.5 4.2 + - - +
140A THR* 2.8 39.2 + - - -
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Residues in contact with PHE 137 (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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72A LEU* 3.6 30.5 - - + +
76A ILE* 5.1 7.0 - - + -
131A LEU 4.4 2.6 + - - +
132A LEU* 4.6 12.3 - - + +
133A SER 2.9 18.0 + - - +
134A SER* 4.3 1.8 - - - +
136A ASN* 1.3 78.6 - - - +
138A GLU* 1.3 75.8 + - + +
140A THR* 3.7 3.8 - - - -
141A LYS* 2.8 47.9 + - + +
188A LEU 3.5 24.7 - - - -
189A VAL* 3.6 4.0 - - + -
190A VAL* 3.5 49.4 - - + -
193A LEU* 3.9 18.2 - - + -
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Residues in contact with GLU 138 (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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134A SER* 3.1 28.4 + - - +
135A SER* 4.4 2.2 - - - +
137A PHE* 1.3 97.3 - - + +
139A ALA* 1.3 59.0 + - - +
141A LYS* 3.6 19.1 + - - +
142A LYS* 2.9 30.7 + - - +
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A SER 3.1 21.8 + - - +
136A ASN* 3.9 4.9 - - - +
138A GLU* 1.3 77.3 - - - +
140A THR* 1.3 62.1 + - - +
142A LYS* 3.5 9.2 + - - +
143A SER* 3.1 22.5 + - - -
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Residues in contact with THR 140 (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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72A LEU* 4.2 7.4 - - + +
75A ASN* 3.6 35.7 + - + +
76A ILE* 3.6 31.8 - - + +
79A SER* 4.3 3.6 + - - -
136A ASN* 2.8 33.5 + - - -
137A PHE 3.7 3.4 - - - -
139A ALA* 1.3 74.7 - - - +
141A LYS* 1.3 64.4 + - - +
143A SER* 3.0 8.6 + - - -
144A VAL* 2.9 22.0 + - - +
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Residues in contact with LYS 141 (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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72A LEU* 3.9 20.6 - - + +
137A PHE* 2.8 34.5 + - + +
138A GLU* 3.6 22.9 + - - +
140A THR* 1.3 74.0 - - - +
142A LYS* 1.3 62.0 + - - +
143A SER 3.3 0.2 + - - -
144A VAL* 3.3 5.0 + - + +
145A LEU* 3.0 36.2 + - + +
185A LEU 3.2 23.6 - - - +
186A GLU* 3.1 26.7 + - - +
187A ASN 4.3 0.8 - - - -
188A LEU 2.6 28.5 + - - +
189A VAL* 5.2 2.6 - - - +
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Residues in contact with LYS 142 (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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138A GLU 2.9 17.7 + - - +
139A ALA* 3.7 8.3 - - - +
141A LYS* 1.3 76.4 - - - +
143A SER* 1.3 60.8 + - - +
145A LEU* 3.5 11.8 + - - +
146A LYS* 3.2 23.6 + - + +
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Residues in contact with SER 143 (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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75A ASN* 4.8 3.4 + - - -
139A ALA 3.1 14.5 + - - -
140A THR* 3.0 14.2 + - - -
142A LYS* 1.3 74.9 - - - +
144A VAL* 1.3 64.5 + - - +
146A LYS* 3.5 5.3 + - - +
147A GLN* 3.1 32.7 + - - +
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Residues in contact with VAL 144 (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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68A GLY 6.0 0.4 - - - +
71A ASN* 4.5 16.6 - - - +
72A LEU* 3.5 26.7 - - + +
75A ASN* 3.6 39.0 - - + +
140A THR 2.9 13.3 + - - +
141A LYS* 3.3 10.8 - - + +
143A SER* 1.3 73.3 - - - +
145A LEU* 1.3 65.4 + - + +
147A GLN* 3.2 11.1 - - + +
148A VAL* 2.8 34.3 + - - +
185A LEU* 4.4 19.3 - - + -
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Residues in contact with LEU 145 (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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141A LYS* 3.0 34.4 + - + +
142A LYS* 3.5 11.2 - - - +
143A SER 3.2 0.2 - - - -
144A VAL* 1.3 79.7 - - + +
146A LYS* 1.3 57.6 + - - +
148A VAL* 4.9 0.2 - - - -
149A GLN* 3.0 29.0 + - - +
182A LEU* 3.6 20.6 - - + +
185A LEU* 3.3 39.9 - - + +
186A GLU* 4.0 24.0 - - + +
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Residues in contact with LYS 146 (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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142A LYS 3.2 12.7 + - - +
143A SER* 3.9 5.4 - - - +
145A LEU* 1.3 76.3 - - - +
147A GLN* 1.3 65.3 + - - +
149A GLN* 3.5 12.3 + - - +
150A ASP* 3.0 52.2 + - - +
292B GLN* 6.0 2.0 - - - +
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Residues in contact with GLN 147 (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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71A ASN* 4.5 11.1 + - - +
74A LYS* 5.6 3.5 + - - -
75A ASN* 3.4 32.8 + - - +
143A SER* 3.1 24.3 + - - +
144A VAL* 3.2 14.8 - - - +
146A LYS* 1.3 76.6 - - - +
148A VAL* 1.3 64.4 + - + +
150A ASP* 3.2 10.3 + - - +
151A PHE* 3.2 20.8 + - - +
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Residues in contact with VAL 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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71A ASN* 4.1 7.6 - - - +
144A VAL 2.8 22.0 + - - +
145A LEU 4.1 2.9 - - - +
147A GLN* 1.3 72.9 - - + +
149A GLN* 1.3 65.8 + - - +
151A PHE* 3.3 9.3 + - + +
152A GLU* 3.0 34.8 + - + +
179A ARG* 3.7 28.9 - - + +
180A GLY 4.0 15.9 - - - +
181A THR* 5.0 0.2 - - - -
182A LEU* 3.9 21.1 - - + +
185A LEU* 3.6 23.3 - - + -
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Residues in contact with GLN 149 (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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145A LEU 3.0 20.1 + - - +
146A LYS* 3.7 12.3 + - - +
147A GLN 3.3 0.2 - - - -
148A VAL* 1.3 77.8 - - - +
150A ASP* 1.3 66.2 + - - +
152A GLU* 3.5 3.3 + - - +
153A ASP* 3.0 32.6 + - + +
182A LEU* 4.0 24.9 - - + +
306D LYS* 4.0 25.8 - - - +
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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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146A LYS* 3.0 47.2 + - - +
147A GLN* 3.2 7.3 + - - +
149A GLN* 1.3 84.2 + - - +
151A PHE* 1.3 55.5 + - - +
153A ASP* 4.3 2.1 - - - +
154A ASN* 2.7 54.3 + - - +
155A ASP 3.9 0.2 + - - -
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Residues in contact with PHE 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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147A GLN 3.2 12.0 + - - +
148A VAL* 3.3 12.5 + - + +
150A ASP* 1.3 76.8 - - - +
152A GLU* 1.3 79.6 + - - +
155A ASP* 3.0 51.6 + - + +
158A ASN* 3.6 26.2 - - + -
159A ARG* 3.7 29.4 - - - +
162A GLU* 4.6 7.2 - - + -
179A ARG* 3.2 57.9 - - + +
34E TYR* 4.1 8.3 - - - -
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Residues in contact with GLU 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 VAL* 3.0 26.9 + - + +
149A GLN* 3.9 4.7 - - - +
151A PHE* 1.3 92.0 - - - +
153A ASP* 1.3 59.4 + - - +
159A ARG* 3.3 42.4 + - + +
163A HIS* 3.5 11.7 - - + -
180A GLY 5.1 2.3 - - - +
181A THR* 6.2 0.2 - - - -
182A LEU* 5.5 9.0 - - + -
33E THR* 5.6 2.5 - - - +
34E TYR* 2.6 45.1 + - + -
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Residues in contact with ASP 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 GLN* 3.0 21.4 + - + +
150A ASP* 3.8 4.5 - - - +
152A GLU* 1.3 80.2 - - - +
154A ASN* 1.3 76.1 + - - +
156A HIS* 3.5 15.6 + - - -
159A ARG* 5.2 0.5 + - - -
256A LEU* 5.8 0.3 - - - +
306D LYS* 3.3 33.0 + - - +
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Residues in contact with ASN 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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150A ASP* 2.7 41.9 + - - +
153A ASP* 1.3 97.4 + - - +
155A ASP* 1.3 59.3 + - - +
156A HIS* 3.0 27.2 + - - -
157A PRO* 5.3 0.2 - - - +
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Residues in contact with ASP 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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150A ASP 3.9 1.0 + - - -
151A PHE* 3.0 34.2 + - + +
154A ASN* 1.3 71.8 - - - +
156A HIS* 1.3 59.3 + - - +
157A PRO* 3.7 9.3 - - - +
158A ASN* 2.9 44.9 + - - +
159A ARG* 2.8 32.3 + - - +
179A ARG* 5.2 1.2 + - - -
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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
------------------------------------------------------------
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