Contacts of the helix formed by residues 143 - 154 (chain A) in PDB entry 5FWV
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 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A LYS 3.3 10.9 + - - +
142A LEU* 1.3 80.3 - - - +
144A ILE* 1.3 65.0 + - - +
145A GLN 3.2 0.5 + - - -
146A THR* 3.1 20.9 + - - +
147A CYS* 3.0 22.3 + - - +
190A CYS* 4.0 5.4 - - - -
192A GLY 3.8 20.0 - - - +
193A ASP* 4.0 6.5 - - + -
196A GLN* 3.5 7.2 - - - +
198A CYS* 4.1 5.6 - - - -
232A ASP* 2.9 39.1 + - - +
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Residues in contact with ILE 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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35A ALA* 3.7 29.8 - - + -
143A THR* 1.3 73.0 - - - +
145A GLN* 1.3 63.1 + - - +
147A CYS* 3.0 4.7 + - - +
148A ILE* 2.9 36.2 + - + +
161A MET* 3.6 17.7 - - - -
190A CYS* 3.9 3.9 - - - -
196A GLN* 3.2 21.0 - - + +
197A PRO* 3.6 28.5 - - + +
198A CYS* 3.9 0.2 - - - -
207A PHE* 3.7 41.5 - - + -
231A PRO* 4.0 11.4 - - + -
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Residues in contact with GLN 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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143A THR* 3.2 2.8 + - - -
144A ILE* 1.3 78.9 - - - +
146A THR* 1.3 54.8 + - - +
148A ILE* 3.2 6.2 + - - +
149A SER* 2.7 39.4 + - - -
152A ARG* 3.3 27.2 + - - -
211A VAL 3.2 18.2 + - - -
212A GLY* 3.9 0.9 - - - +
229A ASP* 3.3 48.5 - - + +
230A PHE 2.8 26.7 + - - -
231A PRO* 4.0 6.2 - - + +
232A ASP* 3.6 17.9 + - - +
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Residues in contact with THR 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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137A LYS* 3.6 21.8 + - - +
139A SER* 4.7 4.9 - - - +
141A LYS* 4.3 10.9 + - + +
142A LEU* 3.9 17.9 - - + -
143A THR* 3.1 27.1 + - - +
145A GLN* 1.3 80.2 - - - +
147A CYS* 1.3 61.2 + - - +
149A SER* 3.5 5.9 + - - -
150A PHE* 3.2 22.7 + - - +
232A ASP* 4.3 3.5 + - - -
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Residues in contact with CYS 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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142A LEU* 4.0 2.9 - - + -
143A THR 3.0 10.2 + - - +
144A ILE 3.0 6.7 + - - +
146A THR* 1.3 75.4 - - - +
148A ILE* 1.3 65.7 + - - +
149A SER 3.3 0.2 + - - -
150A PHE* 3.3 2.6 + - - +
151A CYS* 3.0 28.7 + - - -
159A ALA* 3.9 14.4 - - - -
160A GLY 3.6 12.1 - - - -
161A MET* 3.6 22.7 - - + -
167A CYS* 2.1 58.6 - - + -
168A PHE 3.9 1.8 - - - -
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Residues in contact with ILE 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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144A ILE* 2.9 28.1 + - + +
145A GLN* 3.5 14.4 - - - +
147A CYS* 1.3 76.8 - - - +
149A SER* 1.3 57.8 + - - +
151A CYS* 3.4 1.7 + - - +
152A ARG* 2.8 56.5 + - - +
159A ALA* 3.9 13.7 - - + -
161A MET* 5.2 0.7 - - + -
207A PHE* 3.7 32.5 - - + -
208A ASP 4.0 2.9 - - - +
209A THR* 3.4 17.1 - - - +
211A VAL* 3.5 30.7 - - + +
230A PHE 5.1 0.4 - - - +
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Residues in contact with SER 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 GLN* 2.7 32.5 + - - -
146A THR* 3.8 6.3 - - - -
147A CYS 3.2 0.2 - - - -
148A ILE* 1.3 71.9 - - - +
150A PHE* 1.3 62.2 + - - +
152A ARG* 3.6 18.0 + - - +
153A SER* 3.0 31.7 + - - -
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Residues in contact with PHE 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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135A THR* 3.9 5.6 - - + -
136A SER* 3.7 33.2 - - - -
137A LYS* 3.3 39.5 - - + +
146A THR 3.2 8.8 + - - +
147A CYS 3.6 5.6 - - - +
149A SER* 1.3 75.3 + - - +
151A CYS* 1.3 66.0 + - - +
153A SER* 3.4 7.2 + - - -
154A GLN* 3.2 51.8 + - - +
167A CYS* 4.1 1.8 - - - -
169A CYS* 3.3 34.3 - - - -
1324A CL 4.0 15.0 - - + -
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Residues in contact with CYS 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 CYS* 3.0 20.6 + - - +
148A ILE 3.7 3.1 - - - +
150A PHE* 1.3 82.7 - - - +
152A ARG* 1.3 62.9 + - - +
154A GLN* 3.1 13.3 + - - +
156A PHE* 3.1 20.6 + - + -
158A PHE 3.9 2.0 - - - +
159A ALA* 3.6 9.0 - - + -
168A PHE 3.5 10.8 - - - -
169A CYS* 2.0 58.6 - - + -
209A THR* 3.7 17.3 - - + -
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Residues in contact with ARG 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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145A GLN* 3.3 17.2 + - - -
148A ILE* 2.8 28.5 + - - +
149A SER* 3.6 22.3 + - - +
151A CYS* 1.3 71.0 - - - +
153A SER* 1.3 56.1 + - - +
155A ARG* 2.9 28.6 + - - -
156A PHE 4.1 9.0 - - - -
209A THR* 2.9 30.2 + - - +
210A LEU* 4.7 4.2 - - + +
211A VAL 2.9 27.9 + - - -
212A GLY 3.5 2.4 + - - -
213A ALA* 3.2 39.1 - - - +
214A CYS 5.4 0.2 - - - +
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Residues in contact with SER 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 SER* 3.0 18.1 + - - -
150A PHE* 3.4 11.6 - - - -
152A ARG* 1.3 76.3 - - - +
154A GLN* 1.3 66.0 + - - +
155A ARG* 3.3 14.0 + - - -
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Residues in contact with GLN 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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135A THR* 2.9 41.4 + - + +
150A PHE* 3.2 33.9 + - - +
151A CYS* 3.1 14.1 + - - +
153A SER* 1.3 80.1 - - - +
155A ARG* 1.3 75.8 + - - +
156A PHE* 3.6 18.0 + - + -
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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