Contacts of the helix formed by residues 143 - 152 (chain A) in PDB entry 3FTC
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 GLY 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LYS* 5.1 3.2 + - - +
141A ASP 3.2 5.5 + - - -
142A THR* 1.3 75.7 - - - +
144A TRP* 1.3 68.0 + - - +
145A LEU* 3.2 3.9 + - - -
146A SER* 3.2 18.3 + - - -
147A VAL 3.5 3.6 + - - -
201A PHE* 3.6 17.3 - - - -
204A ARG* 3.9 4.7 - - - -
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Residues in contact with TRP 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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112A GLU* 3.4 38.6 - - + -
143A GLY* 1.3 72.8 - - - -
145A LEU* 1.3 84.5 + - + +
147A VAL* 3.2 3.6 + - - -
148A PHE* 3.0 51.3 + + + +
194A LYS* 3.6 33.4 - - + -
197A LEU* 3.8 26.3 - - + +
198A THR* 4.0 18.0 - - + +
201A PHE* 3.6 32.7 - - + +
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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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108A SER* 3.4 43.1 - - - +
111A ILE* 4.5 4.7 - - + -
112A GLU* 3.8 32.5 - - + +
132A VAL* 6.3 0.7 - - + -
136A LEU* 3.9 20.4 - - + -
143A GLY* 3.2 1.2 - - - -
144A TRP* 1.3 102.9 - - + +
146A SER* 1.3 57.5 + - - +
148A PHE* 3.4 12.1 - - + +
149A VAL* 2.9 46.8 + - + +
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Residues in contact with SER 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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135A LYS* 2.8 30.1 + - - -
136A LEU* 3.1 16.9 + - - +
138A GLY 3.6 0.7 + - - -
142A THR* 3.6 8.8 - - - +
143A GLY* 3.2 14.8 + - - +
144A TRP 3.2 0.2 - - - -
145A LEU* 1.3 79.1 - - - +
147A VAL* 1.3 57.6 + - - +
149A VAL* 3.9 1.2 - - - +
150A ARG* 2.9 58.6 + - - +
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Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A THR* 4.3 3.4 - - + -
143A GLY 3.5 1.7 + - - +
144A TRP 3.2 7.6 + - - +
146A SER* 1.3 73.5 - - - +
148A PHE* 1.3 59.6 + - - +
150A ARG* 3.9 15.6 - - - +
151A THR* 2.6 35.2 + - - -
193A TYR* 4.0 9.4 - - - +
197A LEU* 3.7 25.1 - - + -
201A PHE* 3.9 18.6 - - + -
233A LEU* 3.9 17.8 - - + +
236A PHE* 3.7 40.2 - - + -
237A PHE* 5.4 0.2 - - + -
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Residues in contact with PHE 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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112A GLU* 3.9 19.7 - - + -
115A VAL* 3.4 35.0 - - + -
116A TYR* 3.9 27.4 - + - -
144A TRP* 3.0 37.2 + + + +
145A LEU* 3.4 15.3 - - + +
147A VAL* 1.3 78.7 - - - +
149A VAL* 1.3 61.1 + - - +
151A THR* 3.5 3.1 + - - -
152A PHE* 3.1 28.7 - + - -
190A LEU* 3.7 29.6 - - + -
193A TYR* 3.8 23.3 - + - -
194A LYS* 4.2 9.2 - - + -
197A LEU* 3.6 14.0 - - + +
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Residues in contact with VAL 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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111A ILE* 3.7 26.5 - - + -
115A VAL* 3.7 17.3 - - + -
136A LEU* 4.2 8.7 - - + +
145A LEU* 2.9 31.3 + - + +
146A SER 3.9 3.6 - - - +
148A PHE* 1.3 75.5 - - - +
150A ARG* 1.3 58.0 + - - +
152A PHE* 2.9 6.2 + - - -
153A TYR* 2.8 33.0 + - + +
155A VAL* 3.6 27.1 - - + -
179A LEU* 4.0 22.4 - - + -
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Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LEU 3.2 17.4 + - - +
137A GLN* 3.9 14.6 + - - +
138A GLY* 3.8 11.2 - - - -
142A THR* 3.7 18.0 - - - +
146A SER* 2.9 40.7 + - - +
147A VAL* 3.4 14.5 + - - +
149A VAL* 1.3 72.1 - - - +
151A THR* 1.3 59.6 + - - +
152A PHE 3.1 0.2 - - - -
153A TYR 3.3 9.2 - - - +
155A VAL* 3.8 19.1 - - + +
184A LYS* 2.6 35.5 + - - +
233A LEU* 3.9 41.2 - - + +
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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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147A VAL* 2.6 22.6 + - - +
148A PHE 3.6 8.1 - - - -
149A VAL 3.2 0.4 - - - -
150A ARG* 1.3 77.9 - - - +
152A PHE* 1.3 77.5 + - + +
183A GLU* 3.6 0.9 - - - -
184A LYS 2.8 28.6 + - - -
185A PHE* 3.8 8.9 + - + +
187A VAL* 4.1 8.5 - - + -
193A TYR* 2.7 34.9 + - + +
233A LEU* 4.9 0.2 - - - +
237A PHE* 3.5 29.3 - - + -
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Residues in contact with PHE 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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115A VAL* 3.5 15.0 - - + -
118A LYS* 3.7 30.3 - - + -
148A PHE* 3.1 28.0 - + - -
149A VAL 2.9 2.0 + - - -
151A THR* 1.3 89.7 - - + +
153A TYR* 1.3 71.1 + - + +
181A LYS* 3.5 11.3 - - + +
182A ASN 2.8 36.2 + - - -
183A GLU* 3.7 21.1 - - + +
185A PHE 3.8 17.5 - - - -
187A VAL* 3.7 26.5 - - + -
190A LEU* 3.3 29.8 - - + -
193A TYR* 4.2 8.3 - + - -
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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