Contacts of the helix formed by residues 131 - 145 (chain A) in PDB entry 3S4Y
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 ARG 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLN* 5.0 1.0 - - - +
129A ALA 4.0 0.5 + - - +
130A GLY* 1.3 70.1 - - - +
132A PHE* 1.3 64.7 + - - +
133A ASP* 2.7 36.6 + - - +
134A GLN* 3.1 45.5 + - + +
135A ILE* 3.2 10.2 + - - +
1301A TPP 3.4 16.8 + - - -
159B GLU* 5.5 9.0 - - + +
160B SER* 3.5 7.0 - - - +
182B TRP* 3.2 50.3 - - + +
218B SER* 3.2 18.2 + - - -
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Residues in contact with PHE 132 (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 GLY 3.2 4.6 + - - +
131A ARG* 1.3 71.5 - - - +
133A ASP* 1.3 63.3 + - - +
135A ILE* 3.1 18.6 + - + +
136A MET* 3.2 46.8 + - + +
128B LEU* 4.3 28.5 - - + -
135B ILE* 4.0 23.1 - - + -
139B VAL* 4.0 12.3 - - + -
160B SER* 3.0 24.0 + - - +
162B ILE* 3.5 28.5 - - + -
182B TRP* 3.9 1.4 - - - -
186B ILE* 4.7 1.8 - - + -
236B LEU* 3.7 25.1 - - + -
238B THR* 3.6 20.2 - - + +
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Residues in contact with ASP 133 (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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131A ARG* 2.7 47.6 + - - +
132A PHE* 1.3 78.8 - - - +
134A GLN* 1.3 70.1 + - - +
136A MET* 3.3 5.9 + - - +
137A ALA 2.9 21.8 + - - -
182B TRP* 3.4 28.2 - - + -
183B CYS 4.8 2.0 - - - +
184B GLY* 4.9 0.2 - - - -
186B ILE* 4.8 0.2 - - - -
217B THR* 3.3 27.3 - - + +
218B SER* 2.9 22.1 + - - +
238B THR* 3.9 16.8 + - + -
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Residues in contact with GLN 134 (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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25A ASN* 5.4 1.9 + - - +
127A GLY* 4.5 1.8 - - - -
129A ALA 6.0 0.7 - - - +
131A ARG* 3.1 39.7 + - + +
133A ASP* 1.3 92.9 + - - +
135A ILE* 1.3 64.3 + - - +
137A ALA* 3.5 10.8 - - + +
138A SER* 3.0 26.0 + - - -
1301A TPP 2.9 43.8 + - - -
1302A SO4 3.7 16.6 + - - -
217B THR* 5.7 0.9 - - - +
218B SER* 3.6 4.7 + - - +
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Residues in contact with ILE 135 (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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127A GLY 3.4 13.5 - - - +
128A LEU* 3.7 7.6 - - + +
129A ALA* 3.6 39.7 + - - +
130A GLY 3.6 13.0 - - - +
131A ARG 3.2 9.7 + - - +
132A PHE* 3.1 18.7 + - + +
134A GLN* 1.3 75.0 - - - +
136A MET* 1.3 79.4 + - + +
138A SER* 3.2 5.5 + - - -
139A VAL* 3.1 21.8 + - - +
128B LEU 3.7 20.0 - - - +
132B PHE* 3.9 22.9 - - + -
135B ILE* 4.5 5.4 - - + -
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Residues in contact with MET 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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132A PHE* 3.2 41.8 + - + +
133A ASP 3.5 7.6 - - - +
135A ILE* 1.3 89.7 - - + +
137A ALA* 1.3 61.1 + - - +
139A VAL* 3.3 14.5 + - + +
140A ASN* 2.9 28.1 + - - +
188A VAL* 5.6 2.7 - - + -
132B PHE* 5.0 0.2 - - + -
136B MET* 3.7 30.1 - - + +
186B ILE* 3.7 40.6 - - + -
188B VAL* 4.2 12.3 - - - -
211B PHE* 3.7 12.1 - - + -
215B VAL* 5.0 1.1 - - + -
217B THR* 4.7 2.2 - - + -
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Residues in contact with ALA 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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99A THR* 4.0 20.0 - - + +
101A PHE* 5.3 0.4 - - - -
133A ASP 2.9 13.9 + - - +
134A GLN* 3.3 17.2 + - + +
136A MET* 1.3 77.2 - - - +
138A SER* 1.3 56.8 + - - +
140A ASN* 3.2 7.5 + - - +
141A THR* 2.9 32.3 + - - -
144A GLN* 5.2 0.2 - - - +
215B VAL* 5.7 0.4 - - - -
217B THR* 3.7 23.3 - - - +
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Residues in contact with SER 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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24A LEU* 4.3 6.6 - - - +
101A PHE* 3.8 17.2 - - - -
127A GLY* 2.9 38.9 + - - -
128A LEU* 4.9 3.6 - - - -
134A GLN 3.0 10.8 + - - -
135A ILE 3.2 3.8 + - - -
137A ALA* 1.3 71.0 - - - +
139A VAL* 1.3 67.9 + - - +
141A THR* 3.2 12.8 + - - -
142A LEU* 3.4 13.9 + - - +
155A ILE* 4.1 17.5 - - - -
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Residues in contact with VAL 139 (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 LEU* 5.5 0.2 - - + -
135A ILE* 3.1 13.3 + - + +
136A MET* 3.6 15.3 - - + +
138A SER* 1.3 78.2 - - - +
140A ASN* 1.3 62.8 + - - +
142A LEU* 3.0 23.9 + - - +
143A PHE* 3.5 20.6 - - + -
162A ILE* 3.9 22.2 - - + -
188A VAL* 4.1 13.7 - - + -
236A LEU* 4.3 15.9 - - + -
132B PHE* 3.9 22.0 - - + -
136B MET* 6.1 0.2 - - - -
211B PHE* 3.9 16.6 - - + -
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Residues in contact with ASN 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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136A MET 2.9 17.5 + - - +
137A ALA* 3.2 7.8 + - - +
139A VAL* 1.3 77.1 - - - +
141A THR* 1.3 57.2 + - - +
143A PHE* 2.9 19.0 + - - +
144A GLN* 2.9 39.6 + - - +
210B ALA 4.4 0.2 - - - +
211B PHE* 3.4 19.4 - - + -
212B GLY* 2.8 31.0 + - - +
213B THR 5.3 1.2 - - - +
214B LEU* 5.1 3.6 - - - +
215B VAL* 3.8 27.5 + - + +
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Residues in contact with THR 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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99A THR* 3.9 6.2 + - - +
101A PHE* 3.5 30.6 - - + -
102A THR* 3.0 25.9 + - + +
105A LEU* 3.5 29.4 - - + -
137A ALA 2.9 13.8 + - - -
138A SER 3.2 10.5 + - - -
140A ASN* 1.3 75.7 - - - +
142A LEU* 1.3 52.8 + - + +
144A GLN* 3.1 11.0 + - + -
145A ALA* 2.7 34.1 + - - +
148A ILE* 5.4 0.9 - - + -
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Residues in contact with LEU 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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101A PHE* 4.8 2.7 - - + -
138A SER 3.7 10.1 - - - +
139A VAL* 3.0 10.1 + - - +
141A THR* 1.3 79.1 - - + +
143A PHE* 1.3 60.7 + - + +
145A ALA* 3.6 13.5 + - + +
146A THR* 4.2 8.5 + - - +
153A ILE* 3.7 43.1 - - + +
155A ILE* 3.7 15.5 - - + -
162A ILE* 3.8 33.4 - - + +
163A TYR* 4.7 3.6 - - - -
164A LEU* 3.7 32.8 - - + +
236A LEU* 4.1 15.5 - - + -
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Residues in contact with PHE 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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139A VAL* 3.5 30.7 - - + -
140A ASN 2.9 8.7 + - - +
142A LEU* 1.3 79.4 - - - +
144A GLN* 1.3 60.4 + - - +
146A THR* 3.3 19.3 + - - +
147A HIS* 4.9 1.7 - - - -
164A LEU* 3.9 32.3 - - + -
166A GLN* 5.7 0.2 - - - +
188A VAL* 3.4 28.7 - - + -
189A GLY* 5.3 1.6 - - - -
190A GLN* 6.3 0.9 - - - -
234A PRO* 4.0 25.8 - - + -
236A LEU* 5.9 0.4 - - + -
211B PHE* 4.0 34.1 - + + -
212B GLY* 3.6 24.0 - - - +
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Residues in contact with GLN 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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98A HIS* 4.3 9.5 - - - -
102A THR* 2.7 29.2 + - + -
140A ASN* 2.9 34.9 + - - +
141A THR* 3.1 15.6 + - - +
143A PHE* 1.3 75.0 - - - +
145A ALA* 1.3 64.9 + - - +
147A HIS* 3.0 47.6 + - + +
148A ILE* 3.6 11.6 - - + +
247A UNX 2.5 22.9 - - - -
212B GLY* 5.2 9.9 - - - +
213B THR 5.6 3.8 + - - -
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Residues in contact with ALA 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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105A LEU* 4.5 8.7 - - + -
141A THR 2.7 19.8 + - - +
142A LEU* 3.7 12.3 - - + +
143A PHE 3.3 0.8 - - - -
144A GLN* 1.3 73.4 - - - +
146A THR* 1.3 58.5 + - + +
148A ILE* 2.9 27.7 + - - -
149A THR* 3.0 21.2 + - + +
153A ILE* 3.9 27.8 - - + -
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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