Contacts of the strand formed by residues 143 - 154 (chain A) in PDB entry 3AIH
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 LEU 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A TRP* 3.9 16.6 - - + -
129A GLN* 3.2 6.4 - - - +
130A GLN* 2.7 72.2 + - + +
141A GLU* 3.9 27.1 - - + +
142A VAL* 1.3 78.5 - - - +
144A TYR* 1.3 63.2 + - - +
179A SER* 3.7 24.0 - - - +
180A LYS 5.6 0.7 - - - +
188A ARG* 3.9 16.6 - - - +
3C MAN 3.8 11.0 - - - +
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Residues in contact with TYR 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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127A HIS* 3.8 29.4 + + + -
128A ILE 3.5 5.2 - - - -
129A GLN* 3.1 30.3 + - + -
142A VAL* 4.3 13.9 - - + -
143A LEU* 1.3 75.2 - - - +
145A LEU* 1.3 61.1 + - - +
146A GLY 4.2 3.1 - - - +
147A TYR* 3.1 54.6 - + + +
178A GLY* 3.0 11.0 - - - -
179A SER* 2.7 44.9 + - - +
188A ARG* 3.6 7.7 - - - -
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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
----------------------------------------------------------
120A TYR* 3.8 27.1 - - + -
128A ILE* 2.9 39.4 + - + -
130A GLN* 3.4 41.3 - - + +
143A LEU 4.6 0.7 - - - +
144A TYR* 1.3 74.5 - - - +
146A GLY* 1.3 56.1 + - - +
178A GLY* 4.0 0.2 - - - -
188A ARG* 3.3 30.6 - - - -
189A GLU* 3.3 11.1 + - - -
190A ALA* 4.5 6.7 - - + -
210A VAL* 4.8 0.4 - - + -
218A TYR* 3.9 35.4 - - + +
220A LEU* 4.3 9.9 - - + -
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Residues in contact with GLY 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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127A HIS* 3.4 5.2 - - - +
128A ILE* 3.1 25.9 + - - +
144A TYR* 3.1 5.2 - - - -
145A LEU* 1.3 82.9 - - - +
147A TYR* 1.3 65.9 + - - -
175A TYR* 3.8 9.4 - - - -
176A GLY 3.4 17.9 - - - -
178A GLY* 3.8 7.6 - - - -
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Residues in contact with TYR 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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126A ARG 3.7 4.7 - - - +
127A HIS* 4.4 6.3 - - + -
144A TYR* 3.1 47.5 - + + +
146A GLY* 1.3 75.9 - - - -
148A TYR* 1.3 68.7 + - - +
149A GLN* 3.3 3.1 + - - +
175A TYR* 3.2 3.9 - - - -
176A GLY* 2.8 29.7 + - - +
177A ASN* 3.0 35.2 - - + +
178A GLY* 4.4 2.2 - - - -
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Residues in contact with TYR 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLY* 3.3 44.2 - - - +
126A ARG* 2.8 17.1 + - - +
147A TYR* 1.3 75.5 - - - +
149A GLN* 1.3 71.5 + - - +
150A SER* 3.3 25.0 - - - -
151A ALA* 3.3 31.3 + - + +
173A GLN* 4.5 6.5 - - + -
174A THR 4.1 0.9 - - - -
175A TYR* 3.2 21.6 - + + -
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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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147A TYR 4.1 2.9 - - - +
148A TYR* 1.3 85.7 - - - +
150A SER* 1.3 65.6 + - - +
174A THR* 2.9 25.4 + - - +
175A TYR 5.1 0.8 - - - -
176A GLY* 3.3 28.5 + - - +
177A ASN* 3.9 13.7 + - - -
183B LEU 5.5 0.4 + - - -
184B ASN* 3.9 25.9 + - - +
186B ARG* 6.3 0.4 - - - +
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Residues in contact with SER 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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148A TYR* 3.3 15.9 - - - -
149A GLN* 1.3 84.1 - - - +
151A ALA* 1.3 63.3 + - - +
173A GLN* 3.3 3.3 - - - -
174A THR* 2.7 51.2 + - - +
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Residues in contact with ALA 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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124A TYR* 5.7 0.2 - - - +
148A TYR* 3.3 17.9 + - + +
150A SER* 1.3 80.5 - - - +
152A PHE* 1.3 62.7 + - - +
171A HIS* 4.6 9.0 - - + +
172A SER 3.3 6.5 - - - +
173A GLN* 3.6 22.4 - - + +
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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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151A ALA* 1.3 75.9 - - - +
153A ASP* 1.3 71.5 + - - +
154A TRP* 3.9 35.7 - + + -
170A TYR* 3.8 24.2 - + - -
171A HIS* 3.2 9.2 + - - -
172A SER* 2.9 44.4 + - - +
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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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152A PHE* 1.3 92.0 - - - +
154A TRP* 1.3 66.2 + - - +
155A ASP* 4.3 14.1 - - - +
170A TYR 3.5 8.3 - - - +
171A HIS* 2.7 32.1 + - + +
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Residues in contact with TRP 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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152A PHE* 3.9 27.8 - + + -
153A ASP* 1.3 78.6 - - - +
155A ASP* 1.3 70.4 + - - +
156A ASP 4.3 12.8 + - - +
168A LYS 3.6 24.4 + - - +
169A ARG* 3.4 6.1 - - - +
170A TYR* 2.8 47.4 + - + +
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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