Contacts of the strand formed by residues 180 - 187 (chain A) in PDB entry 1A4J
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 180 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 3.6 5.0 - - - +
141A LEU* 2.8 54.8 + - + +
144A PHE* 3.9 20.9 - - + -
147A ARG 5.6 1.3 - - - +
149A ALA* 4.9 11.9 - - + +
151A VAL* 3.9 14.6 - - + -
166A GLU* 3.7 31.4 - - + +
167A SER 3.2 13.2 - - - +
168A VAL* 4.4 11.2 - - + -
179A SER* 1.3 78.1 - - - +
181A SER* 1.3 73.9 + - - +
182A SER* 4.1 2.9 - - - +
172B PHE* 3.4 6.3 - - - -
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Residues in contact with SER 181 (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 VAL* 4.8 9.0 - - - -
139A CYS 3.4 7.2 - - - -
140A LEU* 4.7 1.8 - - - +
165A GLN 3.9 0.5 + - - +
166A GLU* 3.0 4.7 - - - +
167A SER* 2.8 44.2 + - - -
180A LEU* 1.3 76.6 - - - +
182A SER* 1.3 59.5 + - - +
183A THR* 4.6 5.4 + - - -
172B PHE* 3.5 17.7 - - - +
185B SER* 3.6 23.7 + - - -
187B VAL* 5.9 0.7 - - - -
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 3.6 0.8 - - - -
139A CYS* 2.9 36.2 + - - -
151A VAL* 4.3 20.1 + - - +
153A TRP* 2.9 31.0 + - - -
164A SER* 4.1 6.8 + - - -
165A GLN 3.5 7.1 + - - -
166A GLU* 3.9 15.7 + - - +
180A LEU* 4.1 5.6 - - - +
181A SER* 1.3 73.7 - - - +
183A THR* 1.3 61.7 + - - +
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Residues in contact with THR 183 (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 SER* 4.0 25.1 - - - +
137A VAL 3.3 10.8 - - - +
138A VAL* 4.3 15.1 - - + +
153A TRP* 4.4 0.2 - - - -
164A SER* 3.0 7.1 - - - -
165A GLN* 2.8 40.7 + - - +
181A SER* 4.6 7.6 + - - -
182A SER* 1.3 75.0 + - - +
184A LEU* 1.3 64.9 + - - +
185A THR* 3.8 9.7 + - + +
147B LEU* 5.3 9.8 - - + +
183B SER* 5.8 2.0 + - - +
185B SER* 5.0 4.2 + - - -
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Residues in contact with LEU 184 (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 ALA 3.7 1.6 - - - +
136A SER* 3.6 2.3 - - - -
137A VAL* 2.8 39.8 + - + +
153A TRP* 3.6 42.6 - - + -
155A VAL* 4.2 16.6 - - + -
160A GLN* 4.1 11.0 - - + -
163A ASN* 3.2 42.8 - - - +
164A SER* 4.0 3.6 - - - -
182A SER 3.9 1.2 + - - -
183A THR* 1.3 73.4 - - - +
185A THR* 1.3 59.5 + - - +
186A LEU* 4.0 26.0 - - + -
197A TYR* 4.2 9.2 - - + -
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Residues in contact with THR 185 (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 THR* 5.2 4.5 - - + -
135A ALA 3.8 3.8 - - - +
136A SER* 3.4 26.0 - - - +
163A ASN* 3.1 26.3 + - - +
164A SER* 5.0 0.5 - - - -
165A GLN* 5.5 1.7 + - - +
183A THR* 4.2 11.3 + - + +
184A LEU* 1.3 72.8 - - - +
186A LEU* 1.3 76.6 + - - +
149B LYS* 3.6 19.1 - - - +
177B GLN* 5.1 4.9 + - - +
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Residues in contact with LEU 186 (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 THR* 4.0 6.7 - - - +
135A ALA 3.0 33.5 + - - +
137A VAL* 5.0 2.2 - - + -
155A VAL* 5.0 2.2 - - + -
160A GLN* 4.3 6.1 - - - +
163A ASN* 3.2 31.9 - - - +
184A LEU* 4.0 15.7 - - + -
185A THR* 1.3 81.7 - - - +
187A SER* 1.3 66.7 + - - +
190A ASP* 4.5 8.7 - - + +
191A TYR* 4.2 15.9 - - + +
194A HIS* 6.2 0.4 - - - +
197A TYR* 3.5 38.8 - - + +
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Residues in contact with SER 187 (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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133A GLY 3.8 7.9 - - - -
134A THR* 4.8 2.5 - - - +
135A ALA* 4.6 0.2 - - - -
186A LEU* 1.3 77.9 - - - +
188A LYS* 1.3 54.1 + - - +
189A ALA* 3.8 7.4 + - - +
190A ASP* 3.2 32.7 + - - +
191A TYR* 2.8 32.3 + - - +
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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