Contacts of the strand formed by residues 139 - 146 (chain A) in PDB entry 5MJ3
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 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ALA* 3.6 16.5 - - - +
134A LYS 4.9 1.0 + - - -
135A ASN* 4.6 5.1 - - - +
137A SER* 3.1 21.9 + - - +
138A GLY* 1.3 82.0 + - - +
140A PHE* 1.3 64.9 + - - +
192A GLU* 5.5 8.0 + - - +
193A CYS 3.2 8.5 + - - +
194A GLN* 3.4 53.3 + - + +
229A ILE* 5.3 1.0 - - - +
408A PGE 4.7 20.2 + - - -
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Residues in contact with PHE 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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131A CYS* 4.6 0.7 - - + -
132A GLU 3.5 14.6 - - - +
133A ALA* 4.1 3.8 - - + +
138A GLY 3.9 12.1 - - - -
139A ARG* 1.3 79.1 - - - +
141A THR* 1.3 65.3 + - - +
142A CYS* 3.8 17.9 - - - -
158A SER* 3.7 10.1 - - - -
168A VAL* 4.2 10.1 - - + -
192A GLU* 3.6 4.2 - - - +
193A CYS* 2.9 62.1 + - + +
195A GLU 5.1 0.4 - - - -
208A ILE* 3.7 33.7 - - + -
210A VAL* 3.6 20.9 - - + -
227A PHE* 3.9 13.7 - + - -
229A ILE* 4.7 8.7 - - + -
232A ILE* 4.0 12.3 - - + -
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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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131A CYS* 3.1 2.6 - - - +
132A GLU 2.8 34.7 + - - -
134A LYS* 5.9 3.1 - - - -
140A PHE* 1.3 75.7 + - - +
142A CYS* 1.3 70.4 + - - +
143A TRP* 3.5 41.5 - - + -
190A SER* 4.2 9.6 - - - +
191A VAL 3.3 14.4 - - - +
192A GLU* 4.0 17.7 - - + +
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Residues in contact with CYS 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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129A LEU* 5.4 2.2 - - + -
130A ARG 3.1 5.2 - - - +
131A CYS* 2.1 45.3 - - - -
140A PHE* 3.8 21.5 - - - -
141A THR* 1.3 75.5 - - - +
143A TRP* 1.3 61.9 + - - +
144A TRP* 4.3 10.8 - - + -
190A SER* 3.1 6.6 - - - -
191A VAL* 2.9 47.0 + - + +
193A CYS* 5.6 0.4 - - - -
210A VAL* 4.0 15.3 - - + -
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Residues in contact with TRP 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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120A GLN* 3.9 5.0 - - - +
129A LEU* 3.6 1.7 - - - -
130A ARG* 2.7 50.3 + - + +
132A GLU* 3.8 37.0 - - + -
141A THR* 3.5 43.1 - - + -
142A CYS* 1.3 74.3 - - - +
144A TRP* 1.3 68.2 + - - +
176A SER* 4.2 2.8 + - - -
188A GLU* 3.5 34.4 + - + +
189A TYR 3.1 6.7 - - - -
190A SER* 3.5 23.6 + - - -
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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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117A LEU* 3.3 30.1 - - + -
120A GLN* 4.0 4.7 - - - -
128A PHE 3.4 19.3 - - - +
129A LEU* 3.7 19.5 - - + -
142A CYS* 4.3 10.1 - - + -
143A TRP* 1.3 84.9 - - - +
145A LEU* 1.3 66.3 + - - +
154A PHE* 3.4 33.9 - + + -
156A VAL* 3.6 23.8 - - + -
173A ALA* 3.4 26.5 - - + -
187A TYR 3.9 0.2 - - - +
188A GLU* 3.4 4.2 - - - +
189A TYR* 2.9 52.3 + + + +
191A VAL* 3.8 22.7 - - + -
212A VAL* 3.9 19.5 - - + -
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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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117A LEU* 3.4 9.8 - - - +
118A LYS* 2.9 48.1 + - + +
120A GLN* 4.3 29.8 + - + +
128A PHE 4.7 1.0 + - - -
143A TRP* 6.4 0.2 - - + -
144A TRP* 1.3 76.7 - - - +
146A THR* 1.3 62.1 + - - +
179A ARG* 3.7 15.7 - - - +
181A ARG* 5.7 2.2 - - - +
186A GLU* 3.7 31.9 - - + +
187A TYR 3.3 3.4 - - - +
188A GLU* 3.6 37.0 - - + +
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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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116A ILE* 2.8 26.5 + - - +
117A LEU* 4.4 7.4 - - - -
118A LYS* 4.7 3.8 - - - +
145A LEU* 1.3 76.0 - - - +
147A THR* 1.3 61.9 + - - +
148A ILE* 3.1 33.9 + - - +
152A LEU* 3.9 8.9 - - + +
154A PHE* 4.7 1.6 - - + -
186A GLU* 3.7 4.4 - - - -
187A TYR* 2.8 43.1 + - + +
189A TYR* 3.8 24.5 - - + -
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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