Contacts of the strand formed by residues 133 - 141 (chain A) in PDB entry 4PTJ
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 TRP 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A LEU* 4.0 21.3 - - + +
107A ALA* 3.6 24.0 - - + -
108A GLN 3.6 11.9 - - - -
109A LYS 3.8 2.9 - - - -
110A LEU* 3.5 38.2 - - + +
129A GLU* 3.1 33.3 + - - +
130A PRO* 3.1 15.2 + - + +
131A ASP 3.2 2.2 + - - -
132A ASP* 1.3 89.3 + - + +
134A GLU* 1.3 61.0 + - - +
135A SER 3.9 1.6 + - - -
156A LEU* 3.9 36.5 - - + +
157A GLU 3.4 7.4 - - - -
158A ARG* 3.3 37.7 - - + -
159A ARG* 3.7 13.1 + - - -
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Residues in contact with GLU 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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133A TRP* 1.3 72.8 - - - +
135A SER* 1.3 73.2 + - - +
136A VAL* 3.4 17.7 + - + +
156A LEU* 3.2 3.8 - - - -
157A GLU* 2.8 41.9 + - + +
159A ARG* 3.0 50.1 + - + +
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Residues in contact with SER 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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133A TRP 3.9 1.6 + - - -
134A GLU* 1.3 82.5 - - - +
136A VAL* 1.3 59.1 + - - +
137A PHE 3.6 7.0 + - - -
138A SER* 4.5 5.2 - - - -
154A GLU* 3.1 28.0 - - - +
155A ILE 3.6 1.1 - - - -
156A LEU* 3.5 19.0 - - - +
159A ARG* 5.1 1.4 - - - +
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Residues in contact with VAL 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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134A GLU* 3.4 21.0 + - + +
135A SER* 1.3 75.3 - - - +
137A PHE* 1.3 61.1 + - + +
155A ILE* 2.9 34.3 + - + +
157A GLU* 4.1 28.5 - - + +
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Residues in contact with PHE 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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30A TRP* 4.0 32.3 - + - -
135A SER* 3.6 1.6 + - - -
136A VAL* 1.3 81.1 - - + +
138A SER* 1.3 64.1 + - - +
139A GLU* 3.7 43.7 - - + -
153A PHE* 3.8 9.6 - - + -
154A GLU* 3.2 8.0 - - - +
155A ILE* 3.0 50.9 + - + -
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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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135A SER* 4.5 8.5 - - - -
137A PHE* 1.3 79.2 - - - +
139A GLU* 1.3 62.8 + - - +
140A PHE* 4.3 3.0 + - - +
152A CSD 5.2 6.2 - - - +
153A PHE 3.2 7.7 + - - -
154A GLU* 4.5 6.7 - - - -
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Residues in contact with GLU 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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30A TRP* 5.4 1.2 - - - -
137A PHE* 3.7 32.2 - - + -
138A SER* 1.3 75.5 + - - +
140A PHE* 1.3 61.8 + - - +
141A HIS* 4.1 20.9 + - + +
151A TYR 4.1 0.9 - - - +
152A CSD 3.4 2.0 - - - -
153A PHE* 2.9 60.9 + - + +
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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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116A ASP* 5.6 2.2 - - - -
138A SER* 4.3 2.7 - - - +
139A GLU* 1.3 75.7 - - - +
141A HIS* 1.3 84.4 + - - +
142A ASP* 3.7 35.7 - - - -
150A SER* 4.5 9.0 - - - -
151A TYR 3.6 8.3 - - - +
152A CSD 4.1 17.5 - - + +
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Residues in contact with HIS 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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26A ALA* 5.2 3.8 - - + -
139A GLU* 4.1 26.4 + - + +
140A PHE* 1.3 88.7 - - - +
142A ASP* 1.3 65.6 + - - +
144A ASP* 5.6 2.0 + - - -
150A SER* 3.3 4.0 - - - -
151A TYR* 2.7 75.7 + + + +
153A PHE* 5.0 6.7 - + - -
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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