Contacts of the helix formed by residues 125 - 135 (chain A) in PDB entry 2BEW
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 PRO 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ASP 3.7 7.4 - - - +
124A TYR* 1.3 100.3 - - + +
126A LEU* 1.3 64.5 + - - +
127A GLU* 4.0 13.5 - - + +
128A LEU* 2.8 38.8 + - + +
129A PHE* 3.2 11.5 + - - -
155A ARG* 3.9 13.0 - - - +
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Residues in contact with LEU 126 (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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66A LEU* 4.3 17.5 - - + -
70A MET* 4.0 23.8 - - - -
120A MET* 4.0 23.3 - - + -
124A TYR 3.5 2.4 + - - -
125A PRO* 1.3 70.5 - - - +
127A GLU* 1.3 63.4 + - - +
129A PHE* 3.3 7.5 + - + +
130A MET* 3.0 28.2 + - + +
344A LYS* 3.6 43.3 - - + +
345A VAL* 4.0 14.6 - - + +
348A ALA* 3.6 16.3 - - + +
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Residues in contact with GLU 127 (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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125A PRO* 3.1 10.2 - - + +
126A LEU* 1.3 79.0 - - - +
128A LEU* 1.3 69.0 + - + +
130A MET* 3.8 2.7 - - - +
131A ALA* 2.9 25.5 + - - +
138A SER* 3.9 5.4 + - - -
348A ALA* 4.1 12.4 - - + +
351A GLN* 3.3 30.1 + - - +
352A ALA* 5.4 2.6 - - + +
355A LYS* 2.7 29.0 + - - +
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Residues in contact with LEU 128 (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* 3.4 41.3 + - + +
125A PRO* 2.8 29.0 + - + +
127A GLU* 1.3 91.1 - - + +
129A PHE* 1.3 66.1 + - - +
130A MET 3.2 0.7 - - - -
131A ALA* 3.8 4.0 - - + +
132A GLN* 3.1 23.7 + - - +
138A SER* 3.7 26.2 - - - +
139A ASP* 5.1 1.6 - - - +
140A LEU* 5.2 16.8 - - + +
152A CYS* 5.9 0.4 - - - -
155A ARG* 5.1 4.0 - - - +
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Residues in contact with PHE 129 (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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70A MET* 3.8 29.2 - - + -
74A LEU* 5.4 1.1 - - + -
116A ALA* 3.8 14.6 - - + -
119A LEU* 3.7 22.7 - - + -
120A MET* 3.7 32.5 - - + -
124A TYR* 3.6 39.4 - + + -
125A PRO 3.2 20.0 + - - -
126A LEU* 3.7 10.8 - - - +
128A LEU* 1.3 77.5 - - - +
130A MET* 1.4 63.8 + - - +
132A GLN 3.4 0.3 + - - -
133A CYS* 3.2 20.6 + - - -
150A TYR* 3.5 51.6 - + - +
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Residues in contact with MET 130 (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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70A MET* 3.9 33.4 - - + -
73A ILE* 5.5 0.2 - - + -
74A LEU* 3.7 25.6 - - + -
126A LEU* 3.0 17.8 + - + +
127A GLU 4.3 1.8 - - - +
129A PHE* 1.4 80.0 - - - +
131A ALA* 1.3 61.7 + - - +
133A CYS* 3.2 4.2 + - - +
134A TYR* 3.0 38.9 + - + +
345A VAL* 3.9 24.9 - - + +
348A ALA* 3.6 10.3 - - + +
349A PHE* 3.1 44.0 - - + -
352A ALA* 3.8 15.0 - - + -
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Residues in contact with ALA 131 (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 GLU 2.9 20.4 + - - +
128A LEU* 3.8 7.4 - - - +
129A PHE 3.3 0.2 - - - -
130A MET* 1.3 75.1 - - - +
132A GLN* 1.3 58.4 + - - +
135A GLY* 2.8 24.1 + - - -
136A ASN* 3.1 40.4 + - - +
138A SER* 3.8 11.0 - - - +
139A ASP* 3.5 22.0 - - - +
352A ALA* 4.7 0.4 - - - +
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Residues in contact with GLN 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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124A TYR* 5.5 2.5 - - - +
128A LEU 3.1 15.9 + - - +
129A PHE 3.8 4.0 - - - +
131A ALA* 1.3 79.3 - - - +
133A CYS* 1.3 62.9 + - - +
135A GLY* 3.2 10.7 + - - -
139A ASP* 3.5 28.7 + - - +
141A GLY* 6.0 0.9 - - - -
143A GLY* 5.7 0.2 - - - -
145A GLN* 3.3 22.6 + - - +
146A MET 2.7 23.8 + - - -
147A PRO* 3.3 2.6 - - - +
148A VAL* 2.8 28.8 + - - -
149A HIS* 3.2 26.3 + - - +
150A TYR* 3.8 15.7 - - + -
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Residues in contact with CYS 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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74A LEU* 4.3 9.2 - - + -
83A ILE* 3.7 28.0 - - + +
84A SER 4.8 0.7 + - - -
86A TYR* 4.2 17.7 - - - -
129A PHE 3.2 13.6 + - - +
130A MET* 3.2 8.9 + - - +
132A GLN* 1.3 79.3 - - - +
134A TYR* 1.3 60.3 + - + +
135A GLY 3.7 0.2 + - - -
147A PRO* 3.5 31.3 - - + +
148A VAL 3.9 15.3 - - - -
150A TYR* 3.3 26.2 - - - -
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Residues in contact with TYR 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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74A LEU* 4.5 2.7 - - + -
77A SER* 3.0 17.0 + - - -
82A ARG* 3.4 20.4 - - + -
83A ILE* 3.5 18.4 - - + -
130A MET* 3.0 35.4 + - + +
133A CYS* 1.3 76.8 - - + +
135A GLY* 1.3 64.2 + - - +
136A ASN* 4.2 15.9 - - - +
349A PHE* 3.1 20.1 - + - -
352A ALA* 3.8 26.2 - - + +
353A GLU* 2.7 40.7 + - + -
357A LYS* 3.0 39.1 + - - +
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Residues in contact with GLY 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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131A ALA 2.8 9.8 + - - -
132A GLN 3.2 9.8 + - - -
133A CYS 3.4 0.2 - - - -
134A TYR* 1.3 79.8 - - - +
136A ASN* 1.3 60.7 + - - +
139A ASP* 4.6 0.9 - - - -
143A GLY* 3.8 25.6 - - - -
145A GLN 6.1 0.7 - - - -
357A LYS* 3.6 6.6 - - - +
358A PRO* 3.1 23.6 - - - +
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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