Contacts of the helix formed by residues 127 - 135 (chain B) in PDB entry 4P46
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 SER 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A TYR* 3.3 21.8 - - - +
122A GLN 3.3 29.2 - - - -
123A LEU* 4.2 4.9 - - - +
125B GLU 3.5 3.0 + - - -
126B PRO* 1.3 75.9 - - - +
128B GLU* 1.3 64.9 + - - +
129B ALA* 3.9 7.4 - - - -
130B GLU* 3.1 23.3 + - - +
131B ILE* 3.4 19.8 + - - +
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PRO 3.7 5.4 + - - +
127B SER* 1.3 73.3 - - - +
129B ALA* 1.3 57.3 + - - +
131B ILE* 3.2 23.6 + - - +
132B SER* 2.9 30.9 + - - -
197B TRP* 5.1 4.3 + - - -
238B ARG* 5.3 11.7 + - - +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A TYR* 4.0 2.9 - - + -
198A PHE* 5.0 1.9 - - + -
200A PRO* 3.5 37.2 - - + -
201A SER* 5.1 3.4 - - - +
127B SER* 3.1 7.4 - - - +
128B GLU* 1.3 76.6 - - - +
130B GLU* 1.3 66.7 + - - +
132B SER* 3.2 17.1 + - - -
133B HIS* 3.3 17.8 + - - +
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A TYR* 3.4 35.7 - - + -
135A LEU* 6.2 0.2 - - + -
126B PRO* 5.5 0.7 - - + -
127B SER* 3.1 26.7 + - - +
129B ALA* 1.3 74.7 - - - +
131B ILE* 1.3 64.9 + - + +
134B THR* 2.9 32.4 + - - +
136B LYS 3.8 7.6 - - - +
138B THR* 5.1 14.6 - - - +
191B ARG* 5.7 1.3 - - - +
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PRO* 4.2 7.4 - - + +
127B SER 3.4 14.3 + - - +
128B GLU* 3.2 27.6 + - - +
129B ALA 3.1 0.2 - - - -
130B GLU* 1.3 77.1 - - - +
132B SER* 1.3 60.9 + - - +
135B GLN* 3.0 29.3 + - - +
136B LYS 3.6 7.4 - - - +
137B ALA* 4.0 19.1 - - + -
194B ALA* 3.6 20.2 - - + -
197B TRP* 3.6 33.4 - - + +
198B GLN* 3.9 17.3 - - + +
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Residues in contact with SER 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLU 2.9 16.7 + - - -
129B ALA* 3.2 9.1 + - - -
131B ILE* 1.3 77.0 - - - +
133B HIS* 1.3 57.1 + - - +
135B GLN* 6.3 0.4 - - - -
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Residues in contact with HIS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASP* 2.7 34.7 + - - -
119A ALA* 5.1 0.9 - - + -
121A TYR* 3.1 22.9 + - - +
198A PHE* 4.1 37.0 - + + +
129B ALA 3.3 16.1 + - - +
130B GLU 4.0 1.3 - - - +
131B ILE 3.2 1.0 + - - -
132B SER* 1.3 78.3 - - - +
134B THR* 1.3 64.8 + - + +
135B GLN* 3.8 2.4 - - - +
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Residues in contact with THR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASP* 5.0 2.5 - - - +
121A TYR* 3.5 24.9 - - + +
138A ASP* 4.3 6.5 - - - +
130B GLU* 2.9 16.5 + - - +
133B HIS* 1.3 91.6 - - + +
135B GLN* 1.3 64.2 + - - +
136B LYS* 2.8 50.5 + - - +
191B ARG* 3.7 20.5 + - - +
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Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ILE 3.0 16.9 + - - +
132B SER 6.3 0.4 - - - -
133B HIS 5.4 1.6 - - - +
134B THR* 1.3 78.7 + - - +
136B LYS* 1.3 55.5 + - + +
193B SER* 3.7 5.2 - - - -
194B ALA* 2.7 37.2 + - + +
195B THR* 4.6 1.0 + - - -
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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