Contacts of the helix formed by residues 123 - 135 (chain B) in PDB entry 1P27
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 THR 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B TRP* 3.7 6.9 - - - +
121B TYR* 3.3 4.9 - - - +
122B GLU* 1.3 85.7 + - - +
124B TYR* 1.4 64.8 + - - +
125B LYS* 3.3 23.6 - - + +
126B GLU* 3.4 33.2 + - + +
127B ALA* 3.3 17.0 + - - +
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Residues in contact with TYR 124 (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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66B PRO* 4.0 15.3 - - + +
73B TRP* 3.4 49.3 - + + +
123B THR* 1.4 73.7 - - - +
125B LYS* 1.3 63.9 + - + +
127B ALA* 3.2 4.1 + - - +
128B GLN* 3.0 63.5 + - + +
148B TRP* 3.3 31.1 - + - -
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Residues in contact with LYS 125 (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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123B THR* 3.3 13.9 - - + +
124B TYR* 1.3 86.3 - - + +
126B GLU* 1.3 60.1 + - + +
128B GLN* 4.2 4.0 - - - +
129B ALA* 3.3 23.6 + - + +
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Residues in contact with GLU 126 (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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96B TYR 3.0 25.5 - - - +
97B GLY* 3.6 11.5 - - - -
98B GLU* 3.6 17.2 + - - +
121B TYR* 3.7 10.7 - - + +
122B GLU* 3.6 14.5 + - - +
123B THR* 3.4 39.8 + - + +
125B LYS* 1.3 76.2 - - + +
127B ALA* 1.4 59.3 + - - +
129B ALA* 3.3 5.5 + - - +
130B ALA* 3.0 27.2 + - - +
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Residues in contact with ALA 127 (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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73B TRP* 4.0 18.6 - - + +
75B LEU* 3.5 19.3 - - + +
121B TYR* 3.6 24.4 - - + -
123B THR 3.3 4.1 + - - +
124B TYR 3.2 6.3 + - - +
126B GLU* 1.4 79.1 - - - +
128B GLN* 1.3 57.4 + - - +
130B ALA 3.5 0.3 + - - -
131B MET* 3.0 23.9 + - - +
148B TRP* 3.8 25.1 - - + -
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Residues in contact with GLN 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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124B TYR* 3.0 51.5 + - + +
125B LYS* 4.2 5.2 - - - +
127B ALA* 1.3 75.5 - - - +
129B ALA* 1.3 62.1 + - - +
131B MET* 3.1 8.0 + - + +
132B GLU* 2.9 49.2 + - - +
148B TRP* 4.0 16.2 + - + -
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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
----------------------------------------------------------
96B TYR* 3.4 26.8 - - + +
125B LYS* 3.3 18.3 + - + +
126B GLU* 3.3 6.5 + - - +
128B GLN* 1.3 78.5 - - - +
130B ALA* 1.4 59.6 + - - +
132B GLU* 3.6 4.0 + - - +
133B GLY* 3.0 23.7 + - - -
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Residues in contact with ALA 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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75B LEU* 4.1 5.8 - - + -
93B PHE* 4.4 5.6 - - + -
96B TYR* 3.5 25.5 - - + -
121B TYR* 3.2 34.1 - - + +
126B GLU 3.0 12.0 + - - +
127B ALA 3.7 5.4 - - - +
129B ALA* 1.4 75.8 - - - +
131B MET* 1.3 58.3 + - - +
134B LEU* 2.9 35.6 + - - +
146B VAL* 4.7 0.6 - - - +
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Residues in contact with MET 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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75B LEU* 3.7 12.9 - - + +
127B ALA 3.0 11.3 + - - +
128B GLN* 3.1 9.6 + - - +
130B ALA* 1.3 75.8 - - - +
132B GLU* 1.3 62.1 + - + +
135B ASN* 3.1 33.2 + - + +
146B VAL* 3.5 33.9 - - + +
147B ASP* 3.8 7.9 - - - +
148B TRP* 3.3 63.7 - - + +
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Residues in contact with GLU 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 GLN* 2.9 39.2 + - - +
129B ALA* 4.3 3.6 - - - +
131B MET* 1.3 80.2 - - + +
133B GLY* 1.3 59.7 + - - +
134B LEU 3.6 0.2 - - - -
135B ASN* 4.8 4.5 + - - +
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Residues in contact with GLY 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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96B TYR* 3.9 16.4 + - - -
129B ALA 3.0 17.6 + - - -
130B ALA 4.0 0.2 - - - -
132B GLU* 1.3 79.1 - - - +
134B LEU* 1.3 63.0 + - - +
135B ASN 3.8 0.7 - - - -
137B GLN* 3.1 21.0 - - - +
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Residues in contact with LEU 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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92B LYS* 3.3 50.3 - - + +
93B PHE* 3.6 34.5 - - + -
96B TYR* 3.8 22.4 - - + +
130B ALA 2.9 16.5 + - - +
133B GLY* 1.3 80.6 - - - +
135B ASN* 1.3 65.4 + - - +
136B GLY 3.3 0.9 + - - -
137B GLN* 3.3 23.9 + - + +
144B ILE* 3.6 19.3 - - + +
146B VAL* 3.8 11.7 - - + -
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Residues in contact with ASN 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 MET* 3.1 21.8 + - + +
132B GLU* 4.8 4.3 - - - +
133B GLY 3.8 1.4 - - - +
134B LEU* 1.3 75.8 + - - +
136B GLY* 1.3 61.0 + - - +
137B GLN* 3.2 11.8 + - - +
145B SER* 3.2 16.6 - - - +
146B VAL* 3.0 41.6 + - - +
147B ASP* 5.0 2.0 + - - -
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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