Contacts of the helix formed by residues 127 - 136 (chain A) in PDB entry 1PHP
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 ASP 127 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A GLY* 3.0 31.0 + - - +
125A LYS* 3.3 10.3 - - + +
126A ASN* 1.3 75.7 - - - +
128A PRO* 1.3 69.6 - - - +
129A GLU* 3.0 27.4 + - - +
130A LEU* 2.9 14.0 + - - +
131A ALA* 2.9 25.4 + - - +
154A ALA* 4.3 0.9 - - - +
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Residues in contact with PRO 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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126A ASN 3.3 7.8 - - - +
127A ASP* 1.3 90.1 - - - +
129A GLU* 1.3 58.7 + - + +
131A ALA* 3.7 8.0 - - + +
132A LYS* 2.9 44.7 + - - +
162A TYR* 3.7 18.6 - - - +
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Residues in contact with GLU 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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127A ASP* 3.0 17.8 + - - +
128A PRO* 1.3 77.0 - - + +
130A LEU* 1.3 64.8 - - - +
132A LYS* 2.9 38.1 + - - +
133A ALA* 3.2 22.0 + - - +
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Residues in contact with LEU 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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95A VAL* 4.0 31.4 - - + -
120A TYR* 3.9 26.0 - - + -
122A GLY* 3.5 5.6 - - - +
123A GLU* 3.3 38.6 - - + +
127A ASP* 2.9 20.2 + - + +
129A GLU* 1.3 76.3 - - - +
131A ALA* 1.3 66.3 + - - +
133A ALA* 3.2 6.1 + - + +
134A PHE* 3.1 39.6 + - + -
154A ALA* 4.0 6.5 - - + -
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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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126A ASN* 4.9 0.2 - - - +
127A ASP 2.9 12.6 + - - +
128A PRO* 3.7 10.1 - - + +
130A LEU* 1.3 78.1 - - - +
132A LYS* 1.3 55.6 + - - +
134A PHE* 3.4 9.4 + - - +
135A ALA* 2.9 27.9 + - - +
154A ALA* 4.0 11.3 - - + +
158A GLY* 3.5 37.7 - - - +
159A ILE* 3.6 6.4 - - - +
162A TYR* 3.9 8.7 - - + -
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Residues in contact with LYS 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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128A PRO* 2.9 25.3 + - - +
129A GLU* 2.9 39.1 + - - +
130A LEU 3.3 0.2 - - - -
131A ALA* 1.3 72.6 - - - +
133A ALA* 1.3 57.3 + - - +
135A ALA* 3.1 7.0 + - - +
136A GLU* 2.9 35.0 + - - +
162A TYR* 3.5 41.4 + - + -
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Residues in contact with ALA 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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95A VAL* 3.9 26.9 - - + +
100A LYS* 5.7 0.2 - - - -
129A GLU 3.2 14.3 + - - +
130A LEU* 3.5 11.2 - - + +
132A LYS* 1.3 75.3 - - - +
134A PHE* 1.3 61.0 + - - +
136A GLU* 3.5 29.9 - - - +
137A LEU* 3.6 13.0 - - - +
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Residues in contact with PHE 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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17A PHE* 3.8 29.7 - + + -
94A ALA* 3.7 21.5 - - + -
95A VAL* 3.5 26.5 - - + -
114A LEU* 5.0 0.7 - - + -
117A VAL* 3.9 25.8 - - + -
120A TYR* 5.5 1.8 - + - -
123A GLU* 3.8 18.8 - - - -
130A LEU* 3.1 37.0 + - + -
131A ALA* 3.5 6.1 - - - +
133A ALA* 1.3 72.6 - - - +
135A ALA* 1.3 66.5 - - - +
137A LEU* 3.1 24.8 + - + +
138A ALA* 4.2 1.6 + - - +
154A ALA* 4.1 17.3 - - + -
155A SER* 4.0 10.1 - - - -
159A ILE* 3.7 16.7 - - + +
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Residues in contact with ALA 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 2.9 16.0 + - - +
132A LYS* 3.1 5.1 + - - +
134A PHE* 1.3 77.4 - - - +
136A GLU* 1.3 60.8 + - - +
137A LEU 3.1 1.2 + - - -
138A ALA 3.3 21.5 + - - +
159A ILE* 4.0 7.4 - - + -
162A TYR* 3.6 31.0 - - + -
163A LEU* 3.9 26.4 - - + +
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Residues in contact with GLU 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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15A ARG* 3.5 14.9 + - - -
100A LYS* 2.9 40.9 + - - +
132A LYS* 2.9 15.0 + - - +
133A ALA* 3.5 24.9 - - - +
134A PHE 3.2 0.2 - - - -
135A ALA* 1.3 74.8 - - - +
137A LEU* 1.3 60.1 + - + +
138A ALA 3.6 0.2 + - - -
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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