Contacts of the helix formed by residues 121 - 132 (chain A) in PDB entry 3HPD
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 PHE 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ASN* 1.3 73.4 - - - +
122A GLY* 1.3 60.8 + - - +
125A SER* 2.8 48.2 + - - -
143A GLY* 5.0 3.4 - - - -
146A GLU* 3.7 37.7 - - + -
147A ALA* 3.9 30.3 - - + -
150A LEU* 3.6 25.6 - - + +
164A VAL* 3.7 17.4 - - + +
165A THR 4.0 4.5 + - - +
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Residues in contact with GLY 122 (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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96A ALA 4.3 2.4 - - - +
97A GLY* 5.1 0.3 - - - -
120A ASN* 3.1 6.8 + - - -
121A PHE* 1.3 81.5 - - - +
123A GLU* 1.3 56.6 + - - +
125A SER* 2.9 17.7 + - - -
126A ALA* 3.0 20.4 + - - +
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Residues in contact with GLU 123 (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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92A ASP* 4.4 5.4 - - - +
93A PRO* 3.6 23.5 - - + +
94A VAL* 3.4 9.8 - - - +
95A GLY* 2.9 23.2 + - - +
96A ALA* 3.6 23.7 - - + +
118A LYS* 5.2 0.3 + - - -
119A GLY* 3.4 9.8 - - - -
120A ASN* 2.8 53.2 + - - +
122A GLY* 1.3 73.1 - - - +
124A ILE* 1.3 63.1 + - - +
126A ALA* 3.4 3.5 + - - +
127A LEU* 3.1 27.9 + - - +
300A PO4 4.7 3.4 + - - -
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Residues in contact with ILE 124 (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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93A PRO* 4.3 8.3 - - + -
117A LEU* 3.9 30.5 - - + -
119A GLY* 3.8 32.3 - - - +
120A ASN 3.1 16.4 + - - +
123A GLU* 1.3 74.6 - - - +
125A SER* 1.3 67.0 + - - +
127A LEU* 3.2 6.0 + - + +
128A LEU* 3.0 22.2 + - - +
150A LEU* 4.1 19.1 - - + -
154A ALA* 3.7 28.5 - - + -
158A PHE* 5.8 0.4 - - + -
162A VAL* 4.2 4.0 - - + -
163A ALA 4.2 2.7 - - - +
164A VAL* 4.1 15.5 - - + -
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Residues in contact with SER 125 (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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121A PHE* 2.8 38.4 + - - -
122A GLY* 2.9 15.1 + - - -
124A ILE* 1.3 77.1 - - - +
126A ALA* 1.3 57.1 + - - +
128A LEU* 3.5 0.9 + - - +
129A GLY* 2.9 26.5 + - - -
150A LEU* 3.8 24.1 - - - +
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Residues in contact with ALA 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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96A ALA* 4.3 0.7 - - + -
97A GLY* 3.5 33.2 - - - +
103A THR* 4.5 4.0 - - + +
122A GLY 3.0 19.3 + - - +
123A GLU 3.6 4.9 - - - +
125A SER* 1.3 78.9 + - - +
127A LEU* 1.3 57.5 + - - +
129A GLY* 3.9 0.8 - - - -
130A GLU* 2.9 31.9 + - - +
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Residues in contact with LEU 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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93A PRO* 3.9 29.2 - - + -
96A ALA* 3.9 12.1 - - + -
103A THR* 4.0 12.3 - - + +
106A SER* 3.5 24.0 - - - -
107A LEU* 3.7 19.1 - - + +
110A LEU* 4.0 18.2 - - + -
117A LEU* 4.2 12.8 - - + -
123A GLU 3.1 15.7 + - - +
124A ILE* 3.2 9.8 + - + +
126A ALA* 1.3 75.0 - - - +
128A LEU* 1.3 60.5 + - - +
130A GLU* 4.7 1.1 - - - -
131A GLU* 3.0 31.4 + - - +
158A PHE* 3.6 15.2 - - + -
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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 ILE 3.0 16.8 + - - +
125A SER 4.0 2.9 - - - +
127A LEU* 1.3 76.5 - - - +
129A GLY* 1.3 63.3 + - - +
131A GLU* 3.7 2.5 + - - +
132A GLY* 3.2 18.0 + - - -
150A LEU* 3.6 25.8 - - + -
153A ASN* 3.8 30.5 - - + +
154A ALA* 4.1 8.7 - - + +
157A GLU* 3.6 40.4 - - + +
158A PHE* 4.3 6.7 - - + -
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Residues in contact with GLY 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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125A SER 2.9 17.1 + - - -
126A ALA* 3.9 1.1 - - - -
128A LEU* 1.3 76.3 - - - +
130A GLU* 1.3 64.3 + - - +
132A GLY 3.3 17.7 + - - +
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Residues in contact with GLU 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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103A THR* 3.8 20.1 - - + +
107A LEU* 3.8 20.1 - - + +
126A ALA 2.9 18.4 + - - +
129A GLY* 1.3 76.0 - - - +
131A GLU* 1.3 65.1 + - - +
132A GLY 3.3 5.5 + - - -
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Residues in contact with GLU 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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107A LEU* 3.6 23.9 - - + +
127A LEU 3.0 20.9 + - - +
128A LEU* 3.8 5.6 - - - +
130A GLU* 1.3 78.4 - - - +
132A GLY* 1.3 59.5 + - - +
157A GLU* 3.5 28.9 - - + +
158A PHE* 3.8 23.1 - - + -
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Residues in contact with GLY 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 LEU 3.2 11.1 + - - -
129A GLY 3.3 13.7 + - - +
130A GLU 3.2 4.8 - - - -
131A GLU* 1.3 83.8 - - - +
157A GLU* 5.5 5.8 + - - -
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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