Contacts of the helix formed by residues 127 - 139 (chain A) in PDB entry 1HF0
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 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A LYS 4.5 4.7 - - - +
126A PRO* 1.3 75.2 - - - +
128A SER* 1.3 57.0 + - - +
129A GLU* 3.2 21.7 + - - +
130A GLU* 2.6 37.7 + - - +
131A ILE* 2.7 37.5 + - - +
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Residues in contact with SER 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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127A THR* 1.3 72.3 - - - +
129A GLU* 1.3 70.8 + - - +
131A ILE* 3.0 8.0 - - - +
132A THR 2.9 15.6 + - - -
142A LYS* 2.6 37.6 + - - +
1N C 6.0 9.0 - - - -
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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 THR* 3.2 20.1 + - - +
128A SER* 1.3 79.7 + - - +
130A GLU* 1.3 60.5 + - + +
131A ILE 2.9 1.6 - - - -
132A THR* 2.6 30.1 + - - +
133A MET* 2.8 17.3 + - + +
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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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123A ASN* 3.4 18.0 + - - -
126A PRO* 3.2 15.4 - - + +
127A THR* 2.6 48.9 + - - +
129A GLU* 1.3 78.3 - - + +
131A ILE* 1.3 57.2 + - - +
133A MET* 3.2 25.6 + - + +
134A ILE* 2.8 37.6 + - + +
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Residues in contact with ILE 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 PRO* 4.0 28.3 - - + +
127A THR 2.7 24.2 + - - +
128A SER* 3.0 14.4 - - - +
129A GLU 2.9 0.2 - - - -
130A GLU* 1.3 74.0 - - - +
132A THR* 1.3 57.5 + - - +
134A ILE* 3.3 7.8 + - - +
135A ALA* 2.8 28.6 + - - +
142A LYS* 3.6 31.2 - - + +
145A ILE* 3.5 22.3 - - + +
146A ARG* 3.8 33.0 - - + +
149A PHE* 5.4 3.6 - - + -
1N C 5.9 0.2 - - - -
2N T 5.0 6.3 - - - +
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Residues in contact with THR 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 SER 2.9 4.7 + - - -
129A GLU* 2.6 20.6 + - - -
131A ILE* 1.3 69.4 - - - +
133A MET* 1.3 65.8 + - + +
135A ALA* 3.4 2.7 + - + +
136A ASP* 2.9 36.3 + - - +
142A LYS* 2.7 39.9 - - + +
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Residues in contact with MET 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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129A GLU* 2.8 14.2 + - + +
130A GLU* 3.5 29.6 - - + +
132A THR* 1.3 77.3 - - + +
134A ILE* 1.3 59.7 + - + +
136A ASP* 3.4 5.3 - - - +
137A GLN* 2.7 34.4 + - - +
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Residues in contact with ILE 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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116A LEU* 3.9 16.4 - - + -
119A SER* 3.5 27.8 - - - +
126A PRO* 4.1 19.3 - - + -
130A GLU* 2.8 34.1 + - + +
131A ILE* 3.8 5.8 - - - +
133A MET* 1.3 74.8 - - + +
135A ALA* 1.3 63.4 + - - +
137A GLN* 3.3 13.2 + - - +
138A LEU* 3.0 51.1 + - + +
145A ILE* 4.1 7.6 - - + -
149A PHE* 4.2 9.0 - - + -
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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 ILE 2.8 21.6 + - - +
132A THR* 3.7 4.9 - - - +
134A ILE* 1.3 72.7 - - - +
136A ASP* 1.3 51.5 + - - +
138A LEU* 3.1 1.4 + - - -
139A ASN* 2.6 33.3 + - - -
140A MET* 2.9 29.4 + - - +
142A LYS* 3.8 24.0 - - + +
145A ILE* 3.8 15.0 - - + +
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Residues in contact with ASP 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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132A THR* 2.9 31.9 + - - +
133A MET* 3.4 6.3 - - - +
135A ALA* 1.3 75.8 - - - +
137A GLN* 1.3 60.0 + - - +
138A LEU 2.9 5.5 + - - -
139A ASN* 3.0 24.7 + - - +
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Residues in contact with GLN 137 (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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115A ALA* 5.5 3.3 - - - +
133A MET* 2.7 21.2 + - + +
134A ILE* 3.6 14.5 + - - +
136A ASP* 1.3 72.6 - - - +
138A LEU* 1.3 75.2 + - - +
139A ASN* 5.0 2.6 - - - +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A ILE* 4.5 26.6 - - + +
115A ALA* 3.8 27.1 - - + -
116A LEU* 3.8 22.7 - - + -
134A ILE* 3.0 39.4 + - + +
135A ALA 3.8 0.7 - - - +
136A ASP 3.0 0.4 - - - -
137A GLN* 1.3 96.6 - - + +
139A ASN* 1.3 75.4 + - - +
140A MET* 3.8 17.7 - - + +
145A ILE* 4.3 8.5 - - + -
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Residues in contact with ASN 139 (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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135A ALA 2.6 14.0 + - - -
136A ASP* 3.0 18.3 + - - +
137A GLN 5.0 2.1 - - - +
138A LEU* 1.3 79.6 - - - +
140A MET* 1.3 62.8 + - - +
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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