Contacts of the helix formed by residues 119 - 130 (chain A) in PDB entry 1HK2
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 GLU 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A PRO* 1.3 82.5 - - - +
120A VAL* 1.3 73.0 + - - +
121A ASP* 4.7 3.1 - - + +
122A VAL* 2.7 39.8 + - + +
123A MET* 3.1 5.5 + - - +
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Residues in contact with VAL 120 (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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118A PRO 3.9 2.6 + - - -
119A GLU* 1.3 77.3 + - - +
121A ASP* 1.3 70.5 + - - +
123A MET* 2.8 22.3 + - - +
124A CYS* 3.1 18.8 + - - -
174A LYS* 4.4 12.6 - - + -
175A ALA* 3.2 47.3 - - + +
178A LEU* 4.3 18.3 - - + +
179A LEU* 4.6 17.0 - - + -
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Residues in contact with ASP 121 (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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119A GLU* 3.3 2.8 - - + +
120A VAL* 1.3 84.3 - - - +
122A VAL* 1.3 63.2 + - + +
124A CYS* 3.7 9.6 - - - +
125A THR* 2.8 34.2 + - - +
174A LYS* 4.9 16.8 + - - +
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Residues in contact with VAL 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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118A PRO* 4.2 15.3 - - + -
119A GLU* 2.7 45.2 + - + +
121A ASP* 1.3 75.0 - - + +
123A MET* 1.3 60.9 + - - +
125A THR* 3.6 8.0 - - - -
126A ALA* 3.5 14.7 + - - +
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Residues in contact with MET 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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117A ARG* 4.5 15.7 - - + -
118A PRO* 4.1 32.1 - - + +
119A GLU 3.7 12.1 - - - +
120A VAL* 2.8 12.7 + - - +
122A VAL* 1.3 74.7 - - - +
124A CYS* 1.3 52.8 + - - +
126A ALA* 2.6 31.3 + - - +
127A PHE* 2.7 16.9 + - - +
134A PHE* 3.9 11.5 - - + -
161A TYR* 4.2 10.1 - - - +
165A PHE* 3.6 34.5 - - + -
178A LEU* 4.7 5.4 - - + -
179A LEU* 6.2 1.1 - - - -
182A LEU* 4.7 13.5 - - + -
186A ARG* 5.6 2.9 - - - +
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Residues in contact with CYS 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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120A VAL* 3.1 26.4 + - - +
121A ASP* 3.7 12.1 - - - +
123A MET* 1.3 78.0 - - - +
125A THR* 1.3 58.0 + - - +
127A PHE* 2.7 22.1 + - - -
128A HIS* 2.8 23.8 + - + -
165A PHE* 4.4 2.2 - - - -
168A CYS 5.0 0.4 - - - -
169A CYS* 2.0 59.5 - - + +
174A LYS* 5.3 3.8 - - - -
178A LEU* 4.9 3.6 - - - -
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Residues in contact with THR 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 ASP* 2.8 25.5 + - - +
122A VAL* 3.6 8.3 - - - -
124A CYS* 1.3 75.5 - - - +
126A ALA* 1.3 56.4 + - - +
128A HIS* 3.9 6.2 - - - +
129A ASP* 2.9 35.2 + - + +
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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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122A VAL 3.5 8.7 + - - +
123A MET* 2.6 19.6 + - - +
125A THR* 1.3 72.2 - - - +
127A PHE* 1.3 62.0 + - - -
128A HIS 3.0 2.7 + - - -
129A ASP* 4.3 5.4 - - - -
130A ASN* 3.0 27.4 + - - +
134A PHE* 4.0 16.2 - - + -
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Residues in contact with PHE 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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123A MET 2.7 11.4 + - - +
124A CYS* 2.7 7.9 + - - +
126A ALA* 1.3 72.3 - - - +
128A HIS* 1.3 78.2 + + - +
131A GLU* 3.1 56.5 - - + +
134A PHE* 3.5 31.6 - + + -
135A LEU* 5.4 2.0 - - + -
162A LYS* 3.9 12.6 - - + -
165A PHE* 2.9 62.6 - - + -
166A THR* 3.2 23.8 - - + -
169A CYS* 4.0 4.3 - - - -
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Residues in contact with HIS 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 CYS* 2.8 32.7 + - + +
125A THR* 4.0 4.7 - - - +
127A PHE* 1.3 97.9 + + - +
129A ASP* 1.3 68.2 + - - +
130A ASN* 3.0 5.5 + - - -
131A GLU* 4.1 3.5 + - - +
165A PHE 5.0 0.2 - - - -
169A CYS* 3.4 31.3 + - + +
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Residues in contact with ASP 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 THR* 2.9 28.6 + - + +
126A ALA* 4.2 5.2 - - - +
128A HIS* 1.3 74.0 - - - +
130A ASN* 1.3 66.5 + - + +
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Residues in contact with ASN 130 (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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126A ALA 3.0 18.5 + - - +
128A HIS 3.0 0.8 + - - -
129A ASP* 1.3 87.3 + - + +
131A GLU* 1.3 61.4 + - - +
132A GLU* 3.5 6.9 + - - +
133A THR* 3.4 35.5 + - - -
134A PHE* 3.4 14.2 + - - +
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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