Contacts of the helix formed by residues 121 - 135 (chain A) in PDB entry 2HW7
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 HIS 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A GLN* 4.7 0.4 - - - +
120A GLY* 1.3 69.7 - - - -
122A ILE* 1.3 50.2 + - - +
123A ARG* 2.8 15.9 + - - +
124A SER* 2.9 28.8 + - - +
125A ARG* 3.6 6.1 + - + +
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Residues in contact with ILE 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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115A ILE* 4.8 12.1 - - + -
117A LYS* 4.9 10.5 - - + -
118A GLN* 3.2 43.3 - - + +
120A GLY 2.9 2.0 + - - +
121A HIS* 1.3 75.0 - - - +
123A ARG* 1.3 62.7 + - - +
124A SER 3.2 0.2 - - - -
125A ARG* 3.5 25.1 - - + +
126A VAL* 3.0 36.2 + - + +
155A PHE* 4.9 4.7 - - + -
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Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 5.3 5.6 - - - +
120A GLY 4.0 5.3 + - - +
121A HIS 2.8 5.3 + - - +
122A ILE* 1.3 74.0 - - - +
124A SER* 1.3 61.7 + - - +
126A VAL* 3.7 1.2 + - - +
127A PHE* 3.3 56.5 + - + -
150A GLU* 2.7 45.4 + - - -
155A PHE* 3.9 20.4 - - + -
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Residues in contact with SER 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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121A HIS* 2.9 16.2 + - - +
123A ARG* 1.3 75.7 - - - +
125A ARG* 1.3 59.6 + - - +
127A PHE* 3.2 8.8 + - - +
128A ARG* 2.8 32.4 + - - +
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Residues in contact with ARG 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 HIS* 3.6 4.7 + - + +
122A ILE* 3.1 36.2 + - + +
124A SER* 1.3 78.9 - - - +
126A VAL* 1.3 60.1 + - + +
128A ARG* 3.3 5.5 + - - +
129A GLU* 3.0 28.3 + - - +
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 4.2 19.5 - - + -
122A ILE* 3.0 25.3 + - + +
123A ARG 4.2 1.6 - - - +
125A ARG* 1.3 76.2 - - + +
127A PHE* 1.3 57.8 + - - +
129A GLU* 3.2 11.0 + - - +
130A VAL* 2.9 28.2 + - + +
148A PHE* 4.1 8.7 - - + -
155A PHE* 3.7 48.5 - - + -
157A LEU* 4.0 22.2 - - + -
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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
----------------------------------------------------------
123A ARG* 3.3 54.4 + - - +
124A SER* 3.2 12.4 + - - +
126A VAL* 1.3 74.3 - - - +
128A ARG* 1.3 58.6 - - - +
130A VAL* 3.2 4.8 + - - +
131A GLU* 2.9 37.8 + - - +
148A PHE* 3.7 34.3 - + - -
150A GLU* 3.7 6.7 - - - -
155A PHE* 4.0 14.8 - + - -
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Residues in contact with ARG 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 SER 2.8 19.4 + - - +
125A ARG* 3.8 5.6 - - - +
127A PHE* 1.3 73.1 - - - +
129A GLU* 1.3 57.9 + - - +
131A GLU* 4.0 21.6 + - - +
132A MET* 3.0 40.1 + - + +
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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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31A STU 4.8 2.9 - - - -
113A LYS* 2.9 33.6 + - - -
115A ILE* 4.6 6.2 - - - +
125A ARG 3.0 15.4 + - - +
126A VAL* 3.4 14.4 - - - +
127A PHE 3.2 0.4 - - - -
128A ARG* 1.3 75.7 - - - +
130A VAL* 1.3 57.8 + - - +
132A MET* 2.5 24.4 - - + +
133A LEU* 3.1 29.8 - - + +
157A LEU* 4.3 14.9 - - + +
159A PHE* 4.5 4.7 - - - -
226A ASP* 4.5 14.2 - - - +
227A PHE 6.0 1.3 - - - +
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Residues in contact with VAL 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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126A VAL 2.9 19.4 + - - +
127A PHE* 3.2 5.8 + - - +
129A GLU* 1.3 73.7 - - - +
131A GLU* 1.3 70.8 + - - +
133A LEU* 3.4 7.1 - - - +
134A TYR* 3.1 22.4 + - + +
145A LEU* 4.2 20.1 - - + +
148A PHE* 3.9 44.9 - - + -
157A LEU* 3.8 23.8 - - + -
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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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127A PHE* 2.9 22.6 + - - +
128A ARG* 3.6 26.1 + - - +
130A VAL* 1.3 82.6 - - - +
132A MET* 1.3 58.5 + - - +
134A TYR* 3.2 8.9 + - + +
135A GLN* 3.1 33.7 + - + +
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Residues in contact with MET 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 ARG* 3.0 19.0 + - + +
129A GLU* 2.5 28.5 - - - +
131A GLU* 1.3 74.2 - - + +
133A LEU* 1.3 58.1 + - - +
135A GLN* 4.0 18.6 + - - +
136A CYS* 3.5 22.4 - - - -
201A ILE* 3.6 26.9 - - + -
227A PHE* 3.0 54.5 - - + +
228A GLY* 4.1 10.1 - - - +
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Residues in contact with LEU 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* 3.1 33.2 - - + +
130A VAL* 3.4 5.8 - - - +
131A GLU 3.3 0.8 + - - -
132A MET* 1.3 77.2 - - - +
134A TYR* 1.3 63.3 + - - +
135A GLN 3.3 3.6 - - - +
136A CYS* 3.1 23.3 + - - +
137A GLN* 2.9 28.7 + - - +
143A LEU* 3.9 23.1 - - + +
145A LEU* 4.1 22.2 - - + -
157A LEU* 4.9 2.0 - - + -
159A PHE* 3.9 28.3 - - + -
225A CYS* 6.4 0.7 - - + -
226A ASP 6.3 0.4 - - - +
227A PHE* 4.2 18.8 - - + -
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Residues in contact with TYR 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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130A VAL* 3.1 12.9 + - + +
131A GLU* 3.3 14.1 - - + +
133A LEU* 1.3 78.6 - - - +
135A GLN* 1.3 69.5 + - + +
136A CYS 3.0 1.4 + - - -
137A GLN* 3.1 30.7 + - + +
145A LEU* 5.0 11.7 - - + +
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Residues in contact with GLN 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 GLU* 3.1 19.6 + - + +
132A MET* 4.0 17.1 - - - +
133A LEU 4.4 3.6 - - - +
134A TYR* 1.3 83.3 - - + +
136A CYS* 1.3 59.5 + - - +
137A GLN 3.5 1.5 + - - +
199A LYS* 3.6 26.3 + - - +
201A ILE* 4.5 18.0 - - + +
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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