Contacts of the helix formed by residues 115 - 129 (chain A) in PDB entry 1SHL
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 SER 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ASP 3.6 3.0 + - - -
114A CYS* 1.3 74.2 - - - +
116A CYS* 1.3 65.1 + - - +
117A ALA* 3.5 7.8 + - - +
118A LYS* 3.0 22.3 + - - +
119A MET* 3.0 22.8 + - - +
152A GLY* 4.3 0.9 - - - -
153A LYS* 3.9 13.7 - - - +
154A ASP* 3.4 24.4 + - - -
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Residues in contact with CYS 116 (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 SER* 1.3 72.0 - - - +
117A ALA* 1.3 61.2 + - - +
119A MET* 3.4 10.8 + - - +
120A GLN* 3.1 25.6 + - - +
152A GLY* 3.9 9.3 - - - -
154A ASP* 2.7 22.9 + - - +
155A GLY* 3.4 33.7 - - - -
156A VAL* 3.5 11.9 - - - +
157A THR* 3.2 27.5 + - - +
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Residues in contact with ALA 117 (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 SER* 3.3 6.5 + - - +
116A CYS* 1.3 76.0 - - - +
118A LYS* 1.3 54.1 + - - +
120A GLN* 3.1 8.6 + - - +
121A ASP* 2.7 37.4 + - - +
154A ASP* 4.7 2.9 + - - +
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Residues in contact with LYS 118 (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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111A TYR* 5.0 9.3 - - + -
114A CYS* 3.9 14.1 - - + -
115A SER* 3.0 28.4 + - - +
117A ALA* 1.3 77.1 - - - +
119A MET* 1.3 54.4 + - - +
121A ASP* 4.0 7.1 - - - +
122A LEU* 2.8 71.1 + - + +
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Residues in contact with MET 119 (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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73A ILE* 3.9 15.7 - - + -
75A ASN* 3.5 26.9 - - - -
114A CYS* 3.8 14.1 - - + -
115A SER 3.0 16.8 + - - +
116A CYS* 3.6 8.1 - - - +
117A ALA 3.2 0.2 - - - -
118A LYS* 1.3 75.4 - - - +
120A GLN* 1.3 62.2 + - - +
122A LEU* 3.7 7.5 - - - +
123A LEU* 3.2 33.6 + - + +
141A LEU* 5.4 4.3 - - - -
150A ILE* 4.4 15.3 - - + -
151A TYR 3.9 11.7 - - - +
152A GLY* 4.3 8.3 - - - +
157A THR* 3.9 33.2 - - + -
162A LEU* 3.8 15.9 - - + +
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Residues in contact with GLN 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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116A CYS 3.1 16.2 + - - +
117A ALA* 3.1 12.4 + - - +
119A MET* 1.3 77.9 - - - +
121A ASP* 1.3 57.0 - - - +
123A LEU* 3.8 1.7 - - - +
124A LYS* 2.9 29.7 + - - +
157A THR* 3.4 29.7 - - + +
161A ASP* 3.4 18.0 - - - +
162A LEU* 3.4 29.9 - - - +
165A HIS* 3.2 29.0 + - - +
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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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117A ALA 2.7 20.5 + - - +
118A LYS* 4.0 7.2 - - - +
120A GLN* 1.3 69.6 - - - +
122A LEU* 1.3 60.4 + - - +
124A LYS* 3.1 15.5 + - - +
125A LYS* 2.7 77.5 + - - +
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Residues in contact with LEU 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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71A ILE* 4.2 9.0 - - + +
73A ILE* 3.6 30.5 - - + -
111A TYR* 3.6 46.9 - - + +
114A CYS* 3.9 12.6 - - - -
118A LYS* 2.8 41.6 + - + +
119A MET* 3.7 5.6 - - - +
121A ASP* 1.3 72.0 - - + +
123A LEU* 1.3 60.9 + - + +
125A LYS* 3.9 5.8 - - + +
126A ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 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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71A ILE* 4.7 7.0 - - + -
73A ILE* 5.0 9.9 - - + -
119A MET* 3.2 24.9 + - - +
120A GLN 4.1 2.2 - - - +
121A ASP 3.2 0.4 - - - -
122A LEU* 1.3 82.2 - - + +
124A LYS* 1.3 60.4 + - - +
126A ALA* 3.8 3.4 - - - -
127A SER* 3.0 22.9 + - - -
137A PHE* 4.4 1.6 - - + -
139A CYS* 4.0 24.7 - - + -
141A LEU* 5.0 0.9 - - + -
162A LEU* 3.5 42.6 - - + +
165A HIS* 4.0 3.7 - - + +
166A PHE* 3.3 35.8 - - + -
181A PHE* 3.9 21.5 - - + -
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Residues in contact with LYS 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 GLN 2.9 18.5 + - - +
121A ASP* 3.8 16.5 + - - +
123A LEU* 1.3 74.1 - - - +
125A LYS* 1.3 61.2 + - - +
127A SER* 2.5 23.2 + - - +
128A GLU* 2.9 48.4 + - - +
165A HIS* 3.6 36.3 - - + +
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Residues in contact with LYS 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* 2.7 51.9 + - - +
122A LEU* 3.9 5.4 - - + +
124A LYS* 1.3 74.3 - - - +
126A ALA* 1.3 62.1 + - - +
128A GLU* 2.9 25.6 + - + +
129A GLU* 3.0 21.1 + - - +
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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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69A LYS* 5.2 5.2 - - + +
71A ILE* 3.6 24.7 - - + -
122A LEU 2.9 20.2 + - - +
123A LEU* 3.5 7.6 - - - +
125A LYS* 1.3 76.5 - - - +
127A SER* 1.3 53.2 + - - +
129A GLU* 3.3 20.1 + - - +
131A HIS* 2.8 30.7 + - + -
137A PHE* 4.4 4.9 - - + -
166A PHE* 3.7 12.1 - - + -
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Residues in contact with SER 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 LEU 3.0 11.4 + - - -
124A LYS* 2.5 21.5 + - - +
126A ALA* 1.3 75.5 - - - +
128A GLU* 1.3 61.9 + - - +
129A GLU 3.5 4.7 + - - +
165A HIS* 3.2 40.9 + - - +
166A PHE* 3.5 22.1 - - - -
170A ARG 4.5 4.6 + - - +
171A CYS* 3.1 28.1 - - - +
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Residues in contact with GLU 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 LYS* 2.9 53.3 + - - +
125A LYS* 2.9 19.3 + - - +
127A SER* 1.3 75.8 + - - +
129A GLU* 1.3 65.1 + - - +
170A ARG 5.8 1.1 - - - +
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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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69A LYS* 3.0 38.7 + - - +
125A LYS* 3.0 18.7 + - - +
126A ALA* 3.3 18.8 + - - +
127A SER 3.6 3.5 - - - +
128A GLU* 1.3 82.1 - - - +
130A ASP* 1.3 63.1 + - - +
131A HIS* 3.4 26.5 + - + +
173A THR* 4.0 5.0 + - - -
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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