Contacts of the helix formed by residues 124 - 138 (chain A) in PDB entry 5IZL
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 GLN 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A HIS* 3.0 56.4 + - + +
17A ASP 5.7 0.4 - - - +
18A SER* 5.2 1.2 - - - +
117A ILE* 6.0 0.2 - - - +
118A ASP* 4.2 19.2 - - - +
121A LYS* 3.1 40.8 + - + +
122A GLY 3.1 14.9 + - - +
123A MET* 1.3 76.7 - - - +
125A THR* 1.3 68.1 + - - +
126A GLN 3.4 1.1 - - - -
127A SER* 3.2 15.8 + - - -
128A ALA* 3.3 12.0 + - - +
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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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15A HIS* 3.4 7.5 - - - -
124A GLN* 1.3 77.4 - - - +
126A GLN* 1.3 78.0 + - - +
128A ALA* 3.5 7.2 + - - +
129A GLU* 3.5 20.0 + - - +
440A ASN* 3.8 36.7 - - - +
441A THR 4.4 10.2 - - - +
442A CYS* 6.1 0.2 - - - -
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Residues in contact with GLN 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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14A GLY 4.4 3.6 - - - +
15A HIS* 3.4 34.9 + - - +
16A ILE* 5.4 1.6 + - - +
95A GLY 3.7 18.2 - - - +
96A HIS 5.1 0.2 - - - +
97A ALA* 3.7 23.1 + - - +
100A ILE* 4.6 10.3 - - + -
103A ILE* 5.3 1.1 - - + -
124A GLN 3.4 0.2 - - - -
125A THR* 1.3 85.3 - - - +
127A SER* 1.3 61.7 + - - +
128A ALA 3.2 1.1 - - - -
129A GLU* 2.5 33.2 + - - +
130A CYS* 2.8 36.8 + - - -
443A ARG* 3.2 17.4 - - - +
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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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15A HIS* 3.9 21.4 + - - +
115A LEU* 3.9 16.5 - - - +
116A VAL 4.4 2.8 + - - -
117A ILE* 4.2 15.6 - - - +
122A GLY 4.4 1.2 + - - -
123A MET* 3.7 22.2 - - - +
124A GLN* 3.2 28.0 + - - +
126A GLN* 1.3 77.6 - - - +
128A ALA* 1.3 60.7 + - - +
130A CYS* 3.5 0.4 + - - -
131A LEU* 3.1 23.6 + - - +
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Residues in contact with ALA 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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123A MET* 3.7 17.6 - - + +
124A GLN 3.3 7.6 + - - +
125A THR* 3.7 9.9 - - - +
126A GLN 3.2 0.4 - - - -
127A SER* 1.3 76.9 - - - +
129A GLU* 1.3 66.2 + - + +
131A LEU* 3.2 4.7 + - - +
132A VAL* 3.0 29.1 + - + +
324A TYR* 6.0 4.7 - - + -
442A CYS* 5.3 8.5 - - + -
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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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100A ILE* 3.7 17.5 - - + +
125A THR* 3.5 8.5 + - - +
126A GLN* 2.5 41.8 + - - +
128A ALA* 1.3 77.7 - - - +
130A CYS* 1.3 57.9 + - - +
132A VAL* 3.4 2.9 + - - -
133A ILE* 3.0 34.5 + - - +
441A THR 4.1 4.8 - - - +
442A CYS* 4.4 8.3 - - - -
443A ARG* 2.8 56.9 + - - +
444A LEU* 3.6 20.6 - - + +
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Residues in contact with CYS 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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13A LEU* 3.9 17.5 - - + +
14A GLY 3.8 26.2 - - - -
94A PRO 5.7 0.2 - - - -
100A ILE* 5.1 2.5 - - - -
103A ILE* 4.0 25.6 - - - -
113A MET* 3.5 12.6 - - - +
115A LEU* 3.9 18.4 - - + -
126A GLN* 2.8 31.3 + - - +
129A GLU* 1.3 71.5 - - - +
131A LEU* 1.3 61.2 + - - +
133A ILE* 3.5 10.7 - - - +
134A GLY 3.0 20.1 + - - -
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Residues in contact with LEU 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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113A MET* 4.9 4.5 - - + -
115A LEU* 4.6 9.5 - - + +
123A MET* 4.1 22.9 - - + -
127A SER 3.1 17.2 + - - +
128A ALA* 3.2 4.9 + - - +
130A CYS* 1.3 74.8 - - - +
132A VAL* 1.3 62.7 + - + +
134A GLY* 2.8 17.4 + - - -
135A GLN* 2.9 32.4 + - - +
141A LEU* 4.2 9.9 - - + -
170A THR* 4.6 12.3 - - + +
171A LEU* 4.1 31.2 - - + -
174A THR* 4.8 4.7 - - + -
176A PHE* 4.1 22.4 - - + -
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Residues in contact with VAL 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 ALA* 3.0 14.9 + - + +
129A GLU 3.7 7.2 - - - +
131A LEU* 1.3 76.3 - - + +
133A ILE* 1.3 63.3 + - - +
135A GLN* 3.1 25.5 + - - +
136A ILE* 3.1 37.9 - - + +
322A ILE* 3.7 33.7 - - + -
324A TYR* 5.1 5.8 - - + -
442A CYS* 4.2 13.0 - - - -
444A LEU* 3.8 17.9 - - + -
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Residues in contact with ILE 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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13A LEU* 4.8 3.6 - - + -
100A ILE* 4.4 11.7 - - + -
103A ILE* 4.0 23.8 - - + +
104A ILE* 3.7 34.3 - - + -
107A ALA* 3.6 28.9 - - + -
129A GLU 3.0 18.0 + - - +
130A CYS* 3.5 12.1 - - - +
132A VAL* 1.3 76.0 - - - +
134A GLY* 1.3 63.3 + - - +
136A ILE* 3.2 9.4 + - - +
137A ALA* 3.0 23.7 + - + +
429A ILE* 5.8 7.2 - - + -
444A LEU* 3.7 15.0 - - + -
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Residues in contact with GLY 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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113A MET* 3.5 28.9 - - - -
130A CYS 3.0 6.7 + - - -
131A LEU* 2.8 10.6 + - - -
133A ILE* 1.3 76.8 - - - +
135A GLN* 1.3 59.9 + - - -
137A ALA* 5.1 0.2 - - - -
138A CYS* 3.1 31.7 + - - +
176A PHE* 3.5 12.1 - - - -
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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 LEU* 2.9 27.3 + - + +
132A VAL* 3.1 21.3 + - - +
134A GLY* 1.3 76.1 - - - +
136A ILE* 1.3 61.6 + - + +
174A THR* 3.5 39.1 - - - +
175A LYS* 3.0 32.9 + - + +
176A PHE* 3.7 18.1 - - + -
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Residues in contact with ILE 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 VAL* 3.1 26.5 + - + +
133A ILE* 3.2 4.9 + - - +
134A GLY 3.1 0.6 - - - -
135A GLN* 1.3 82.8 - - + +
137A ALA* 1.3 57.4 + - - +
175A LYS* 5.4 0.4 - - - -
322A ILE* 3.8 22.2 - - + -
427A LEU* 3.2 29.8 - - + +
429A ILE* 4.5 19.1 - - + -
444A LEU* 5.8 1.6 - - + -
447A HIS* 3.5 58.6 - - + +
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Residues in contact with ALA 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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107A ALA* 3.7 33.6 - - + +
108A GLN* 4.8 8.5 - - + +
110A ILE 5.1 1.6 - - - +
133A ILE* 3.0 15.3 + - + +
134A GLY 3.3 0.6 + - - -
135A GLN 3.5 0.8 - - - -
136A ILE* 1.3 81.0 - - + +
138A CYS* 1.3 66.1 + - - +
139A GLN* 5.1 2.8 - - - +
175A LYS* 5.3 0.8 + - - -
427A LEU* 5.0 6.7 - - + -
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Residues in contact with CYS 138 (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 ALA* 3.7 11.7 - - - -
110A ILE* 3.0 55.0 - - - -
111A ASP 3.7 9.9 - - - +
113A MET* 4.3 15.9 - - + -
134A GLY 3.1 15.1 + - - +
137A ALA* 1.3 80.3 - - - +
139A GLN* 1.3 63.4 + - - +
140A LYS 4.2 11.4 - - - +
175A LYS* 3.1 24.6 + - - -
176A PHE* 4.6 1.6 - - + -
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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