Contacts of the helix formed by residues 123 - 133 (chain A) in PDB entry 1SOI
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 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ASP* 3.3 20.5 + - - -
122A VAL* 1.3 79.4 - - - +
124A ARG* 1.3 59.0 + - - +
125A GLU* 3.6 13.9 + - - +
126A ASP* 3.2 32.8 + - - +
127A PHE* 2.9 28.2 + - - +
145A TYR* 4.0 0.9 - - - -
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Residues in contact with ARG 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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24A ARG 6.2 0.2 - - - +
25A GLY 4.8 4.4 + - - +
26A ASP* 4.4 2.0 + - - -
123A SER* 1.3 73.4 - - - +
125A GLU* 1.3 88.3 + - - +
127A PHE* 3.3 3.1 + - - +
128A ALA* 3.1 20.3 + - - +
145A TYR* 3.4 18.6 + - - +
149A LEU* 3.8 12.5 - - + +
155A PRO* 3.1 48.4 + - - +
156A ALA 3.2 22.8 + - - -
157A LEU* 3.2 25.9 - - + +
158A PRO* 3.3 24.0 - - + +
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Residues in contact with GLU 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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123A SER* 3.6 14.4 + - - +
124A ARG* 1.3 109.8 + - - +
126A ASP* 1.3 64.4 + - - +
128A ALA* 3.4 6.2 + - - +
129A GLN* 3.3 23.5 + - - +
158A PRO* 3.9 19.7 - - + +
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Residues in contact with ASP 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* 3.7 17.9 - - + -
123A SER* 3.2 22.1 + - - +
125A GLU* 1.3 77.6 - - - +
127A PHE* 1.3 60.6 + - - +
129A GLN* 3.2 13.4 + - - +
130A LEU* 2.9 32.0 + - + +
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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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27A ILE* 4.1 3.8 - - + -
29A LEU* 3.9 21.1 - - + -
122A VAL* 3.7 8.7 - - + +
123A SER 2.9 17.4 + - - +
124A ARG 3.6 4.0 - - - +
125A GLU 3.3 0.2 - - - -
126A ASP* 1.3 76.9 - - - +
128A ALA* 1.3 62.0 + - - +
130A LEU* 3.1 5.4 + - - +
131A TYR* 2.8 32.7 + - + +
136A ILE* 3.6 31.0 - - + -
141A THR* 3.8 17.7 - - + -
142A LYS* 3.8 46.4 - - + -
145A TYR* 3.5 36.3 - + + -
157A LEU* 4.0 9.6 - - + -
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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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124A ARG 3.1 11.2 + - - +
125A GLU 3.5 10.1 - - - +
127A PHE* 1.3 85.3 - - - +
129A GLN* 1.3 57.1 + - + +
131A TYR* 3.6 6.0 + - - +
132A ALA* 3.1 28.4 + - - +
142A LYS* 6.1 3.6 - - - +
157A LEU* 5.1 5.2 - - + -
158A PRO* 4.0 31.2 - - + +
159A VAL* 5.9 2.2 - - + -
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Residues in contact with GLN 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 GLU 3.3 13.0 + - - +
126A ASP* 3.2 17.9 + - - +
127A PHE 3.1 0.6 - - - -
128A ALA* 1.3 77.6 - - + +
130A LEU* 1.3 65.6 + - + +
132A ALA* 3.3 8.4 + - - +
133A ALA* 2.9 26.0 + - - +
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Residues in contact with LEU 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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29A LEU* 4.8 3.1 - - + -
45A TRP* 4.5 23.1 - - + +
122A VAL* 4.0 28.9 - - + -
126A ASP* 2.9 18.7 + - + +
127A PHE* 3.5 8.3 - - - +
129A GLN* 1.3 76.9 - - + +
131A TYR* 1.3 60.4 + - - +
133A ALA* 3.3 4.0 + - + -
134A GLY 3.2 3.8 + - - -
135A GLN* 2.9 50.0 + - + +
136A ILE* 4.0 22.4 - - + -
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Residues in contact with TYR 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* 2.8 27.1 + + + +
128A ALA* 3.8 7.2 - - - +
130A LEU* 1.3 74.0 - - - +
132A ALA* 1.3 67.1 + - + +
134A GLY* 3.0 15.6 + - - -
136A ILE* 3.8 26.4 - - + +
139A TYR* 3.7 32.4 + - + +
142A LYS* 3.6 54.9 - - + +
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Residues in contact with ALA 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 3.1 16.0 + - - +
129A GLN* 3.8 9.2 - - - +
131A TYR* 1.3 85.8 - - + +
133A ALA* 1.3 58.5 + - - +
134A GLY 3.4 0.9 + - - -
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Residues in contact with ALA 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 GLN 2.9 17.5 + - - +
130A LEU* 3.8 5.8 - - - +
131A TYR 3.1 0.4 - - - -
132A ALA* 1.3 76.4 - - - +
134A GLY* 1.3 55.0 + - - +
135A GLN* 2.7 36.9 + - + +
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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