Contacts of the helix formed by residues 139 - 153 (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 TYR 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A TYR* 3.7 32.4 + - + +
136A ILE* 4.5 2.8 + - - -
137A ARG 4.1 1.8 + - - -
138A MET* 1.3 72.1 - - - +
140A GLN* 1.3 98.6 + - + +
141A THR 3.0 0.4 - - - -
142A LYS* 3.0 17.9 + - - +
143A LEU* 3.5 23.4 + - + +
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Residues in contact with GLN 140 (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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83A TYR* 3.5 59.5 - - + +
138A MET* 3.0 14.1 + - + +
139A TYR* 1.3 124.7 + - + +
141A THR* 1.3 61.6 + - - +
143A LEU* 3.1 15.1 + - + +
144A PHE* 2.9 35.1 + - + -
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Residues in contact with THR 141 (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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19A VAL* 5.2 0.9 - - - +
27A ILE* 4.6 5.3 - - + +
29A LEU* 4.1 11.0 - - + -
46A HIS* 4.8 3.7 - - - +
47A ILE* 3.8 37.7 + - + +
83A TYR* 5.6 0.2 + - - -
127A PHE* 3.8 23.1 - - + -
136A ILE* 3.7 12.5 - - + +
138A MET* 2.9 23.2 + - - +
140A GLN* 1.3 78.9 - - - +
142A LYS* 1.3 57.1 + - - +
144A PHE* 3.5 5.3 + - - +
145A TYR* 2.8 27.9 + - - +
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Residues in contact with LYS 142 (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* 3.8 19.4 - - + -
128A ALA* 6.1 3.7 - - - +
131A TYR* 3.6 49.3 - - + +
136A ILE* 5.1 0.4 - - - +
139A TYR* 3.0 11.9 + - - +
141A THR* 1.3 76.9 - - - +
143A LEU* 1.3 71.2 + - + +
145A TYR* 3.7 1.5 - - - +
146A ALA* 2.9 24.4 + - + +
157A LEU* 3.7 31.0 - - + +
158A PRO 5.6 3.2 + - - -
159A VAL 6.3 0.8 - - - -
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Residues in contact with LEU 143 (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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139A TYR* 3.5 26.7 + - + +
140A GLN* 3.1 23.6 + - + +
142A LYS* 1.3 82.2 - - + +
144A PHE* 1.3 64.8 + - + +
146A ALA* 3.4 6.5 + - - +
147A ASP* 3.1 32.5 + - - +
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Residues in contact with PHE 144 (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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19A VAL* 3.8 21.1 - - + -
80A LEU* 3.8 36.5 - - + +
81A GLY* 3.8 22.2 - - - -
82A ALA 4.5 1.8 - - - -
83A TYR* 3.7 32.1 - + + -
97A VAL* 4.0 19.7 - - + -
140A GLN* 2.9 32.7 + - + +
141A THR* 4.1 2.9 - - - +
143A LEU* 1.3 77.7 - - + +
145A TYR* 1.3 60.6 + - - +
147A ASP* 3.2 20.3 + - - +
148A ALA* 2.9 28.9 + - - +
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Residues in contact with TYR 145 (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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19A VAL* 4.3 8.5 - - + +
21A LEU* 3.4 32.5 - - + -
25A GLY 2.7 21.7 + - - -
27A ILE* 3.7 30.4 + - + +
124A ARG* 3.4 20.7 + - - +
127A PHE* 3.5 40.8 - + + -
141A THR 2.8 18.8 + - - +
142A LYS* 3.3 5.4 + - - +
144A PHE* 1.3 75.6 - - - +
146A ALA* 1.3 58.7 + - - +
148A ALA* 3.2 1.4 + - - +
149A LEU* 2.9 45.0 + - + +
157A LEU* 3.6 21.8 - - + -
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Residues in contact with ALA 146 (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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142A LYS* 2.9 19.1 + - + +
143A LEU* 3.5 7.4 - - - +
145A TYR* 1.3 77.9 - - - +
147A ASP* 1.3 62.3 + - - +
149A LEU* 3.4 12.0 + - - +
150A ARG* 3.1 40.9 + - - +
156A ALA* 6.4 1.6 - - + +
157A LEU* 4.8 11.6 - - + +
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Residues in contact with ASP 147 (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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80A LEU* 4.3 18.8 - - + +
143A LEU* 3.1 12.7 + - - +
144A PHE* 3.2 34.1 + - - +
146A ALA* 1.3 75.4 - - - +
148A ALA* 1.3 59.2 + - - +
150A ARG* 2.7 28.2 + - - +
151A GLU* 2.8 35.8 + - + +
302A SM 2.4 29.4 - - - -
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Residues in contact with ALA 148 (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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19A VAL* 3.5 19.1 - - + -
21A LEU* 3.8 10.1 - - + -
80A LEU* 4.5 3.8 - - + +
99A LEU* 3.5 30.1 - - + -
144A PHE 2.9 12.6 + - - +
145A TYR 3.2 8.0 + - - +
147A ASP* 1.3 77.9 - - - +
149A LEU* 1.3 62.1 + - - +
151A GLU* 3.3 5.2 + - - +
152A LYS* 3.0 30.0 + - - +
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Residues in contact with LEU 149 (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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21A LEU* 4.2 6.7 - - + -
25A GLY* 3.9 12.1 - - - +
124A ARG* 3.8 11.7 - - + +
145A TYR* 2.9 47.4 + - + +
146A ALA* 3.7 6.7 - - - +
148A ALA* 1.3 76.2 - - - +
150A ARG* 1.3 61.4 + - + +
152A LYS 3.5 0.2 + - - -
153A GLY 3.0 3.5 + - - -
154A PHE* 2.8 56.0 + - + +
155A PRO 3.8 22.0 - - - +
156A ALA* 4.5 3.1 - - - -
157A LEU* 3.8 32.1 - - + +
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Residues in contact with ARG 150 (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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146A ALA* 3.1 32.0 + - - +
147A ASP* 2.7 36.1 + - - +
149A LEU* 1.3 77.7 - - + +
151A GLU* 1.3 64.2 + - + +
153A GLY* 3.1 13.4 + - - -
154A PHE 4.8 3.6 - - - +
156A ALA* 6.0 7.0 - - + -
302A SM 3.0 13.3 - - - -
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Residues in contact with GLU 151 (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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78A LYS* 2.8 42.4 + - - +
80A LEU* 4.6 11.8 - - + +
99A LEU* 4.0 22.0 - - + -
147A ASP* 2.8 24.8 + - + +
148A ALA* 3.6 4.7 - - - +
150A ARG* 1.3 77.8 - - + +
152A LYS* 1.3 61.8 + - - +
153A GLY 3.6 0.2 + - - -
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Residues in contact with LYS 152 (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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21A LEU* 4.2 16.4 - - + -
77A VAL* 6.4 1.3 - - + -
99A LEU* 4.1 24.2 - - + -
101A GLU* 4.6 20.9 - - + +
148A ALA 3.0 17.9 + - - +
151A GLU* 1.3 77.5 - - - +
153A GLY* 1.3 61.4 + - - +
154A PHE* 3.4 34.6 + - + -
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Residues in contact with GLY 153 (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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149A LEU 3.0 4.9 + - - -
150A ARG* 3.1 11.9 + - - -
151A GLU 3.3 1.4 + - - -
152A LYS* 1.3 78.9 - - - +
154A PHE* 1.3 63.3 + - - +
155A PRO* 4.6 1.4 - - - +
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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