Contacts of the helix formed by residues 147 - 162 (chain A) in PDB entry 1O1M
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 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A VAL 3.8 3.2 + - - -
146A LEU* 1.3 75.6 - - - +
148A PRO* 1.3 70.3 - - - +
149A ALA* 3.4 9.3 + - - +
150A ASP* 3.0 33.3 + - - -
151A LYS* 2.9 26.2 + - - +
271A LYS* 4.6 2.8 - - - +
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Residues in contact with PRO 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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146A LEU 4.5 0.7 - - - +
147A SER* 1.3 89.6 - - - +
149A ALA* 1.3 60.3 + - - +
151A LYS* 3.8 14.7 - - + +
152A THR* 2.9 30.4 + - - +
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Residues in contact with ALA 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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147A SER* 3.1 8.9 + - - +
148A PRO* 1.3 81.5 - - - +
150A ASP* 1.3 57.3 + - - +
152A THR* 3.3 6.6 + - - -
153A ASN* 2.9 40.5 + - - +
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Residues in contact with ASP 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 LEU* 4.1 15.0 - - + -
147A SER* 3.0 31.0 + - - +
149A ALA* 1.3 77.2 - - - +
151A LYS* 1.3 57.7 + - - +
153A ASN* 3.2 2.4 + - - +
154A VAL* 2.9 35.6 + - - +
267A ALA* 5.1 0.3 - - - +
268A SER* 2.7 36.3 + - - +
271A LYS* 2.7 41.4 + - - +
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Residues in contact with LYS 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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146A LEU* 3.1 33.4 - - + +
147A SER 2.9 16.0 + - - +
148A PRO* 3.8 12.6 - - + +
150A ASP* 1.3 78.2 - - - +
152A THR* 1.3 63.3 + - - +
154A VAL* 3.3 5.0 + - - +
155A LYS* 3.0 41.7 + - - +
217A VAL* 3.4 35.7 - - + -
218A ASP* 2.6 25.4 + - - +
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Residues in contact with THR 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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148A PRO* 2.9 19.1 + - - +
149A ALA* 3.6 6.9 - - - -
151A LYS* 1.3 77.8 - - - +
153A ASN* 1.3 60.4 + - - +
155A LYS* 3.5 7.0 + - - +
156A ALA* 3.0 30.5 + - + +
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Residues in contact with ASN 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 ALA* 2.9 26.4 + - - +
150A ASP 3.6 4.0 - - - +
152A THR* 1.3 78.6 - - - +
154A VAL* 1.3 57.6 + - - +
156A ALA* 3.4 5.9 + - - +
157A ALA* 3.0 29.8 + - - +
264A ALA* 3.7 18.6 + - - +
265A VAL* 3.9 28.8 - - + +
268A SER* 3.0 29.8 + - - +
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Residues in contact with VAL 154 (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 LEU* 5.6 2.2 - - + -
150A ASP* 2.9 22.4 + - + +
151A LYS* 3.8 5.6 - - - +
152A THR 3.3 0.2 - - - -
153A ASN* 1.3 73.8 - - - +
155A LYS* 1.3 62.0 + - + +
157A ALA* 3.9 0.7 - - - +
158A TRP* 2.9 29.6 + - + +
214A VAL* 3.8 27.8 - - + -
217A VAL* 5.3 4.7 - - + -
268A SER* 3.8 15.7 - - - +
269A LEU* 4.1 19.4 - - + +
272A PHE* 3.7 42.2 - - + -
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Residues in contact with LYS 155 (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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151A LYS* 3.0 36.7 + - - +
152A THR* 4.0 6.1 - - - +
154A VAL* 1.3 73.4 - - + +
156A ALA* 1.3 61.7 + - - +
159A GLY* 2.8 29.1 + - - -
214A VAL* 4.0 35.0 - - + +
215A ALA* 6.2 0.4 - - - +
217A VAL* 5.1 9.3 - - + +
218A ASP* 5.7 2.7 + - - -
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Residues in contact with ALA 156 (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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152A THR* 3.0 20.7 + - + +
153A ASN* 3.7 7.0 - - - +
155A LYS* 1.3 78.8 - - - +
157A ALA* 1.3 61.4 + - - +
159A GLY* 3.9 1.1 - - - -
160A LYS* 3.2 19.9 + - - +
265A VAL* 6.1 2.0 - - + -
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Residues in contact with ALA 157 (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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153A ASN 3.0 16.3 + - - +
154A VAL 4.2 1.8 - - - +
156A ALA* 1.3 76.8 - - - +
158A TRP* 1.3 63.7 + - - +
160A LYS* 3.0 16.8 + - - +
161A VAL* 3.1 16.6 + - - +
253A LEU* 5.7 1.8 - - + -
257A LEU* 4.0 13.3 - - + +
260A GLU* 5.1 10.5 - - + -
265A VAL* 4.2 20.4 - - + -
269A LEU* 4.3 17.9 - - + -
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Residues in contact with TRP 158 (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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154A VAL* 2.9 19.5 + - + +
155A LYS 4.3 0.9 - - - +
157A ALA* 1.3 75.7 - - - +
159A GLY* 1.3 66.6 + - - +
161A VAL* 3.0 34.7 + - + +
162A GLY* 3.1 11.4 + - - -
165A ALA* 4.4 17.7 - - + +
168A TYR* 6.2 1.8 - - + -
207A ALA* 3.9 11.7 - - + -
210A LEU* 3.7 38.8 - - + -
211A THR* 2.9 35.5 + - + +
214A VAL* 4.0 31.4 - - + -
249A LEU* 4.6 15.0 - - + -
253A LEU* 4.4 24.5 - - + -
269A LEU* 5.5 7.6 - - + -
272A PHE* 5.9 4.7 - + - -
273A LEU* 6.3 0.4 - - + -
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Residues in contact with GLY 159 (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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155A LYS 2.8 18.8 + - - -
156A ALA 3.9 1.6 - - - -
158A TRP* 1.3 77.9 - - - +
160A LYS* 1.3 58.0 + - - +
162A GLY* 3.4 13.6 + - - -
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Residues in contact with LYS 160 (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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156A ALA 3.2 12.3 + - - +
157A ALA* 3.0 12.6 + - - +
159A GLY* 1.3 73.9 - - - +
161A VAL* 1.3 65.4 + - - +
164A HIS* 5.1 5.1 + - - -
168A TYR* 5.8 0.2 + - - -
257A LEU* 4.4 20.5 - - + +
260A GLU* 3.7 32.1 - - + +
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Residues in contact with VAL 161 (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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157A ALA 3.1 13.2 + - - +
158A TRP* 3.0 28.8 + - + +
160A LYS* 1.3 77.1 - - - +
162A GLY* 1.3 64.0 + - - +
163A ALA 3.3 0.7 + - - -
164A HIS* 3.0 30.7 + - - +
165A ALA* 3.4 35.7 - - + +
168A TYR* 3.7 22.2 - - + -
253A LEU* 3.8 27.4 - - + -
257A LEU* 4.1 10.1 - - + -
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Residues in contact with GLY 162 (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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158A TRP* 3.1 9.9 + - - -
159A GLY* 3.7 12.8 - - - -
160A LYS 3.4 1.0 - - - -
161A VAL* 1.3 77.3 - - - +
163A ALA* 1.3 62.2 + - - -
165A ALA* 3.1 22.0 + - - +
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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