Contacts of the helix formed by residues 139 - 150 (chain A) in PDB entry 1ORN
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 ASP 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A LYS* 4.1 17.3 - - + -
137A ALA 3.7 2.1 + - - +
138A VAL* 1.3 72.5 - - - +
140A THR* 1.3 64.9 + - - +
141A HIS* 3.1 23.7 + - - +
142A VAL* 2.9 32.1 + - - +
143A GLU* 3.0 26.2 + - - +
158A VAL* 5.5 1.3 - - - +
178A HIS* 5.8 0.7 - - + -
182A ILE* 3.9 11.9 - - + +
18C PED 2.6 39.2 + - - +
19C G 3.9 5.6 - - - -
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Residues in contact with THR 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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139A ASP* 1.3 85.9 - - - +
141A HIS* 1.3 69.3 + - + +
143A GLU* 3.9 7.7 - - - +
144A ARG* 3.0 35.3 + - - +
17C A 2.8 38.9 + - + +
18C PED 4.3 3.1 - - - +
19C G 2.9 28.4 + - - +
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Residues in contact with HIS 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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139A ASP* 3.1 20.9 + - - +
140A THR* 1.3 77.2 - - + +
142A VAL* 1.3 66.6 + - - +
144A ARG* 2.9 29.6 + - - +
145A VAL* 2.9 31.8 + - - +
181A MET 4.9 0.7 - - - -
182A ILE* 4.1 21.8 - - + +
185A GLY* 3.6 6.3 - - - -
186A ARG* 3.6 32.3 + - + -
17C A 3.3 28.5 + - - -
18C PED 2.9 38.4 + - - -
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Residues in contact with VAL 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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136A ILE* 5.0 2.0 - - + -
137A ALA 3.7 15.0 - - - +
138A VAL* 4.1 17.3 - - + -
139A ASP* 2.9 30.7 + - - +
141A HIS* 1.3 71.4 - - - +
143A GLU* 1.3 62.4 + - - +
145A VAL* 4.7 0.7 - - - -
146A SER* 2.9 32.4 + - - +
161A VAL* 4.4 0.7 - - + -
165A LEU* 4.0 19.5 - - + -
178A HIS* 4.0 6.3 - - - +
181A MET* 3.9 34.2 - - + +
182A ILE* 3.8 19.5 - - + -
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Residues in contact with GLU 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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138A VAL* 4.0 13.4 - - + +
139A ASP 3.0 18.6 + - - +
140A THR* 3.9 7.0 - - - +
142A VAL* 1.3 78.4 - - - +
144A ARG* 1.3 63.8 + - - +
146A SER* 3.3 5.4 + - - -
147A LYS* 2.8 63.3 + - + +
156A ASP 4.3 2.8 - - - +
158A VAL* 3.8 20.9 + - + +
161A VAL* 4.5 9.0 - - + -
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Residues in contact with ARG 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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140A THR* 3.0 34.1 + - - +
141A HIS* 2.9 31.5 + - - +
143A GLU* 1.3 79.1 - - - +
145A VAL* 1.3 56.2 + - - +
147A LYS* 3.4 4.6 + - - +
148A ARG* 2.9 69.1 + - + +
154A TRP* 5.4 7.0 - - + -
185A GLY* 2.9 25.7 + - - -
189A CYS 3.1 18.6 + - - -
191A ALA* 3.5 23.9 - - - +
17C A 2.8 22.0 + - - -
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Residues in contact with VAL 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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14A MET* 3.7 31.0 - - + -
141A HIS 2.9 21.0 + - - +
142A VAL 4.0 2.5 - - - +
144A ARG* 1.3 76.6 - - - +
146A SER* 1.3 64.3 + - - +
148A ARG* 4.0 4.3 - - - +
149A LEU* 3.1 30.2 + - + +
151A PHE* 5.3 0.4 - - + -
181A MET* 4.0 17.9 - - + +
184A PHE* 3.8 13.9 - - + -
185A GLY* 3.6 31.9 - - - +
189A CYS* 4.1 13.4 - - + +
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Residues in contact with SER 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 VAL* 2.9 23.3 + - - +
143A GLU 3.6 4.3 - - - -
145A VAL* 1.3 78.3 - - - +
147A LYS* 1.3 58.5 + - - +
150A GLY 3.1 5.7 + - - -
151A PHE* 2.8 53.2 + - - +
152A CYS* 3.7 8.3 + - - -
161A VAL* 3.5 25.9 - - - +
165A LEU* 4.3 2.4 - - - +
181A MET* 3.4 15.4 - - - +
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Residues in contact with LYS 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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143A GLU* 2.8 53.5 + - + +
144A ARG* 4.0 2.0 - - - +
146A SER* 1.3 75.0 - - - +
148A ARG* 1.3 64.2 + - - +
150A GLY* 3.5 9.0 + - - -
152A CYS* 3.8 24.3 - - - +
153A ARG 3.6 12.3 - - - +
154A TRP* 2.9 75.2 + - + +
155A ASP 4.4 0.6 - - - -
156A ASP* 2.8 27.7 + - - -
161A VAL* 4.5 2.7 - - - -
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Residues in contact with ARG 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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144A ARG* 2.9 41.0 + - + +
145A VAL 4.0 2.9 - - - +
147A LYS* 1.3 77.6 - - - +
149A LEU* 1.3 61.6 + - - +
150A GLY* 4.5 0.2 - - - -
154A TRP* 3.8 20.7 + - + -
189A CYS* 3.3 36.8 + - - -
190A LYS 2.8 20.8 + - - -
191A ALA 3.0 26.3 + - - -
194A PRO* 3.7 10.9 - - - +
205A CYS* 3.5 13.3 - - - -
206A ARG* 4.1 5.4 + - - +
207A GLU* 3.5 43.0 + - + +
211A ARG* 3.4 21.1 - - - +
300A SF4 4.0 5.6 - - - -
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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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2A LEU* 3.1 24.1 - - - +
10A CYS* 4.0 7.9 - - - -
14A MET* 3.6 31.4 - - + -
145A VAL* 3.1 23.8 + - + +
148A ARG* 1.3 77.5 - - - +
150A GLY* 1.3 58.8 + - - +
151A PHE* 3.6 24.7 - - + -
184A PHE* 4.4 0.2 - - + -
201A LEU* 3.8 15.0 - - + -
204A LEU* 4.1 17.0 - - + +
205A CYS* 3.5 22.7 - - + -
206A ARG* 4.9 3.3 + - - +
300A SF4 3.5 30.1 - - - -
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Residues in contact with GLY 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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1A MET* 3.4 11.5 - - - +
2A LEU* 2.9 29.8 + - - +
146A SER 3.1 4.7 + - - -
147A LYS 3.5 4.6 + - - -
148A ARG 3.3 3.8 - - - -
149A LEU* 1.3 80.7 - - - +
151A PHE* 1.3 66.8 + - - +
152A CYS 3.1 12.5 + - - -
206A ARG* 6.1 2.7 - - - -
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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