Contacts of the helix formed by residues 143 - 156 (chain C) in PDB entry 5DO7
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 THR 143 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142C LEU* 1.3 78.3 - - - +
144C VAL* 1.3 65.4 + - - +
145C ARG* 3.6 4.9 + - - +
146C GLU* 2.8 49.9 + - - +
147C THR* 2.8 21.7 + - - -
181C ALA 3.9 7.4 + - - -
182C ASP* 4.0 16.1 + - + +
183C ARG 3.1 22.9 - - - +
184C LEU* 4.4 1.6 - - - +
185C ILE* 4.0 4.0 - - - +
377C ARG* 5.5 1.3 - - - +
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Residues in contact with VAL 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C THR* 1.3 72.7 - - - +
145C ARG* 1.3 58.8 - - - +
147C THR* 3.2 4.4 + - - +
148C LEU* 2.8 51.9 + - + +
172C MET* 4.2 10.1 - - - -
177C LEU* 4.4 10.3 - - + +
180C VAL* 4.2 15.0 - - + +
181C ALA* 3.2 14.6 + - - +
183C ARG 3.6 3.3 + - - +
185C ILE* 3.7 7.2 - - + +
193C ILE* 3.2 35.7 - - + -
201C VAL* 3.6 22.4 - - + -
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Residues in contact with ARG 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C THR* 3.3 1.5 + - - +
144C VAL* 1.3 74.2 - - - +
146C GLU* 1.3 72.9 + - - +
148C LEU* 3.8 3.4 - - - +
149C HIS* 2.8 32.6 + - + +
165C GLN* 2.6 53.1 + - + +
168C VAL* 4.2 8.0 - - + +
169C GLU* 5.0 9.2 - - - -
172C MET* 3.6 32.1 - - + -
181C ALA* 2.8 12.2 + - - +
182C ASP* 2.9 46.9 + - - +
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Residues in contact with GLU 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C SER 5.1 0.2 - - - +
142C LEU* 3.8 8.2 - - + -
143C THR* 2.8 53.7 + - - +
145C ARG* 1.3 89.0 + - - +
147C THR* 1.3 66.6 + - - +
149C HIS* 3.0 10.4 + - + +
150C TYR* 2.8 45.9 + - + +
373C ARG* 6.3 0.4 - - - +
377C ARG* 2.8 45.2 + - - +
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Residues in contact with THR 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C LEU* 4.3 27.2 - - + +
139C LEU* 4.4 8.7 + - + +
142C LEU* 3.8 21.1 - - + +
143C THR 2.8 16.8 + - - -
144C VAL* 3.8 8.1 - - - -
146C GLU* 1.3 71.1 - - - +
148C LEU* 1.3 58.9 + - + +
150C TYR* 3.2 8.2 + - - +
151C THR* 2.8 35.7 + - + +
185C ILE* 4.4 10.5 - - - +
201C VAL* 5.4 6.7 - - + -
374C ARG* 4.2 19.4 + - - +
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Residues in contact with LEU 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C VAL* 2.8 41.4 + - + +
145C ARG 4.0 0.2 - - - +
147C THR* 1.3 76.0 - - + +
149C HIS* 1.3 55.5 + - - +
151C THR* 3.0 7.4 + - - +
152C ALA* 2.8 38.1 + - - +
168C VAL* 3.7 18.6 - - + -
171C VAL* 4.9 0.4 - - + -
172C MET* 4.0 18.8 - - + +
177C LEU* 5.0 0.9 - - + -
201C VAL* 4.5 9.6 - - + +
204C ALA* 3.5 37.5 - - + +
205C ALA* 3.5 22.7 - - + +
208C LEU* 3.8 15.3 - - + +
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Residues in contact with HIS 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ARG* 2.8 26.3 + - + +
146C GLU* 3.0 9.6 + - + +
148C LEU* 1.3 71.3 - - - +
150C TYR* 1.3 62.3 + + - +
152C ALA* 4.1 0.6 - - - +
153C LEU* 2.7 71.9 + - + +
161C PRO* 3.4 28.3 + - + +
164C PHE* 4.2 8.8 - - + +
165C GLN* 3.6 33.1 + - + +
168C VAL* 4.1 10.0 - - + +
373C ARG* 3.9 26.1 + - - -
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Residues in contact with TYR 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LEU* 4.5 5.2 - - + -
146C GLU* 2.8 49.0 + - + +
147C THR* 3.7 5.8 - - - +
149C HIS* 1.3 79.1 - + - +
151C THR* 1.3 70.3 + - - +
153C LEU* 4.0 2.4 - - + +
154C LEU* 2.8 25.2 + - - +
370C VAL* 3.8 24.5 - - + +
373C ARG* 3.0 49.7 + - - -
374C ARG* 3.8 54.5 - - + +
377C ARG* 3.5 26.2 - - - +
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Residues in contact with THR 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C LEU* 6.4 1.1 - - + -
147C THR* 2.8 24.6 + - + +
148C LEU* 3.0 24.6 + - - +
150C TYR* 1.3 75.0 - - - +
152C ALA* 1.3 49.5 + - - +
154C LEU* 2.8 7.3 + - - +
155C ALA* 2.8 34.1 + - - +
205C ALA* 4.1 19.7 - - + +
208C LEU* 3.5 12.9 - - - +
374C ARG* 4.4 10.4 - - - +
452C GLU* 3.7 24.5 - - - +
457C LEU* 4.4 13.6 - - + +
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Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C LEU 2.8 22.8 + - - +
149C HIS 4.1 1.8 - - - +
151C THR* 1.3 73.0 - - - +
153C LEU* 1.3 62.5 + - - +
155C ALA* 2.9 17.1 + - - +
156C ILE* 3.0 20.0 + - + +
164C PHE* 4.3 12.9 - - + +
167C LYS* 6.3 2.7 - - + -
168C VAL* 4.4 10.3 - - + -
208C LEU* 3.3 32.5 - - + -
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Residues in contact with LEU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C HIS* 2.7 58.2 + - + +
150C TYR* 4.0 3.4 - - + +
152C ALA* 1.3 73.8 - - - +
154C LEU* 1.3 59.2 + - - +
156C ILE 3.4 11.8 - - - +
161C PRO* 4.2 14.1 - - + -
164C PHE* 3.8 34.7 - - + -
362C PRO* 5.3 0.7 - - - +
370C VAL* 3.5 31.0 - - + -
373C ARG* 5.3 4.5 - - - +
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Residues in contact with LEU 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C TYR 2.8 19.8 + - - +
151C THR* 3.2 5.2 - - - +
153C LEU* 1.3 79.5 - - - +
155C ALA* 1.3 59.6 + - - +
362C PRO* 3.1 24.9 - - + +
367C LYS* 4.1 18.2 - - + +
370C VAL* 4.1 20.6 - - + -
371C LEU* 3.9 21.1 - - + -
374C ARG* 5.7 0.7 - - - +
452C GLU* 6.0 0.2 - - - +
457C LEU* 3.1 48.9 - - + +
458C TYR* 3.5 28.9 - - + -
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Residues in contact with ALA 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C THR 2.8 17.8 + - - +
152C ALA* 2.9 8.2 + - - +
154C LEU* 1.3 79.5 - - - +
156C ILE* 1.3 71.5 + - + +
208C LEU* 5.7 3.6 - - + +
209C GLN* 3.7 27.6 - - - +
360C ASP* 3.9 3.1 - - - +
362C PRO* 2.8 26.3 - - - +
457C LEU* 3.9 8.1 - - + +
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Residues in contact with ILE 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ALA* 3.0 9.5 + - + +
153C LEU 3.4 9.7 - - - +
154C LEU 3.4 1.6 - - - -
155C ALA* 1.3 92.3 - - + +
157C ARG* 1.3 62.2 + - - +
158C ARG* 3.7 31.9 - - + +
164C PHE* 3.1 27.7 - - + -
167C LYS* 5.8 8.3 - - + -
208C LEU* 3.4 29.6 - - + +
209C GLN* 4.9 3.8 - - - -
358C THR* 5.2 1.3 - - + -
360C ASP* 3.3 30.7 - - - +
362C PRO* 4.1 6.7 - - - -
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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