Contacts of the helix formed by residues 139 - 147 (chain C) in PDB entry 5D0A
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 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C LEU* 3.6 28.4 - - - +
57C ARG* 3.5 17.6 + - - +
138C LEU* 1.3 73.2 - - - +
140C ASP* 1.3 62.3 + - - +
141C ARG 3.5 0.2 + - - -
142C ALA* 2.9 21.2 + - - +
143C VAL* 3.1 24.1 + - - +
503C B12 2.9 33.9 + - - -
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Residues in contact with ASP 140 (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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132C MET* 4.7 1.9 - - - +
133C VAL* 4.9 0.4 - - - -
134C ASP* 2.8 25.6 + - - -
136C GLY 5.7 0.5 + - - -
138C LEU 3.7 2.4 - - - +
139C SER* 1.3 72.0 - - - +
141C ARG* 1.3 58.3 + - - +
143C VAL* 3.6 2.3 + - - +
144C ALA* 3.0 29.5 + - - +
169C LEU* 3.7 15.2 - - + +
171C GLU* 2.6 42.4 - - - +
503C B12 2.8 61.2 + - + +
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Residues in contact with ARG 141 (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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139C SER* 3.1 2.3 + - - +
140C ASP* 1.3 77.0 - - - +
142C ALA* 1.3 60.5 + - - +
144C ALA 3.3 0.2 + - - -
145C GLU* 2.8 31.7 + - - +
156C CYS* 2.9 27.5 + - - +
157C MET* 3.3 24.2 - - - -
158C ILE* 3.5 23.1 - - + +
169C LEU* 3.9 5.6 - - + -
503C B12 2.9 143.5 + - + +
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Residues in contact with ALA 142 (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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30C PHE* 3.8 19.5 - - + -
33C LEU* 3.8 24.2 - - + -
139C SER* 2.9 27.8 + - - +
141C ARG* 1.3 75.9 - - - +
143C VAL* 1.3 62.8 + - - +
145C GLU* 3.5 5.1 + - - +
146C ARG* 3.1 24.1 + - - +
503C B12 3.7 13.0 - - - -
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Residues in contact with VAL 143 (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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25C THR* 4.3 7.0 - - + +
30C PHE* 3.8 24.7 - - + -
70C ILE* 3.7 26.2 - - + -
72C ALA* 3.9 11.9 - - + -
138C LEU* 3.9 28.9 - - + -
139C SER 3.1 15.2 + - - +
140C ASP 3.7 4.5 - - - +
142C ALA* 1.3 74.0 - - - +
144C ALA* 1.3 65.1 + - - +
146C ARG* 3.1 4.3 + - - +
147C ALA* 2.9 23.0 + - - +
171C GLU* 3.9 17.7 - - + +
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Residues in contact with ALA 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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72C ALA* 4.3 5.6 - - + -
140C ASP 3.0 18.1 + - - +
141C ARG 3.8 2.5 - - - +
143C VAL* 1.3 77.3 - - - +
145C GLU* 1.3 62.0 + - - +
147C ALA 3.3 0.9 + - - -
148C GLY 3.2 4.0 + - - -
149C ILE* 2.9 53.1 + - + -
150C GLY 4.5 1.3 - - - -
158C ILE* 4.2 6.3 - - + -
169C LEU* 3.7 26.9 - - + -
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Residues in contact with GLU 145 (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 ARG 2.8 18.4 + - - +
142C ALA* 3.7 5.2 - - - +
144C ALA* 1.3 77.2 - - - +
146C ARG* 1.3 63.0 + - + +
148C GLY* 3.3 9.5 + - - -
150C GLY 3.6 16.2 - - - +
151C PHE* 5.0 1.5 - - - -
152C SER* 2.9 31.5 + - - +
158C ILE* 3.9 9.3 - - + +
183C PRO* 3.8 22.8 - - + +
184C ILE 4.9 0.2 + - - -
503C B12 3.7 15.1 - - - +
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Residues in contact with ARG 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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24C PHE 4.1 2.4 - - - +
25C THR* 2.9 25.4 + - - +
26C THR* 3.1 31.0 + - - -
27C ALA 4.2 0.2 - - - -
28C ASP* 2.8 37.2 + - - +
29C THR 3.4 15.0 + - - -
30C PHE* 3.3 37.8 - - + +
142C ALA 3.1 18.1 + - - +
143C VAL 3.1 2.7 + - - +
145C GLU* 1.3 78.7 - - - +
147C ALA* 1.3 58.5 + - - +
148C GLY 3.3 1.3 + - - -
180C PRO* 5.7 0.3 - - - +
181C ASP 4.1 10.7 - - - +
183C PRO* 4.4 17.3 - - + +
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Residues in contact with ALA 147 (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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23C GLY* 3.5 19.5 - - - +
24C PHE 3.4 32.3 - - - +
25C THR* 4.0 5.4 - - + +
72C ALA* 3.7 17.3 - - + -
143C VAL 2.9 15.1 + - - +
144C ALA 3.3 2.4 + - - +
145C GLU 3.2 0.2 - - - -
146C ARG* 1.3 76.8 - - - +
148C GLY* 1.3 61.4 + - - +
149C ILE* 3.3 0.9 - - + -
181C ASP* 3.5 20.0 - - - +
182C VAL 4.9 0.2 - - - -
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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