Contacts of the helix formed by residues 145 - 149 (chain C) in PDB entry 4EOO
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 145 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C LYS* 3.8 9.7 + - - +
51C GLU* 4.7 1.1 - - - -
55C LEU* 6.3 0.2 - - - +
64C VAL* 4.8 2.4 - - - +
80C PHE* 6.2 1.0 - - - -
125C HIS* 3.4 13.2 + - - +
127C ASP* 3.9 9.4 - - - +
132C ASN* 3.4 18.8 + - - -
144C ALA* 1.3 82.8 - - + +
146C PHE* 1.3 58.4 + - - +
147C GLY* 3.1 19.7 + - - -
148C LEU 4.5 3.0 + - - -
301C ATP 3.0 48.6 + - - +
302C MG 2.5 22.9 - - - -
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Residues in contact with PHE 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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47C THR 4.7 0.2 - - - +
50C ARG* 5.2 0.2 - - - +
51C GLU* 3.7 39.6 + - + +
54C LEU* 5.2 4.7 - - + -
55C LEU* 3.5 22.1 - - + +
58C LEU* 3.6 22.7 - - + -
63C ILE* 3.8 27.6 - - + -
64C VAL* 5.0 0.4 - - + -
118C CYS* 3.9 22.2 - - - -
123C VAL* 4.2 8.7 - - + -
125C HIS* 3.7 27.4 - + + -
143C LEU* 3.9 17.9 - - + -
144C ALA* 4.1 4.7 - - - -
145C ASP* 1.3 73.7 - - - +
147C GLY* 1.3 62.1 + - - +
148C LEU 3.2 3.6 - - - +
149C ALA* 3.3 35.7 + - + +
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Residues in contact with GLY 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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47C THR* 3.6 33.6 - - - +
50C ARG* 5.9 2.3 - - - +
51C GLU* 4.1 16.6 - - - -
145C ASP* 3.1 18.8 + - - -
146C PHE* 1.3 77.1 - - - +
148C LEU* 1.3 65.3 + - - +
149C ALA 3.5 1.0 - - - +
301C ATP 5.5 1.8 - - - -
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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
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47C THR* 5.3 6.3 - - + -
50C ARG* 5.8 0.2 - - - -
125C HIS 3.6 7.2 + - - +
126C ARG* 2.8 55.7 + - + +
127C ASP* 4.1 31.8 + - + +
145C ASP* 4.5 2.6 + - - -
146C PHE* 3.2 1.0 - - - +
147C GLY* 1.3 84.1 - - - +
149C ALA* 1.3 61.3 + - - +
162C GLU 4.8 3.8 - - - +
163C VAL* 4.4 13.0 - - + -
164C VAL 4.0 14.1 - - - +
165C THR* 5.8 1.3 - - + +
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Residues in contact with ALA 149 (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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50C ARG* 3.6 22.2 + - - +
54C LEU* 4.0 13.7 - - + -
123C VAL* 4.2 1.1 - - + -
124C LEU 3.1 18.2 - - - +
125C HIS 3.5 7.9 + - - +
126C ARG* 4.0 1.4 + - - -
146C PHE* 3.3 41.4 + - + +
147C GLY 3.5 0.5 - - - +
148C LEU* 1.3 83.0 - - - +
150C ARG* 1.3 64.2 + - - +
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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