Contacts of the helix formed by residues 130 - 135 (chain E) in PDB entry 4DOH
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 TYR 130 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C ASP* 3.9 27.4 - - - +
167C ILE* 4.7 5.6 - - + +
170C GLN* 3.8 23.7 - - - +
174C GLU* 5.3 0.5 + - - -
104E TYR 3.0 27.8 - - - -
105E GLU* 4.4 10.2 + - - +
106E HIS 3.5 7.2 - - - -
107E GLN* 3.5 32.8 - - + -
128E ARG* 5.4 1.1 - - + +
129E PHE* 1.3 73.4 - - - +
131E PRO* 1.3 67.6 - - - +
132E PHE* 3.6 16.9 - - + -
133E LEU* 2.9 45.5 + - + -
134E GLU* 3.0 27.9 + - + +
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Residues in contact with PRO 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E MET* 3.3 27.1 - - + -
52E ASN* 3.9 3.1 - - - +
101E THR 3.9 5.6 - - - +
103E ASP 3.8 13.0 - - - +
104E TYR* 4.0 1.1 - - - +
106E HIS 3.6 9.4 - - - +
108E TYR* 3.7 20.6 - - + -
129E PHE* 3.5 40.6 - - + +
130E TYR* 1.3 85.9 - - - +
132E PHE* 1.3 63.7 + - - +
135E THR* 2.9 32.1 + - - +
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Residues in contact with PHE 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C GLN* 3.5 32.5 - - + -
50E MET* 4.8 2.7 - - - -
104E TYR* 3.3 40.9 - + + +
105E GLU* 6.1 0.2 - - - -
130E TYR* 3.1 19.3 + - + -
131E PRO* 1.3 81.2 - - - +
133E LEU* 1.3 74.1 + - + +
175E ILE* 3.9 24.5 - - + -
176E TYR* 2.6 51.6 + + - -
225E PRO* 6.0 0.2 - - + -
227E ARG* 2.8 12.7 + - - -
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Residues in contact with LEU 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ARG* 4.6 6.5 - - - +
166C ASP* 4.0 25.8 - - + +
170C GLN* 3.5 22.4 - - - +
130E TYR* 2.9 43.1 + - + +
132E PHE* 1.3 94.7 - - + +
134E GLU* 1.3 63.9 + - + +
225E PRO* 3.5 39.3 - - + +
226E PRO 5.4 1.0 - - - +
227E ARG* 3.7 20.3 + - - +
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Residues in contact with GLU 134 (chain E).
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* 4.4 21.7 + - - +
45E PHE* 5.8 0.5 - - - +
47E SER* 4.6 3.5 - - - +
128E ARG 3.7 13.2 - - - +
129E PHE* 3.9 20.5 - - + -
130E TYR* 3.0 38.3 + - + +
133E LEU* 1.3 84.5 - - + +
135E THR* 1.3 69.0 + - - +
136E GLN* 3.3 6.9 + - - +
227E ARG* 5.0 5.4 - - - +
228E ARG* 5.2 7.8 + - - +
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Residues in contact with THR 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E SER* 2.5 29.4 + - - -
48E ILE 3.5 0.3 + - - -
49E ASN 3.4 5.5 + - - -
50E MET* 3.1 33.8 + - - +
131E PRO* 2.9 16.8 + - - +
133E LEU 3.8 0.4 - - - -
134E GLU* 1.3 77.6 - - - +
136E GLN* 1.3 68.0 + - - +
137E ILE* 3.9 0.8 + - + -
172E MET* 4.5 5.2 - - + -
176E TYR* 3.5 30.3 - - + +
227E ARG* 2.8 29.0 + - - +
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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