Contacts of the helix formed by residues 133 - 139 (chain C) in PDB entry 1REP
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 PRO 133 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C HIS 5.1 4.1 - - - +
57C ASP* 3.8 17.5 - - - +
116C ILE* 3.4 26.9 - - + -
130C HIS* 4.0 7.4 - - + +
131C ILE 2.8 8.9 - - - +
132C ASN* 1.3 86.9 - - - +
134C TYR* 1.3 66.0 + - + +
135C LEU 2.9 5.9 + - - -
136C ILE* 3.1 26.5 + - + +
137C PRO* 4.0 2.9 - - - +
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Residues in contact with TYR 134 (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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112C PHE* 4.1 22.7 - + + -
132C ASN* 2.7 27.4 + - - +
133C PRO* 1.3 80.6 - - + +
135C LEU* 1.3 59.5 + - - +
136C ILE 3.6 0.4 - - - -
137C PRO* 3.9 12.4 - - - +
138C PHE* 3.9 16.6 - - - -
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Residues in contact with LEU 135 (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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94C VAL* 3.9 23.1 - - + -
96C PHE* 3.8 17.7 - - + -
112C PHE* 3.4 38.1 - - + -
113C PRO 4.0 17.5 - - - +
114C TRP* 4.2 10.3 - - + +
131C ILE* 4.5 2.5 - - + -
132C ASN* 2.8 19.7 + - + +
134C TYR* 1.3 78.1 - - - +
136C ILE* 1.3 65.6 + - - +
137C PRO 3.4 2.0 - - - -
138C PHE* 3.4 7.6 + - + +
139C PHE* 3.2 52.8 + - + -
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Residues in contact with ILE 136 (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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46C ILE* 4.2 28.9 - - + -
56C HIS* 4.1 37.0 - - + +
58C GLY* 3.9 28.9 - - - +
131C ILE* 5.1 4.5 - - + -
132C ASN 4.7 5.2 - - - +
133C PRO* 3.1 17.0 - - + +
135C LEU* 1.3 73.8 - - - +
137C PRO* 1.3 72.8 - - + +
139C PHE* 2.8 20.7 + - + +
140C ILE* 3.0 19.7 + - + +
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Residues in contact with PRO 137 (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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133C PRO 4.0 5.2 - - - +
134C TYR* 3.9 12.6 - - - +
135C LEU 3.5 2.7 - - - -
136C ILE* 1.3 95.8 - - + +
138C PHE* 1.3 63.8 + - + +
140C ILE* 2.5 31.6 + - + +
142C LEU* 2.9 33.4 - - + +
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Residues in contact with PHE 138 (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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21C SER* 2.9 33.4 + - - -
23C ASP* 4.1 18.2 - - + -
24C LEU* 4.7 3.1 - - - +
96C PHE* 3.5 68.4 - + + -
110C GLU* 5.4 4.3 - - + -
112C PHE* 4.2 22.4 - + - -
134C TYR 3.9 23.1 - - - -
135C LEU* 3.8 7.6 - - + +
136C ILE 3.2 0.6 - - - -
137C PRO* 1.3 78.1 - - + +
139C PHE* 1.3 60.3 + - - +
140C ILE 2.9 6.1 + - - -
142C LEU* 4.9 1.1 - - - -
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Residues in contact with PHE 139 (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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19C VAL 4.1 4.2 - - - +
20C GLN* 4.3 2.1 - - - +
21C SER 4.5 3.8 - - - +
24C LEU* 3.4 37.0 - - + -
39C LEU* 4.1 15.0 - - + -
43C VAL* 3.6 30.9 - - + +
46C ILE* 4.3 23.6 - - + -
47C ARG* 4.0 3.5 + - - -
96C PHE* 4.1 5.4 - + - -
114C TRP* 3.4 26.9 - + - -
131C ILE* 3.8 23.1 - - + -
135C LEU* 3.3 36.6 - - + +
136C ILE* 2.8 15.8 + - + +
138C PHE* 1.3 73.2 - - + +
140C ILE* 1.3 70.0 + - + +
141C GLY 4.2 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