Contacts of the strand formed by residues 148 - 152 (chain R) in PDB entry 1E50
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 LEU 148 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72R CYS* 5.7 0.2 - - - -
75R LEU* 3.8 15.7 - - + -
89R PHE* 3.6 29.6 - - + -
105R VAL* 3.5 26.9 - - + -
106R MET 2.9 6.5 - - - +
107R ALA* 4.3 5.8 - - + -
134R LEU* 5.3 0.7 - - + -
136R PHE* 4.3 10.3 - - + -
146R PHE 4.7 0.9 - - - +
147R THR* 1.3 81.6 - - - +
149R THR* 1.3 65.2 + - - +
150R ILE* 4.1 6.1 - - + +
160R ALA 4.3 0.4 - - - -
161R THR* 3.6 4.2 - - - -
162R TYR* 3.2 39.8 + - + -
165R ALA* 3.5 23.3 - - + -
166R ILE* 4.1 17.7 - - + -
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Residues in contact with THR 149 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104R THR 3.3 9.7 - - - +
105R VAL* 3.8 1.2 - - - -
106R MET* 2.8 39.6 + - + +
147R THR* 4.0 6.9 + - - +
148R LEU* 1.3 81.0 + - - +
150R ILE* 1.3 60.6 + - - +
151R THR* 3.4 12.5 + - - +
159R VAL* 3.6 27.8 - - + -
160R ALA 3.3 4.5 - - - -
161R THR* 4.5 6.2 + - - +
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Residues in contact with ILE 150 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R THR* 3.7 28.9 - - + -
70R PHE* 5.3 4.3 - - + -
71R LEU 5.2 0.9 - - - +
72R CYS* 3.9 13.5 - - + -
89R PHE* 4.8 3.8 - - + -
91R VAL* 3.4 38.6 - - + -
103R VAL* 3.4 22.9 - - + -
104R THR 3.3 5.4 - - - +
105R VAL* 4.6 11.0 - - + +
148R LEU* 5.1 7.0 - - + -
149R THR* 1.3 73.7 - - - +
151R THR* 1.3 60.0 + - - +
152R VAL* 3.8 8.0 - - + +
158R GLN 3.6 1.9 - - - +
159R VAL* 3.4 2.9 - - - -
160R ALA* 2.8 49.0 + - + +
161R THR 6.0 0.4 - - - -
162R TYR* 5.9 1.6 - - + -
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Residues in contact with THR 151 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102R LEU 3.7 1.4 - - - +
103R VAL* 3.7 0.4 - - - -
104R THR* 2.9 37.2 + - - -
106R MET* 5.3 6.0 - - - -
149R THR* 3.8 18.7 + - - +
150R ILE* 1.3 75.6 + - - +
152R VAL* 1.3 57.2 + - - +
153R PHE* 2.9 42.3 + - + -
157R PRO* 4.4 13.7 - - + -
158R GLN 3.6 4.9 - - - +
159R VAL* 4.4 11.5 - - + +
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Residues in contact with VAL 152 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70R PHE* 3.3 44.4 - - + -
97R VAL* 4.0 14.8 - - + -
101R THR* 3.5 18.8 - - + -
102R LEU 3.7 3.8 - - - -
103R VAL* 4.1 24.7 - - + -
124R MET* 4.7 2.9 - - + -
150R ILE* 4.8 7.6 - - + +
151R THR* 1.3 67.5 - - - +
153R PHE* 1.3 51.5 + - - +
154R THR* 2.6 33.5 + - - +
157R PRO* 3.7 0.7 - - - +
158R GLN* 2.9 30.6 + - + +
160R ALA* 6.2 0.4 - - + -
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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