Contacts of the strand formed by residues 102 - 108 (chain G) 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 102 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100G GLY 3.1 7.1 + - - +
101G THR* 1.3 75.4 - - - +
103G VAL* 1.3 61.9 + - - +
104G THR* 5.6 1.6 - - + -
121G THR* 4.2 18.4 - - + -
122G ALA 3.5 14.1 - - - +
123G ALA* 4.4 10.5 - - + -
153G PHE* 2.8 51.5 + - + +
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Residues in contact with VAL 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G VAL* 4.3 5.8 - - + -
101G THR 3.7 10.8 - - - +
102G LEU* 1.3 79.0 - - - +
104G THR* 1.3 71.6 + - - +
121G THR* 3.5 0.7 - - - +
122G ALA 2.8 35.4 + - - +
124G MET* 4.1 16.6 - - + -
129G ALA* 3.6 26.5 - - + -
131G PHE* 3.5 23.8 - - + -
150G ILE* 4.0 19.5 - - + -
151G THR 3.1 10.1 - - - +
152G VAL* 4.4 10.5 - - + -
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Residues in contact with THR 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G LEU* 5.4 1.8 - - + -
103G VAL* 1.3 81.0 - - - +
105G VAL* 1.3 67.9 + - - +
106G MET* 5.0 7.5 - - - +
120G ALA 3.2 7.2 - - - -
121G THR* 3.7 22.7 - - + +
131G PHE* 4.2 0.4 - - - -
149G THR 3.5 0.9 - - - +
150G ILE* 3.3 6.2 - - - +
151G THR* 2.9 41.9 + - - -
153G PHE* 3.4 30.1 - - + -
65H SER* 5.0 2.6 - - - -
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Residues in contact with VAL 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G PHE* 3.5 21.5 - - + -
91G VAL* 4.8 0.2 - - + -
104G THR* 1.3 75.6 - - - +
106G MET* 1.3 72.3 + - - +
117G LEU* 3.2 19.4 - - + +
120G ALA* 3.0 22.3 + - + +
131G PHE* 3.4 32.3 - - + -
134G LEU* 4.7 9.4 - - + -
136G PHE* 5.3 0.4 - - + -
148G LEU* 3.9 36.3 - - + -
149G THR 3.4 5.2 - - - +
150G ILE* 4.7 7.2 - - + -
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Residues in contact with MET 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G THR* 5.0 7.2 - - - +
105G VAL* 1.3 81.3 - - - +
107G ALA* 1.3 60.9 + - - +
114G SER* 5.9 1.3 - - - +
115G ALA 5.9 0.2 - - - -
117G LEU* 3.6 7.2 - - - -
148G LEU* 3.2 6.9 - - - +
149G THR* 2.7 46.5 + - + +
151G THR* 4.2 7.2 - - - +
30H THR* 5.4 0.4 - - - -
54H GLU* 4.9 21.8 - - - +
63H ASN* 3.6 26.9 - - + +
64H LEU* 3.5 45.1 - - - +
65H SER* 3.5 10.8 - - - +
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Residues in contact with ALA 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G MET* 1.3 77.7 - - - +
108G GLY* 1.3 54.9 + - - +
114G SER* 3.2 0.5 + - - -
115G ALA* 2.7 39.2 + - + -
117G LEU* 3.9 9.1 - - + +
136G PHE* 4.2 10.3 - - + -
146G PHE* 3.9 21.3 - - + -
147G THR 3.3 5.6 - - - +
148G LEU* 3.6 19.7 - - + -
63H ASN* 3.2 12.6 + - - -
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Residues in contact with GLY 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G ALA* 1.3 75.9 - - - +
109G ASN* 1.3 62.3 + - - +
112G ASN 3.1 13.2 - - - -
113G TYR 3.8 3.8 - - - -
146G PHE* 3.6 9.2 - - - -
147G THR* 2.9 35.8 + - - -
61H GLY 3.3 18.8 + - - -
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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