Contacts of the strand formed by residues 103 - 108 (chain R) in PDB entry 1G3I
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 SER 103 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5R SER* 5.2 6.3 - - - -
7R ARG* 3.3 21.7 + - - -
12R VAL* 5.3 0.9 - - - -
71R LEU* 4.8 0.2 - - - -
96R ILE* 6.3 0.7 - - - -
97R VAL 3.2 7.9 - - - -
98R ALA* 3.3 17.7 - - - -
102R GLU* 1.3 79.9 + - - +
104R LEU* 1.3 75.2 + - - +
115R PRO* 3.3 26.5 - - - +
119R GLN* 5.0 6.1 + - - +
121R LEU* 4.5 7.2 - - - -
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Residues in contact with LEU 104 (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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71R LEU* 5.4 3.8 - - + -
72R LEU* 3.8 29.6 - - + +
75R ALA* 4.1 13.2 - - + -
96R ILE* 3.2 6.8 - - - +
97R VAL* 2.4 56.2 + - + +
102R GLU* 4.3 12.3 - - + +
103R SER* 1.3 89.0 - - - +
105R ILE* 1.3 62.2 + - - +
106R ILE* 5.1 0.4 - - + -
112R VAL* 3.4 26.9 - - + -
113R VAL 3.5 16.6 - - - +
114R GLN* 3.6 26.2 - - + +
115R PRO* 4.2 0.2 - - + -
121R LEU* 3.4 12.6 - - - +
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Residues in contact with ILE 105 (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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27Q MET* 4.5 19.5 - - + -
94R MET* 4.4 13.0 - - + -
95R LEU 3.0 11.9 - - - +
96R ILE* 4.2 2.7 - - + -
104R LEU* 1.3 77.7 - - - +
106R ILE* 1.3 69.3 + - - +
107R THR* 4.4 4.5 + - + +
111R ASP 3.8 0.5 - - - +
112R VAL* 3.5 3.8 - - - +
113R VAL* 2.9 65.8 + - + +
121R LEU* 3.9 20.0 - - + -
122R ALA 4.8 3.8 - - - +
123R ILE* 3.3 32.3 - - + -
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Residues in contact with ILE 106 (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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56R LEU* 4.4 7.5 - - + +
60R PHE* 3.5 40.8 - - + -
75R ALA* 4.0 14.4 - - + +
78R LEU* 4.8 17.7 - - + -
79R ALA 5.5 2.0 - - - +
82R TRP* 5.1 2.0 - - + -
94R MET* 3.4 1.9 - - - -
95R LEU* 2.7 49.5 + - + +
97R VAL* 4.0 17.3 - - + -
104R LEU* 5.1 0.2 - - + -
105R ILE* 1.3 80.9 - - - +
107R THR* 1.3 73.2 + - - +
111R ASP 3.4 15.7 - - - +
112R VAL* 4.5 15.0 - - + -
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Residues in contact with THR 107 (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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27Q MET* 6.0 5.8 - - + -
56R LEU* 3.9 2.2 - - - -
82R TRP* 3.9 3.3 - - - -
93R ALA 3.9 4.5 - - - -
94R MET* 4.1 26.2 - - + -
105R ILE* 5.2 6.1 - - + +
106R ILE* 1.3 85.5 - - - +
108R GLY* 1.3 59.5 + - - +
109R ILE* 2.9 23.9 + - + +
110R GLY* 3.0 18.2 + - - -
111R ASP* 2.2 46.1 + - - +
113R VAL* 5.9 4.5 - - + -
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Residues in contact with GLY 108 (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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56R LEU* 3.3 22.5 - - - +
82R TRP* 3.3 21.6 + - - -
90R LYS* 3.7 1.2 - - - -
91R LEU* 2.9 43.4 + - - -
93R ALA 3.0 13.3 + - - -
107R THR* 1.3 71.5 - - - +
109R ILE* 1.3 57.4 + - - +
110R GLY 3.3 0.7 - - - -
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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