Contacts of the strand formed by residues 103 - 107 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5L SER* 4.2 11.4 + - - -
7L ARG* 3.8 11.5 + - - +
12L VAL* 4.3 2.1 - - - +
96L ILE* 5.4 0.2 - - - +
97L VAL 3.4 6.3 - - - -
98L ALA* 3.4 13.4 - - - +
102L GLU* 1.3 82.0 + - - +
104L LEU* 1.3 74.8 + - - +
115L PRO* 3.3 21.0 - - - +
119L GLN* 3.7 25.3 + - - +
121L LEU* 3.9 14.3 - - - +
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Residues in contact with LEU 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443F ILE* 4.7 4.9 - - + -
71L LEU* 3.6 17.2 - - + +
72L LEU* 3.5 36.8 - - + -
75L ALA* 3.7 21.8 - - + -
96L ILE* 3.3 4.9 - - - -
97L VAL* 2.6 47.4 + - + +
102L GLU* 4.0 8.1 - - + +
103L SER* 1.3 96.8 - - - +
105L ILE* 1.3 61.2 + - - +
106L ILE* 5.1 0.9 - - + -
112L VAL* 4.7 4.7 - - + -
113L VAL 3.7 21.1 - - - +
114L GLN* 4.3 13.5 - - + -
121L LEU* 3.5 10.6 - - - +
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Residues in contact with ILE 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G MET* 4.2 24.9 - - + -
94L MET* 5.0 5.8 - - + -
95L LEU 3.3 13.9 - - - +
96L ILE* 4.3 4.9 - - + -
104L LEU* 1.3 78.4 - - - +
106L ILE* 1.3 64.6 + - - +
107L THR* 5.1 3.4 - - + +
111L ASP 3.8 1.0 - - - +
112L VAL* 3.5 3.3 - - - -
113L VAL* 3.0 55.2 + - + +
121L LEU* 4.2 20.6 - - + -
122L ALA 4.4 5.2 - - - +
123L ILE* 3.3 30.1 - - + -
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Residues in contact with ILE 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56L LEU* 3.8 7.3 - - + +
60L PHE* 3.5 41.3 - - + -
75L ALA* 3.9 21.5 - - + +
78L LEU* 4.6 20.0 - - + -
79L ALA* 5.4 1.8 - - + -
82L TRP* 5.3 2.7 - - + -
94L MET* 3.2 3.3 - - - -
95L LEU* 2.7 46.9 + - + +
97L VAL* 4.2 17.0 - - + -
104L LEU* 5.1 0.7 - - + -
105L ILE* 1.3 78.2 - - - +
107L THR* 1.3 75.2 + - - +
111L ASP 3.6 12.1 - - - +
112L VAL* 4.4 7.9 - - + -
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Residues in contact with THR 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G MET* 5.4 8.1 - - + -
56L LEU* 4.4 2.9 - - - -
82L TRP* 4.2 4.9 - - - -
93L ALA 3.7 4.0 - - - -
94L MET* 4.1 24.7 - - - +
105L ILE* 5.1 4.5 - - + +
106L ILE* 1.3 86.6 - - - +
108L GLY* 1.3 58.9 + - - +
109L ILE* 2.8 24.0 - - + +
110L GLY* 3.0 17.3 + - - -
111L ASP* 2.2 40.6 + - - +
113L VAL* 5.7 4.7 - - + -
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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