Contacts of the strand formed by residues 103 - 108 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Q SER* 5.2 6.3 - - - -
7Q ARG* 3.2 23.0 + - - +
12Q VAL* 5.3 0.4 - - - -
71Q LEU* 4.4 0.4 - - - +
96Q ILE* 6.3 0.7 - - - -
97Q VAL 3.2 7.6 - - - -
98Q ALA* 3.2 17.9 - - - -
102Q GLU* 1.3 80.3 + - - +
104Q LEU* 1.3 75.4 + - - +
115Q PRO* 3.3 23.7 - - - +
119Q GLN* 3.7 10.8 + - - +
121Q LEU* 4.6 6.3 - - - -
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Residues in contact with LEU 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71Q LEU* 5.4 3.4 - - + -
72Q LEU* 3.8 30.1 - - + +
75Q ALA* 4.1 13.0 - - + -
96Q ILE* 3.2 6.4 - - - +
97Q VAL* 2.4 55.1 + - + +
102Q GLU* 4.4 11.4 - - + +
103Q SER* 1.3 89.9 - - - +
105Q ILE* 1.3 62.1 + - - +
106Q ILE* 5.1 0.4 - - + -
112Q VAL* 3.4 25.8 - - + -
113Q VAL 3.5 16.6 - - - +
114Q GLN* 3.6 26.0 - - + +
115Q PRO* 4.2 0.2 - - + -
121Q LEU* 3.4 12.5 - - - +
443W ILE* 4.8 0.4 - - + -
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Residues in contact with ILE 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P MET* 4.4 20.2 - - + -
94Q MET* 4.4 15.7 - - + -
95Q LEU 3.0 11.4 - - - +
96Q ILE* 4.3 2.0 - - + -
104Q LEU* 1.3 78.2 - - - +
106Q ILE* 1.3 66.3 + - - +
107Q THR* 4.3 3.9 - - + +
111Q ASP 3.8 0.5 - - - +
112Q VAL* 3.5 4.2 - - - +
113Q VAL* 2.9 66.0 + - + +
121Q LEU* 3.9 20.9 - - + -
122Q ALA 4.8 3.1 - - - +
123Q ILE* 3.3 32.3 - - + -
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Residues in contact with ILE 106 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Q LEU* 4.4 5.8 - - + +
60Q PHE* 3.5 41.3 - - + -
75Q ALA* 4.1 18.6 - - + +
78Q LEU* 4.8 17.0 - - + -
79Q ALA 5.4 2.2 - - - +
82Q TRP* 5.1 4.3 - - + -
94Q MET* 3.4 2.8 - - - -
95Q LEU* 2.7 50.3 + - + +
97Q VAL* 4.0 18.6 - - + -
105Q ILE* 1.3 80.2 - - - +
107Q THR* 1.3 72.9 + - - +
108Q GLY 4.1 0.2 + - - -
111Q ASP 3.4 15.0 - - - +
112Q VAL* 4.5 9.4 - - + -
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Residues in contact with THR 107 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P MET* 5.9 7.0 - - + -
56Q LEU* 3.9 2.5 - - - -
82Q TRP* 3.9 3.5 - - - -
93Q ALA 3.9 4.3 - - - -
94Q MET* 3.9 26.9 - - - -
105Q ILE* 5.2 6.3 - - + +
106Q ILE* 1.3 82.6 - - - +
108Q GLY* 1.3 59.8 + - - +
109Q ILE* 3.2 23.1 + - + +
110Q GLY* 2.9 18.4 + - - -
111Q ASP* 2.2 46.6 + - - +
113Q VAL* 5.9 4.0 - - + -
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Residues in contact with GLY 108 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Q LEU* 3.3 21.8 - - - +
82Q TRP* 3.3 21.6 + - - -
90Q LYS* 3.7 1.2 - - - -
91Q LEU* 3.0 42.1 + - - -
93Q ALA 3.0 13.5 + - - -
107Q THR* 1.3 71.5 - - - +
109Q ILE* 1.3 57.9 + - - +
110Q 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