Contacts of the strand formed by residues 103 - 107 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I SER* 4.3 11.4 + - - -
7I ARG* 3.8 7.0 + - - +
12I VAL* 4.4 1.9 - - - +
96I ILE* 5.4 0.5 - - - +
97I VAL 3.5 6.0 + - - -
98I ALA* 3.5 11.1 - - - +
102I GLU* 1.3 81.3 + - - +
104I LEU* 1.3 71.3 + - - +
115I PRO* 3.2 24.6 - - - +
119I GLN* 3.6 29.1 + - - +
121I LEU* 3.7 15.8 - - - +
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Residues in contact with LEU 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443C ILE* 5.2 0.9 - - + -
71I LEU* 3.8 10.9 - - + +
72I LEU* 3.6 35.7 - - + +
75I ALA* 3.6 30.3 - - + -
96I ILE* 3.5 3.1 - - - -
97I VAL* 2.6 43.3 + - + +
102I GLU* 4.3 5.6 - - - +
103I SER* 1.3 87.3 - - - +
105I ILE* 1.3 62.4 + - - +
106I ILE* 5.1 0.4 - - + -
112I VAL* 4.6 9.0 - - + -
113I VAL 3.7 22.9 - - - +
114I GLN* 4.0 17.5 - - + -
121I LEU* 3.2 16.0 - - - +
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Residues in contact with ILE 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94I MET* 4.8 5.4 - - - -
95I LEU 3.2 12.8 - - - +
96I ILE* 4.5 3.1 - - + -
104I LEU* 1.3 80.3 - - - +
106I ILE* 1.3 67.1 + - - +
107I THR* 5.0 3.6 - - + +
111I ASP 3.7 1.4 - - - +
112I VAL* 3.6 4.0 - - - -
113I VAL* 3.0 56.9 + - + +
121I LEU* 4.3 19.7 - - + -
122I ALA 4.7 5.8 - - - +
123I ILE* 3.4 29.4 - - + -
27J MET* 4.1 26.5 - - + -
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Residues in contact with ILE 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56I LEU* 4.0 13.3 - - + +
60I PHE* 3.3 43.5 - - + -
75I ALA* 4.0 20.9 - - + +
78I LEU* 4.6 11.4 - - + -
79I ALA* 5.6 1.6 - - + +
82I TRP* 4.6 5.4 - - + -
94I MET* 3.1 3.9 - - - +
95I LEU* 2.6 45.4 + - + +
97I VAL* 4.1 17.3 - - + -
104I LEU* 5.1 0.7 - - + -
105I ILE* 1.3 78.6 - - - +
107I THR* 1.3 74.9 + - - +
111I ASP 3.8 9.6 - - - +
112I VAL* 4.5 9.4 - - + -
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Residues in contact with THR 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56I LEU* 4.3 3.4 - - - -
82I TRP* 3.9 4.0 - - - -
93I ALA 3.7 5.4 - - - -
94I MET* 4.1 22.7 - - - +
105I ILE* 5.0 5.2 - - + +
106I ILE* 1.3 87.1 - - - +
108I GLY* 1.3 59.6 + - - +
109I ILE* 3.0 23.0 - - + +
110I GLY* 3.0 16.6 + - - -
111I ASP* 2.1 41.7 + - - +
113I VAL* 5.7 3.8 - - + -
27J MET* 5.2 10.3 - - + -
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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