Contacts of the strand formed by residues 104 - 109 (chain B) in PDB entry 1G82
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 104 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B SER* 3.8 4.5 - - - -
100B ILE* 2.9 32.2 + - + -
101B ALA* 2.7 29.9 + - + +
102B VAL 3.9 7.6 - - - +
103B GLY* 1.3 80.5 - - - +
105B VAL* 1.3 64.1 + - - +
135B VAL* 3.9 15.0 - - + -
136B PHE 3.4 15.5 - - - +
137B ARG* 3.8 10.5 - - + -
151B ASN* 3.5 40.2 - - + +
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 3.5 29.2 - - + -
98B ILE 3.1 18.4 - - - +
99B SER* 4.7 1.6 - - - +
100B ILE* 3.7 3.6 - - - +
104B LEU* 1.3 78.1 - - - +
106B SER* 1.3 80.2 + - - +
107B ILE* 4.7 3.8 - - + -
134B CYS 3.6 0.3 - - - +
135B VAL* 3.4 1.0 - - - -
136B PHE* 2.9 36.1 + - + +
138B GLU* 3.8 31.2 - - + +
148B TYR* 3.9 18.8 - - + -
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Residues in contact with SER 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 3.6 0.9 - - - -
98B ILE* 2.7 49.5 + - - +
100B ILE* 3.4 22.1 - - - +
105B VAL* 1.3 77.2 + - - +
107B ILE* 1.3 63.8 + - - +
115B TYR* 4.7 5.2 - - - -
130B LEU* 3.8 13.2 - - - +
134B CYS* 2.7 24.4 + - - -
135B VAL* 3.5 9.0 - - - +
136B PHE* 4.9 0.4 - - - -
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Residues in contact with ILE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 4.3 11.4 - - + -
74B LEU* 5.2 1.8 - - + -
76B ILE* 5.4 1.7 - - + +
95B LEU* 3.6 38.8 - - + -
96B GLU 3.4 3.6 - - - +
97B PHE* 3.9 36.1 - - + -
105B VAL* 4.6 4.7 - - + -
106B SER* 1.3 76.3 - - - +
108B ARG* 1.3 61.6 + - - +
109B GLY 5.3 0.2 - - - +
114B LEU 4.2 0.2 - - - +
115B TYR* 3.4 4.1 - - - +
116B LEU* 3.0 55.3 + - + +
134B CYS 4.7 1.6 + - - -
136B PHE* 5.0 6.2 - - + -
148B TYR* 4.6 16.4 - - + -
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Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 4.2 2.9 - - - -
96B GLU* 2.7 55.2 + - + +
98B ILE* 4.1 7.9 - - + +
107B ILE* 1.3 74.1 - - - +
109B GLY* 1.3 72.6 + - - +
110B VAL* 3.0 2.8 + - - +
113B GLY* 3.2 36.2 + - - +
114B LEU 3.5 6.7 - - - +
115B TYR* 3.0 43.3 + - + +
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Residues in contact with GLY 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ILE* 4.0 18.1 - - - +
92B PHE* 5.3 1.8 - - - -
94B ILE 3.9 0.4 - - - -
95B LEU* 3.8 19.5 - - - -
108B ARG* 1.3 70.3 - - - +
110B VAL* 1.3 66.0 + - - -
111B ASP 3.0 3.6 - - - -
112B SER* 3.9 4.0 - - - -
113B GLY* 2.8 24.8 + - - -
114B LEU 3.0 15.5 + - - -
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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