Contacts of the strand formed by residues 72 - 76 (chain C) 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 PHE 72 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C LEU 3.6 0.3 - - - +
67C TYR* 4.1 2.0 - - - -
68C CYS* 2.7 35.1 + - - +
70C THR* 3.3 27.2 - - + +
71C GLY* 1.3 80.5 - - - +
73C HIS* 1.3 63.1 + - - +
74C LEU 3.9 0.7 + - - -
84C GLY* 3.6 13.2 - - - -
85C THR* 3.5 31.0 - - - +
86C ARG* 3.7 35.9 - - + -
166C LEU* 3.9 7.7 - - + +
167C ASN 4.1 0.9 - - - -
168C LYS 3.6 13.0 - - - -
169C ASP* 3.5 18.4 - - - -
170C GLY* 3.4 24.0 - - - -
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Residues in contact with HIS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TRP* 3.9 27.8 - + - -
65C GLN* 3.7 36.9 + - + +
66C LEU 3.1 18.8 - - - +
67C TYR* 3.8 11.2 - + + -
72C PHE* 1.3 73.9 - - - +
74C LEU* 1.3 68.3 + - - +
75C GLU* 3.3 3.8 + - - +
84C GLY* 3.3 4.3 - - - -
85C THR* 2.8 40.2 + - + +
86C ARG* 4.1 3.0 + - - -
87C LYS 3.1 24.0 + - - +
88C ASP* 4.4 2.7 - - - -
90C SER* 5.5 0.9 - - - +
93C GLY* 5.3 5.2 - - - -
166C LEU* 4.0 2.0 - - - -
190C ARG* 3.3 26.4 + - - -
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Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 3.0 38.3 + - + +
73C HIS* 1.3 72.0 - - - +
75C GLU* 1.3 62.5 + - - +
76C ILE* 4.9 6.5 - - + -
82C ILE* 3.7 27.6 - - + -
83C GLN 3.6 2.7 - - - -
92C PHE 4.0 0.2 - - - +
93C GLY* 3.4 17.0 - - - +
95C LEU* 4.1 18.8 - - + +
107C ILE* 5.3 0.4 - - + -
116C LEU* 4.0 29.8 - - + -
124C LEU* 4.7 8.5 - - + -
164C VAL* 4.8 7.4 - - + -
166C LEU* 3.8 26.6 - - + +
187C PHE* 4.5 7.2 - - + -
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Residues in contact with GLU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C HIS 3.7 0.9 - - - +
74C LEU* 1.3 77.9 - - - +
76C ILE* 1.3 65.2 + - - +
77C PHE* 3.6 29.7 + - + -
82C ILE* 3.5 7.8 - - - +
83C GLN* 2.8 42.5 + - - +
84C GLY 3.3 13.2 + - - +
85C THR* 3.0 45.0 - - + +
90C SER* 3.7 13.0 + - - +
92C PHE* 3.1 22.0 - - + +
93C GLY* 4.2 0.9 - - - -
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Residues in contact with ILE 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LEU* 4.9 5.4 - - + -
75C GLU* 1.3 76.6 - - - +
77C PHE* 1.3 63.3 + - - +
81C THR 3.9 2.2 - - - -
82C ILE* 3.9 18.8 - - + -
92C PHE* 2.9 23.8 + - - +
95C LEU* 3.9 15.7 - - + -
107C ILE* 4.1 14.8 - - + +
109C GLY* 3.7 27.6 - - - +
112C SER* 3.6 28.3 + - - +
114C LEU* 4.0 21.3 - - + +
116C LEU* 4.1 20.6 - - + +
126C GLY* 4.2 8.1 - - - -
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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