Contacts of the helix formed by residues 79 - 84 (chain B) in PDB entry 3G3B
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 PRO 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B CYS* 4.3 0.2 - - - -
65B ASN* 3.3 12.3 - - + +
77B ASN 4.9 0.2 - - - +
78B ILE* 1.3 96.0 - - + +
80B CYS* 1.3 65.0 + - - +
81B SER* 3.8 17.3 - - - +
82B ALA* 3.1 22.0 + - + +
83B LEU* 3.9 1.7 + - - +
19C SER* 3.2 26.2 - - - +
85H SER* 5.1 7.0 - - - +
86H SER* 6.1 2.5 - - - +
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Residues in contact with CYS 80 (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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53B TYR* 3.4 40.3 - - + +
60B SER* 3.7 3.8 - - - -
64B CYS* 2.0 61.5 - - - -
65B ASN 2.7 17.8 + - - -
66B ASP* 3.6 14.4 - - + -
79B PRO* 1.3 72.6 - - - +
81B SER* 1.3 57.1 + - - +
83B LEU* 2.9 29.6 + - - +
84B LEU* 3.8 2.6 + - - +
41H GLN* 5.5 0.4 - - - +
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Residues in contact with SER 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 5.5 0.6 - - - -
79B PRO* 3.8 11.4 - - - +
80B CYS* 1.3 74.0 - - - +
82B ALA* 1.3 62.1 + - - +
83B LEU 3.0 5.4 - - - -
84B LEU* 3.1 22.2 + - - +
41H GLN* 6.1 1.3 - - - +
81H SER* 3.5 38.2 + - - -
82H ALA* 5.5 0.7 - - - -
84H LEU* 3.9 8.7 - - - -
85H SER* 3.4 34.2 - - - -
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Residues in contact with ALA 82 (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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78B ILE* 4.0 22.9 - - + -
79B PRO* 3.1 21.7 + - + +
81B SER* 1.3 80.5 + - - +
83B LEU* 1.3 60.9 + - - +
84B LEU 3.3 0.2 - - - -
85B SER* 3.5 19.9 - - - -
87B ASP 4.5 2.4 - - - +
90B ALA* 3.6 18.6 - - + +
91B SER 5.0 0.2 + - - -
19C SER* 4.3 12.6 - - - +
81H SER* 5.3 1.1 - - - -
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Residues in contact with LEU 83 (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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40B THR* 3.3 12.0 - - - +
53B TYR* 4.0 13.7 - - + +
54B GLY* 3.3 12.1 - - - -
55B ILE 4.6 0.2 + - - -
58B ILE* 3.9 30.5 - - + -
64B CYS* 3.9 31.2 - - + -
78B ILE* 3.9 17.9 - - + -
79B PRO 4.6 0.9 - - - +
80B CYS 2.9 11.5 + - - +
82B ALA* 1.3 77.1 - - - +
84B LEU* 1.3 58.0 + - - +
85B SER 3.5 2.2 - - - +
90B ALA* 3.7 37.7 - - + +
91B SER* 3.7 21.9 + - - +
94B CYS* 4.6 2.2 - - + -
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Residues in contact with LEU 84 (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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40B THR* 3.2 27.7 + - - +
41B GLN* 3.6 25.6 + - + +
42B ALA 3.7 19.1 - - - +
43B THR* 3.8 13.9 - - - +
53B TYR* 3.8 20.9 - - + -
54B GLY 3.8 8.1 - - - +
80B CYS 4.1 6.1 - - - +
81B SER* 3.1 19.8 + - - +
83B LEU* 1.3 77.0 - - - +
85B SER* 1.3 67.7 + - - +
86B SER 3.8 0.3 + - - -
41H GLN* 5.4 6.1 - - + -
81H SER* 3.9 10.5 - - - -
84H LEU* 3.8 29.4 - - + -
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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