Contacts of the helix formed by residues 75 - 82 (chain B) in PDB entry 4B8Z
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 GLY 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B GLY* 1.3 73.7 - - - -
76B LEU* 1.3 66.4 + - - -
77B PHE* 3.3 3.1 - - - -
78B ARG* 3.0 12.4 + - - +
79B ASN* 3.0 15.2 + - - -
184B ASP 2.8 15.4 + - - -
185B GLY 3.4 26.2 - - - -
186B HIS* 3.9 6.1 - - - -
901B GDP 3.4 6.7 - - - -
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLY* 1.3 67.5 - - - -
77B PHE* 1.3 73.5 + - + +
79B ASN* 3.1 22.1 + - + +
80B ILE* 3.0 26.7 + - + +
139B SER* 3.7 29.4 - - - -
140B ASN* 6.2 1.6 - - + -
276B SER* 3.7 16.2 - - - +
277B ASP 4.1 0.2 - - - +
278B GLY* 3.7 27.4 - - - +
279B GLN 5.3 0.4 - - - +
901B GDP 2.8 69.4 + - - +
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Residues in contact with PHE 77 (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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75B GLY 3.3 0.6 - - - -
76B LEU* 1.3 84.5 - - + +
78B ARG* 1.4 61.2 + - - +
79B ASN 3.4 0.2 - - - -
80B ILE* 3.9 12.2 + - + +
81B LYS* 3.6 26.1 + - - +
183B GLU 4.0 16.4 - - - +
208B TRP* 3.4 39.5 - + + -
275B LYS* 4.3 0.7 - - + -
276B SER* 3.6 31.0 - - - -
901B GDP 3.5 36.6 - - - -
273D THR* 4.2 5.8 - - + +
274D THR* 3.6 49.4 - - + +
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Residues in contact with ARG 78 (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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72B MET* 3.6 37.6 - - - +
73B VAL 3.4 20.8 + - - +
74B GLY* 4.1 7.2 - - - -
75B GLY 3.0 11.7 + - - +
77B PHE* 1.4 75.2 - - - +
79B ASN* 1.3 59.5 + - - +
81B LYS* 3.3 5.5 + - - -
82B TYR* 3.0 50.7 + - + -
86B PHE* 3.6 15.5 - - + -
179B ASN* 5.8 1.6 - - - +
183B GLU 4.5 2.9 + - - -
184B ASP* 3.8 48.3 + - - +
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Residues in contact with ASN 79 (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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74B GLY 3.0 20.2 + - - -
75B GLY 3.0 22.4 + - - -
76B LEU* 3.1 10.8 + - - +
78B ARG* 1.3 76.0 - - - +
80B ILE* 1.3 56.9 + - - +
81B LYS 3.3 0.7 + - - -
83B ASN* 2.8 38.3 + - - +
86B PHE* 3.4 34.2 - - - +
139B SER 3.4 12.1 - - - +
140B ASN* 3.7 19.7 - - + +
143B TYR* 3.4 19.5 - - - +
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Residues in contact with ILE 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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76B LEU* 3.0 28.4 + - + +
77B PHE* 3.9 9.6 - - + +
79B ASN* 1.3 73.2 - - - +
81B LYS* 1.3 60.5 + - - +
83B ASN* 3.7 9.7 + - - +
139B SER* 3.3 35.4 - - - +
276B SER* 5.7 7.0 - - - +
210D THR* 3.5 27.9 - - + +
212D ASN* 6.0 0.2 + - - -
273D THR* 2.9 48.5 + - + +
275D LYS 5.3 1.3 - - - +
277D ASP* 5.3 1.8 - - - +
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Residues in contact with LYS 81 (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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77B PHE 3.6 13.4 + - - +
78B ARG* 3.3 10.5 + - - +
79B ASN 3.2 0.4 - - - -
80B ILE* 1.3 81.8 - - - +
82B TYR* 1.4 97.0 + - + +
83B ASN 3.9 1.2 + - - -
183B GLU* 5.6 7.0 - - + +
273D THR* 3.7 26.5 - - + +
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Residues in contact with TYR 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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72B MET* 4.6 4.0 - - + -
78B ARG* 3.0 49.1 + - + +
79B ASN 3.5 3.3 + - - -
81B LYS* 1.4 112.6 - - + +
83B ASN* 1.3 57.1 + - - +
84B LEU 3.3 3.1 - - - +
85B ASP* 3.3 29.8 + - + +
86B PHE* 3.0 33.6 + + + -
183B GLU* 5.8 0.3 + - - -
184B ASP* 5.2 3.6 - - - -
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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
------------------------------------------------------------
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