Contacts of the helix formed by residues 81 - 86 (chain H) in PDB entry 6B0B
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 ASP 81 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ASN* 6.1 0.2 - - - +
38H TYR* 5.1 3.0 - - + -
73H VAL 4.6 0.2 - - - +
75H HIS* 3.4 40.9 + - + +
79H ILE 3.2 3.9 + - - +
80H PRO* 1.3 67.4 - - - +
82H TYR* 1.3 66.3 + - - +
83H LEU* 3.3 5.0 + - - +
84H LYS* 2.7 60.1 + - + +
85H LEU* 3.2 31.3 + - + +
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Residues in contact with TYR 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H HIS* 5.0 3.4 + - - +
80H PRO* 3.1 8.5 + - - +
81H ASP* 1.3 73.2 + - - +
83H LEU* 1.3 85.6 + - + +
85H LEU* 3.6 10.5 + - - +
86H SER* 3.7 10.8 + - - -
91H PHE* 6.5 0.2 - - + -
156H ALA* 4.8 4.3 - - - -
157H LEU* 4.5 25.6 - - + -
181H TYR* 4.3 9.7 + - + -
182H LYS* 4.3 5.9 - - - +
183H ALA* 3.4 33.7 + - + +
187H VAL* 3.5 38.0 - - + +
188H GLN 4.0 9.4 - - - +
189H LEU* 3.6 30.2 - - + +
190H PRO* 4.3 20.2 - - + -
193H TYR* 5.6 3.8 - - - +
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Residues in contact with LEU 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H LYS* 3.3 39.9 - - + +
71H ALA* 4.7 9.2 - - - -
73H VAL* 5.0 7.0 - - + -
75H HIS* 5.4 7.4 - - + +
81H ASP* 3.2 6.9 + - - +
82H TYR* 1.3 99.0 - - + +
84H LYS* 1.3 63.4 + - + +
86H SER* 2.7 25.6 + - - -
87H PHE* 3.8 10.5 - - - -
91H PHE* 4.6 21.5 - - + -
157H LEU* 5.0 8.3 - - + -
181H TYR* 4.7 19.5 - - + -
183H ALA* 6.4 0.2 - - + -
193H TYR* 6.2 0.2 - - - +
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Residues in contact with LYS 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ASN* 3.0 21.6 - - - +
8H ILE* 4.7 10.0 - - + +
37H PRO* 3.1 48.9 + - + +
38H TYR* 3.7 40.0 - - + +
71H ALA 4.3 14.0 + - - +
73H VAL 3.2 13.3 + - - -
75H HIS 4.9 1.4 - - - +
81H ASP* 2.7 43.3 + - + +
83H LEU* 1.3 78.4 - - + +
85H LEU* 1.3 63.6 + - + +
86H SER 3.2 1.0 + - - -
87H PHE* 3.3 25.7 + - + +
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Residues in contact with LEU 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ASN* 3.6 30.7 - - + +
80H PRO* 5.2 8.5 - - + -
81H ASP* 3.2 28.9 + - + +
82H TYR* 4.1 5.4 - - - +
83H LEU 3.3 0.4 - - - -
84H LYS* 1.3 76.7 - - + +
86H SER* 1.3 62.5 + - - +
87H PHE 3.2 9.4 - - - +
185H LYS* 3.3 19.6 + - - +
187H VAL* 3.9 30.3 - - + -
188H GLN* 5.5 4.7 - - + +
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Residues in contact with SER 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H TYR 3.7 6.4 + - - -
83H LEU* 2.7 24.1 + - - -
85H LEU* 1.3 78.4 - - - +
87H PHE* 1.3 62.3 + - - +
89H GLU* 3.3 12.4 + - - +
90H GLY 2.9 34.8 + - - +
91H PHE* 3.5 18.8 - - - -
183H ALA* 3.7 25.1 - - - -
185H LYS* 4.5 10.8 - - - +
187H VAL* 5.5 0.9 - - - -
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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