Contacts of the strand formed by residues 80 - 85 (chain H) in PDB entry 1R8Y
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 SER 80 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58H HIS* 3.1 29.5 + - - +
59H ARG* 3.6 16.1 + - - +
60H VAL 2.9 23.7 + - - +
78H GLY 4.0 0.2 + - - -
79H PHE* 1.3 73.9 - - - +
81H VAL* 1.3 60.6 + - - +
82H MET 4.2 0.2 + - - -
109H ASN 5.5 4.3 - - - -
130H PHE* 5.9 0.3 - - - -
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Residues in contact with VAL 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H VAL* 3.4 16.4 - - + +
62H ASP* 4.9 3.8 - - + -
71H SER* 3.8 19.1 - - - +
74H LEU* 4.1 11.0 - - + -
75H VAL* 3.2 40.3 - - + +
79H PHE* 3.8 9.8 + - + +
80H SER* 1.3 77.4 - - - +
82H MET* 1.3 66.0 + - - +
83H SER* 3.5 20.0 - - - +
109H ASN 4.3 5.7 + - - +
110H TRP* 3.3 8.9 - - - +
111H VAL* 3.3 22.5 + - - +
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Residues in contact with MET 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H ARG* 5.1 5.2 - - - +
60H VAL 2.8 9.0 + - - +
61H LEU* 3.3 18.7 - - + +
62H ASP 2.9 23.9 + - - -
80H SER 4.2 0.4 + - - -
81H VAL* 1.3 72.7 - - - +
83H SER* 1.3 66.2 + - - +
84H VAL* 4.5 10.1 - - + -
111H VAL* 3.4 33.4 - - + +
113H GLU* 5.4 4.9 - - + -
124H VAL* 3.9 28.0 - - + -
125H LEU 5.3 6.7 - - - +
130H PHE* 4.1 19.0 - - + -
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Residues in contact with SER 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H ASP* 3.3 7.2 - - - -
65H CYS* 3.7 22.4 - - - -
71H SER* 3.1 23.0 + - - -
81H VAL* 3.5 1.0 - - - +
82H MET* 1.3 73.6 - - - +
84H VAL* 1.3 65.6 + - - +
110H TRP* 2.7 30.8 + - - -
111H VAL 2.8 8.9 + - - +
112H ILE* 3.3 5.7 - - - +
113H GLU 3.1 22.7 + - - +
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Residues in contact with VAL 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H LEU* 4.4 9.6 - - + -
62H ASP 2.9 9.4 + - - +
63H VAL* 3.5 22.6 - - + +
65H CYS* 2.9 26.7 + - - +
82H MET* 4.5 10.8 - - - -
83H SER* 1.3 78.8 - - - +
85H ASP* 1.3 61.9 + - - +
91H LEU* 4.6 0.4 - - - -
113H GLU* 3.2 27.1 - - + +
114H GLU 4.6 0.2 - - - -
115H ALA* 3.6 30.1 - - + +
120H LEU* 4.5 4.7 - - + -
124H VAL* 4.0 17.3 - - + -
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Residues in contact with ASP 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G GLU* 2.5 34.3 - - - +
63H VAL 4.7 4.0 - - - -
64H ALA* 3.8 2.3 - - - -
65H CYS* 3.7 5.5 + - + -
66H GLY* 2.9 28.5 + - - +
84H VAL* 1.3 74.6 - - - +
86H ALA* 1.3 75.1 + - - +
87H SER* 2.8 18.1 + - - +
90H MET* 5.3 0.7 - - - -
91H LEU* 3.7 29.4 - - + +
113H GLU 3.4 4.4 + - - -
114H GLU* 3.3 9.2 - - - +
115H ALA 2.8 25.6 + - - -
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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