Contacts of the strand formed by residues 70 - 75 (chain H) in PDB entry 2A3W
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 GLU 70 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H LYS* 3.8 6.1 - - - +
66H GLU* 3.6 23.4 + - + +
67H ARG* 2.9 61.5 + - + +
68H VAL 5.1 0.9 - - - +
69H GLY* 1.3 80.2 - - - +
71H TYR* 1.3 68.4 + - - +
81H THR* 3.7 26.8 - - + +
82H SER 3.5 2.0 - - - -
83H LYS* 3.9 34.7 + - + +
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Residues in contact with TYR 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H LEU* 4.6 5.8 - - + -
63H VAL* 5.3 2.7 - - + -
64H TYR 3.9 2.5 - - - -
65H LYS* 3.5 35.1 + - + +
70H GLU* 1.3 79.4 - - - +
72H SER* 1.3 62.8 - - - +
81H THR* 3.3 2.4 - - - -
82H SER 2.8 37.6 + - - +
84H VAL* 3.7 18.8 - - + -
86H GLU* 2.6 34.7 + - - -
92H VAL* 3.5 19.2 - - - +
94H ILE* 3.6 25.1 - - + -
107H PHE* 3.6 31.9 - + + -
109H ILE* 3.6 27.6 - - + -
114H LEU* 4.5 1.8 - - + -
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Residues in contact with SER 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H LEU 3.6 0.2 - - - +
63H VAL* 3.4 5.4 - - - +
64H TYR* 2.8 44.1 + - - -
66H GLU* 2.7 32.3 + - - +
70H GLU 4.3 0.2 - - - -
71H TYR* 1.3 72.0 - - - +
73H LEU* 1.3 60.9 + - - +
74H TYR* 4.2 15.5 - - - -
79H LYS* 4.0 2.1 - - - +
80H VAL 3.2 6.3 - - - -
81H THR* 2.6 24.8 + - - +
107H PHE* 3.7 5.5 - - - -
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Residues in contact with LEU 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H PHE* 4.2 3.6 - - + -
61H LEU* 3.8 25.1 - - + -
62H LEU 3.3 13.0 - - - +
63H VAL* 4.1 11.2 - - + -
72H SER* 1.3 73.9 - - - +
74H TYR* 1.3 65.1 + - - +
75H ILE* 3.8 26.5 - - + -
78H HIS 3.8 0.2 - - - +
79H LYS* 3.4 2.4 - - - -
80H VAL* 2.9 38.6 + - + +
96H VAL* 4.0 17.3 - - + -
98H TRP* 4.2 8.3 - - + -
105H ALA* 3.7 28.5 - - + -
107H PHE* 3.7 17.7 - - + -
119H LEU* 4.1 3.2 - - + +
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Residues in contact with TYR 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C CPJ 3.1 38.3 - - - +
59H ASN* 3.8 26.7 - - + +
61H LEU* 3.3 5.9 - - - -
62H LEU* 2.8 64.2 + - + +
64H TYR* 4.0 18.8 - + + -
66H GLU* 4.0 5.1 + - - -
72H SER* 4.2 5.6 - - - -
73H LEU* 1.3 78.9 - - - +
75H ILE* 1.3 66.6 + - - +
77H ARG 3.9 14.8 - - - -
78H HIS 3.0 9.0 - - - +
79H LYS* 3.4 46.1 - - + -
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Residues in contact with ILE 75 (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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33H PHE* 3.6 36.8 - - + -
60H GLU 3.4 3.6 - - - +
61H LEU* 4.5 3.8 - - + -
73H LEU* 3.8 21.1 - - + -
74H TYR* 1.3 81.5 - - - +
76H GLY* 1.3 69.8 + - - +
77H ARG 3.2 0.7 - - - -
78H HIS 2.8 18.3 + - - +
98H TRP* 3.8 37.5 - - + -
119H LEU* 3.8 15.1 - - + +
120H ARG* 3.0 16.5 - - + +
123H TYR* 3.8 18.4 - - + -
125H VAL* 4.4 9.9 - - + -
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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
------------------------------------------------------------
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