Contacts of the strand formed by residues 66 - 72 (chain A) in PDB entry 2C68
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 LEU 66 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ILE* 3.8 11.0 - - + +
55A LEU* 3.7 39.7 + - + +
56A LYS* 3.7 37.5 - - + +
59A ASN* 5.0 3.3 + - - +
64A VAL 3.4 4.8 + - - +
65A LYS* 1.3 81.3 + - - +
67A LEU* 1.3 61.3 + - - +
68A ASP 3.6 24.9 - - - +
69A VAL* 4.3 8.3 - - + -
78A LEU* 4.2 11.9 - - + -
79A VAL 3.7 8.5 - - - +
80A PHE* 3.8 31.2 - - + -
148A LEU* 6.1 0.2 - - + -
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 3.5 26.9 - - - +
29A VAL 5.7 0.4 - - - +
30A VAL* 3.9 15.3 - - + -
56A LYS* 4.8 5.2 - - - +
65A LYS* 3.6 39.3 - - + +
66A LEU* 1.3 75.5 - - - +
68A ASP* 1.3 74.3 + - + +
79A VAL* 2.6 20.1 + - + +
80A PHE* 3.6 8.1 - - - +
81A GLU* 3.5 30.7 - - + +
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Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LYS* 4.6 11.1 + - - +
66A LEU* 3.6 7.4 - - - +
67A LEU* 1.3 90.4 - - - +
69A VAL* 1.3 68.7 + - - +
70A ILE* 4.1 6.1 - - + -
78A LEU 3.6 0.2 - - - -
79A VAL* 2.7 50.3 + - + +
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 5.1 10.8 - - + -
52A ILE* 3.0 37.2 - - + +
53A SER* 4.9 3.8 - - - +
56A LYS* 4.2 26.9 + - + +
66A LEU* 4.3 7.2 - - + -
68A ASP* 1.3 79.9 + - - +
70A ILE* 1.3 65.8 + - - +
71A HIS* 4.1 2.6 + - + -
76A LEU* 3.7 27.1 - - + -
77A TYR 3.6 3.1 - - - -
78A LEU* 3.9 7.4 - - + -
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Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 4.6 12.3 - - - +
3A ASN* 4.7 7.4 - - - +
4A PHE* 3.6 32.5 - - + -
68A ASP* 4.7 7.4 - - + -
69A VAL* 1.3 75.5 - - - +
71A HIS* 1.3 61.1 + - - +
72A THR* 3.8 26.0 - - + +
75A LYS 3.8 1.2 - - - +
76A LEU* 3.6 4.4 - - - +
77A TYR* 2.8 56.7 + - + +
79A VAL* 3.7 19.5 - - + -
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Residues in contact with HIS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 3.1 46.2 + - + -
49A ILE* 3.6 27.1 - - + +
69A VAL* 4.1 3.8 + - + -
70A ILE* 1.3 73.5 - - - +
72A THR* 1.3 67.2 + - - +
74A ASN* 3.8 20.8 + - - -
75A LYS 2.9 25.0 + - - -
76A LEU* 4.1 11.2 - - + +
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Residues in contact with THR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 5.6 3.5 - - - +
70A ILE* 3.8 24.2 - - + +
71A HIS* 1.3 79.4 + - - +
73A GLU* 1.3 76.6 + - - +
74A ASN 3.2 2.2 - - - -
75A LYS* 2.8 33.6 + - - +
77A TYR* 4.5 11.3 - - - -
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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