Contacts of the strand formed by residues 61 - 67 (chain F) in PDB entry 1I3R
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 61 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82E ASP* 4.1 17.8 - - - +
57F PHE* 3.2 5.6 - - - -
58F TYR 2.9 32.4 + - - +
59F ASN 3.5 0.6 + - - -
60F LEU* 1.3 84.7 - - + +
62F GLU* 1.3 67.3 + - - +
63F ASN* 3.6 4.3 + - + +
77F THR* 4.4 18.6 + - + +
79F LEU* 6.3 4.5 - - + -
111G LYS* 4.5 20.3 + - - +
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Residues in contact with GLU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E HIS* 5.5 0.8 - - - +
55F ARG* 3.1 37.5 + - + -
56F TYR 3.2 15.3 - - - +
57F PHE* 3.6 21.6 - - + -
61F GLU* 1.3 73.2 - - - +
63F ASN* 1.3 58.7 + - - +
64F LEU 4.2 7.6 - - - +
65F ARG* 2.9 41.2 + - - +
76F VAL* 3.5 23.0 - - + +
77F THR* 3.4 20.1 - - - +
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Residues in contact with ASN 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E MET* 3.8 16.0 - - - +
13F LYS* 4.8 5.0 + - - +
56F TYR* 2.9 19.7 + - - +
57F PHE 4.1 1.4 - - - -
58F TYR* 3.5 36.6 - - - +
61F GLU* 4.0 3.2 + - + +
62F GLU* 1.3 73.6 - - - +
64F LEU* 1.3 74.5 + - - +
76F VAL* 2.7 24.3 + - - -
77F THR* 3.1 22.5 + - - +
79F LEU* 4.1 6.8 - - + +
80F GLY* 3.3 28.0 - - - +
83F ASP* 4.8 1.4 - - - +
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Residues in contact with LEU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F LYS* 5.6 0.7 - - - -
55F ARG* 3.8 0.5 - - - -
56F TYR* 3.0 46.7 + - + +
62F GLU* 4.2 2.8 - - - +
63F ASN* 1.3 90.1 + - - +
65F ARG* 1.3 68.1 + - - +
73F PHE* 4.1 9.6 - - + -
74F ARG 3.7 20.0 - - - +
75F ALA* 3.8 1.3 - - - -
76F VAL* 3.7 5.3 - - - +
80F GLY* 3.3 22.7 - - - +
83F ASP* 3.9 13.0 - - + +
84F ALA* 3.8 22.9 - - + +
87F TRP* 3.6 32.3 - - + -
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Residues in contact with ARG 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ARG* 4.7 6.9 - - - +
53F LEU* 4.2 31.7 - - + +
54F VAL 3.1 15.0 - - - +
55F ARG* 4.3 12.0 - - + +
56F TYR* 4.7 1.8 - - - -
62F GLU* 2.9 32.7 + - - +
64F LEU* 1.3 78.3 - - - +
66F PHE* 1.3 60.8 + - - +
67F ASP* 4.1 7.2 + - + +
72F GLU 4.2 0.5 - - - +
73F PHE* 3.4 8.8 - - - +
74F ARG* 3.0 40.5 + - + +
76F VAL* 3.9 13.7 - - + +
51H ARG* 5.5 2.4 - - - +
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Residues in contact with PHE 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F LEU* 3.3 14.3 - - + +
53F LEU* 4.2 2.0 - - - -
54F VAL* 2.9 46.2 + - + +
65F ARG* 1.3 74.7 - - - +
67F ASP* 1.3 58.0 + - - +
68F SER* 3.9 21.3 - - - -
71F GLY* 3.6 33.9 - - - -
72F GLU* 3.8 18.6 - - - -
73F PHE* 3.7 30.5 - + + -
94F LEU* 4.4 6.7 - - + -
97F LYS* 4.1 34.5 - - + -
98F ARG* 4.1 20.6 - - + -
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Residues in contact with ASP 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ARG* 2.5 47.4 + - - +
52F LEU 3.4 3.1 - - - -
53F LEU* 4.0 8.7 - - + +
65F ARG* 4.1 8.4 + - + -
66F PHE* 1.3 74.4 - - - +
68F SER* 1.3 57.0 + - - +
69F ASP* 2.9 19.0 + - - +
70F VAL* 2.7 49.3 + - + +
71F GLY* 2.9 10.9 + - - -
72F GLU 4.3 4.6 + - - -
44H TYR* 5.1 2.4 + - - -
49H ARG* 5.2 1.9 + - - -
51H ARG* 4.1 4.7 + - - -
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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