Contacts of the strand formed by residues 61 - 67 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ASP* 4.9 12.5 - - - +
143A HIS* 4.9 0.4 - - - +
57B PHE* 3.3 6.4 - - - -
58B TYR 3.2 30.2 + - - +
59B ASN 3.5 2.2 + - - -
60B LEU* 1.3 88.4 - - + +
62B GLU* 1.3 69.5 + - - +
63B ASN* 3.4 4.7 + - + +
77B THR* 4.2 19.5 + - + +
79B LEU* 6.1 0.7 - - - +
111C LYS* 4.2 22.8 + - - -
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A HIS* 6.0 0.2 + - - -
55B ARG* 3.0 38.6 + - + +
56B TYR 3.3 12.8 - - - +
57B PHE* 3.7 21.3 - - + -
61B GLU* 1.3 75.6 - - - +
63B ASN* 1.3 61.1 + - - +
64B LEU 4.0 9.0 - - - +
65B ARG* 2.5 45.6 + - - +
76B VAL* 3.9 19.4 - - + +
77B THR* 3.5 19.1 - - - +
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Residues in contact with ASN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET* 4.3 9.0 - - - +
13B LYS* 5.0 4.6 + - - +
56B TYR* 2.9 16.5 + - - +
57B PHE 3.9 1.6 - - - -
58B TYR* 3.6 36.8 - - - +
61B GLU* 3.9 2.6 + - + +
62B GLU* 1.3 74.5 - - - +
64B LEU* 1.3 76.3 + - - +
75B ALA* 3.6 0.2 - - - -
76B VAL* 2.8 25.4 + - - -
77B THR* 3.0 30.8 + - - +
79B LEU* 4.1 9.6 - - + +
80B GLY* 3.6 21.0 - - - +
83B ASP* 4.6 3.6 - - - +
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LYS* 5.5 0.4 - - - -
55B ARG* 3.7 0.9 - - - -
56B TYR* 2.9 44.7 + - + +
62B GLU* 3.8 3.7 - - - +
63B ASN* 1.3 94.1 + - - +
65B ARG* 1.3 67.8 + - - +
73B PHE* 4.0 12.1 - - + -
74B ARG 3.3 33.4 - - - +
75B ALA* 3.9 2.7 - - - +
76B VAL* 3.9 3.9 - - - +
80B GLY* 3.8 17.9 - - - +
83B ASP* 3.8 17.7 - - + +
84B ALA* 4.0 11.7 - - + -
87B TRP* 3.6 31.4 - - + -
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Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ARG* 5.0 5.5 - - - +
53B LEU* 4.1 29.5 - - + +
54B VAL 3.0 16.6 - - - +
55B ARG* 3.7 13.8 - - + +
56B TYR* 4.4 2.0 - - - -
62B GLU* 2.5 40.6 + - - +
64B LEU* 1.3 81.2 - - - +
66B PHE* 1.3 60.5 + - - +
67B ASP* 4.4 9.4 + - - +
72B GLU 4.2 0.2 - - - +
73B PHE* 3.4 9.1 - - - -
74B ARG* 3.0 42.6 + - + +
76B VAL* 4.0 11.5 - - + +
51D ARG* 6.0 0.8 - - - +
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Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LEU* 3.3 28.2 - - + +
53B LEU* 3.5 1.7 - - - -
54B VAL* 2.9 41.3 + - + +
65B ARG* 1.3 74.4 - - - +
67B ASP* 1.3 57.3 + - - +
68B SER* 3.9 23.8 - - - -
71B GLY 3.7 25.1 - - - -
72B GLU* 3.8 18.8 - - - -
73B PHE* 3.7 31.0 - + + -
94B LEU* 4.4 6.5 - - + -
97B LYS* 4.0 37.0 - - + -
98B ARG* 4.1 14.4 - - + -
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ARG* 2.7 41.1 + - - +
52B LEU 3.5 3.4 - - - -
53B LEU* 4.3 9.0 - - + +
65B ARG* 4.1 10.0 + - + +
66B PHE* 1.3 74.0 - - - +
68B SER* 1.3 59.3 + - - +
69B ASP* 2.9 34.2 + - - +
70B VAL* 2.9 38.6 + - + +
71B GLY* 3.0 10.4 + - - -
72B GLU 4.2 5.5 + - - -
44D TYR* 4.9 4.2 + - - -
51D ARG* 4.4 5.7 + - - -
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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