Contacts of the strand formed by residues 61 - 68 (chain B) in PDB entry 3A46
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 PHE 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B THR* 3.2 6.2 - - - -
58B LYS 3.0 35.5 + - - +
59B GLY 3.4 0.2 - - - -
60B LYS* 1.3 78.7 - - - +
62B LEU* 1.3 58.9 + - - +
63B TRP* 3.6 26.2 - + + -
79B TRP* 3.7 48.7 - + + -
80B ASN 3.7 15.7 - - - -
81B THR* 3.9 16.2 - - + -
128B LEU* 3.8 16.8 - - + -
131B LYS* 3.9 30.5 - - + +
132B LEU* 3.9 16.8 - - + -
135B LEU* 3.8 13.6 - - + +
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Residues in contact with LEU 62 (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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7B VAL* 4.0 7.6 - - + +
11B ALA* 3.9 27.4 - - + +
14B LEU* 3.9 18.4 - - + -
55B VAL* 4.1 5.4 - - + -
56B ASP 3.4 10.8 - - - +
57B THR* 3.9 6.7 - - + -
60B LYS 3.8 0.6 + - - -
61B PHE* 1.3 76.3 - - - +
63B TRP* 1.3 71.0 + - - +
64B PHE* 3.6 32.5 - - + -
79B TRP* 3.9 0.2 - - - -
80B ASN* 2.8 50.6 + - + +
82B PHE* 4.1 24.2 - - + -
88B TRP* 4.7 0.4 - - - +
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Residues in contact with TRP 63 (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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54B ASN* 6.1 1.2 - - - +
55B VAL* 3.3 3.8 - - - +
56B ASP* 2.9 80.4 + - + +
57B THR* 3.7 26.5 - - - -
58B LYS* 3.8 2.7 - - + -
61B PHE* 3.6 30.3 - + + -
62B LEU* 1.3 77.8 - - - +
64B PHE* 1.3 76.2 + - - +
65B GLU* 4.5 9.1 + - + +
77B TYR* 4.1 9.1 - + - -
78B ILE 3.1 15.0 - - - +
79B TRP* 4.4 1.6 - - + -
128B LEU* 3.6 29.5 - - + +
132B LEU* 3.5 37.9 - - + -
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Residues in contact with PHE 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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14B LEU* 3.8 26.7 - - + -
18B PHE* 5.4 5.4 - + + -
52B VAL* 4.5 13.9 - - + -
54B ASN 3.3 4.9 - - - +
55B VAL* 3.5 26.5 - - + +
62B LEU* 3.6 23.6 - - + -
63B TRP* 1.3 76.4 - - - +
65B GLU* 1.3 60.9 + - - +
66B LEU* 3.7 16.9 - - + +
77B TYR* 3.2 10.9 - - - +
78B ILE* 3.0 55.9 + - + -
80B ASN* 5.3 0.9 - - + -
88B TRP* 3.8 32.8 - + - -
100B LEU* 4.5 12.3 - - + -
102B PHE* 5.3 7.4 - + - -
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Residues in contact with GLU 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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52B VAL* 3.6 1.4 - - - +
53B SER* 2.8 41.3 + - - +
54B ASN* 2.7 35.5 + - + +
63B TRP* 4.2 9.3 + - + +
64B PHE* 1.3 72.6 - - - +
66B LEU* 1.3 69.6 + - - +
67B PHE* 6.3 0.2 - - + -
75B LYS* 3.3 29.4 + - + +
76B TRP 3.5 2.9 - - - +
77B TYR* 3.5 27.6 + - + -
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Residues in contact with LEU 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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23B LEU* 3.8 31.6 - - + -
44B PHE* 4.2 6.5 - - + -
50B LEU* 3.9 28.9 - - + +
51B LYS 3.1 10.1 - - - +
52B VAL* 4.0 21.5 - - + -
53B SER* 4.3 1.3 - - - +
64B PHE* 3.7 28.7 - - + +
65B GLU* 1.3 83.0 - - - +
67B PHE* 1.3 62.1 + - - +
75B LYS* 3.3 6.6 - - - +
76B TRP* 2.7 45.0 + - - +
78B ILE* 4.1 14.1 - - + -
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Residues in contact with PHE 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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50B LEU* 3.8 9.4 - - - -
51B LYS* 2.9 70.2 + - + +
52B VAL 4.9 0.2 - - - -
53B SER* 3.6 33.7 - - - +
66B LEU* 1.3 75.5 - - - +
68B ASP* 1.3 71.1 + - - +
69B PRO* 3.7 21.7 - - + +
72B LYS* 3.6 38.4 - - + +
74B ASN 3.7 10.3 - - - +
75B LYS* 4.7 5.8 - - + -
76B TRP 4.9 0.2 - - - +
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Residues in contact with ASP 68 (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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47B ASN 5.6 1.1 - - - +
49B PRO 5.1 5.8 - - - +
50B LEU* 4.1 16.9 - - + +
67B PHE* 1.3 76.7 - - - +
69B PRO* 1.3 66.2 - - - +
70B ASN* 3.0 28.5 + - - +
71B ASP* 2.6 42.4 + - + +
72B LYS* 2.8 14.2 + - - -
74B ASN* 4.0 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
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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