Contacts of the strand formed by residues 50 - 58 (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 LEU 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B THR* 3.5 5.1 - - - -
23B LEU* 2.8 33.5 + - - +
44B PHE* 3.7 31.4 - - + -
47B ASN* 3.2 28.9 - - + +
48B LEU* 3.9 9.6 - - + +
49B PRO* 1.3 74.7 - - - +
51B LYS* 1.3 60.6 + - - +
66B LEU* 3.9 16.8 - - + +
67B PHE 3.8 21.1 - - - +
68B ASP* 4.1 15.0 - - + +
69B PRO* 5.6 1.1 - - - -
74B ASN* 5.8 0.9 - - - +
76B TRP* 3.8 33.2 - - + +
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Residues in contact with LYS 51 (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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20B GLY* 3.2 37.0 - - - +
21B LYS 3.5 5.6 - - - +
22B THR* 4.3 9.6 - - + +
50B LEU* 1.3 73.0 - - - +
52B VAL* 1.3 65.8 + - - +
53B SER 3.3 1.2 + - - -
66B LEU* 3.1 4.9 - - - -
67B PHE* 2.9 63.8 + - + +
69B PRO* 4.2 21.9 - - + +
4C G 4.5 3.8 + - - -
5C A 3.4 22.8 + - - -
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Residues in contact with VAL 52 (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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18B PHE* 3.5 20.0 - - + +
19B LYS* 4.2 5.5 - - - +
20B GLY* 2.7 31.5 + - - -
21B LYS 3.0 15.0 + - - +
23B LEU* 4.7 1.3 - - + -
51B LYS* 1.3 70.1 - - - +
53B SER* 1.3 61.3 + - - +
54B ASN 3.8 22.2 - - - +
55B VAL* 4.1 15.3 - - + -
64B PHE* 4.5 10.3 - - + -
65B GLU 3.6 6.1 - - - +
66B LEU* 4.0 20.0 - - + -
67B PHE* 4.9 0.2 - - - -
102B PHE* 3.7 26.2 - - + -
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Residues in contact with SER 53 (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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19B LYS* 2.8 23.1 + - - +
51B LYS 3.3 2.6 + - - -
52B VAL* 1.3 74.0 - - - +
54B ASN* 1.3 75.9 + - - +
65B GLU* 2.8 41.2 + - - +
67B PHE* 3.6 29.2 - - - +
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Residues in contact with ASN 54 (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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15B GLU* 2.6 25.3 - - - +
19B LYS* 3.7 11.1 + - - +
52B VAL* 3.5 5.7 - - - +
53B SER* 1.3 93.1 + - - +
55B VAL* 1.3 68.0 + - - +
56B ASP* 4.2 5.6 - - + +
63B TRP* 4.5 1.8 - - - +
64B PHE* 3.3 3.3 - - - -
65B GLU* 2.7 52.5 + - + +
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Residues in contact with VAL 55 (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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11B ALA* 3.9 29.2 - - + +
14B LEU* 3.9 22.2 - - + +
15B GLU* 2.8 48.7 + - + +
18B PHE* 5.5 0.9 - - + -
19B LYS* 5.8 0.2 - - - -
52B VAL* 4.1 9.2 - - + -
54B ASN* 1.3 80.1 - - - +
56B ASP* 1.3 62.8 + - - +
62B LEU* 4.1 9.9 - - + -
63B TRP 3.3 9.4 - - - +
64B PHE* 3.5 26.9 - - + -
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Residues in contact with ASP 56 (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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11B ALA* 4.6 1.6 - - - -
54B ASN* 4.2 6.9 - - + -
55B VAL* 1.3 76.0 - - - +
57B THR* 1.3 87.0 + - - +
62B LEU* 3.7 1.0 - - - +
63B TRP* 2.9 66.3 + - + +
141B LYS* 2.9 20.1 + - - -
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Residues in contact with THR 57 (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* 3.6 28.9 - - + +
8B ALA* 3.8 16.6 + - - +
11B ALA* 3.3 26.5 - - + -
56B ASP* 1.3 94.6 + - - +
58B LYS* 1.3 63.6 + - - +
59B GLY 4.6 3.0 + - - -
61B PHE 3.2 9.6 - - - -
62B LEU* 3.9 7.0 - - + -
63B TRP* 3.7 7.4 - - - -
138B ASP* 4.4 1.8 + - - -
141B LYS* 2.7 38.1 + - - +
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Residues in contact with LYS 58 (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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57B THR* 1.3 75.6 - - - +
59B GLY* 1.3 66.9 + - - +
60B LYS 3.2 0.5 + - - -
61B PHE* 3.0 24.6 + - - +
63B TRP* 3.8 2.8 - - + -
132B LEU* 2.7 59.5 + - + +
133B ASN* 4.4 4.8 + - - +
135B LEU* 3.0 23.4 + - + +
136B GLY 3.3 23.6 - - - -
137B PRO* 4.6 5.3 - - - +
138B ASP* 3.5 11.9 - - + +
169B SER* 4.2 5.8 - - - +
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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