Contacts of the strand formed by residues 50 - 57 (chain A) in PDB entry 3I0W
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 LYS 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLY 3.7 0.3 - - - +
46A ILE* 3.3 5.9 - - - +
47A ALA 3.0 33.1 + - - +
48A PHE 3.6 8.3 - - - +
49A GLU* 1.3 84.1 - - - +
51A VAL* 1.3 62.8 + - - +
52A VAL* 4.0 3.2 + - + +
65A ASN* 2.7 32.0 + - - +
66A ILE* 4.2 3.7 - - - +
70A GLU* 2.8 36.3 + - - +
75A TRP* 4.0 20.9 - - + +
148A LEU* 3.8 3.9 - - - +
291A EDO 3.4 21.5 - - - +
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Residues in contact with VAL 51 (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 ILE* 3.9 18.8 - - + -
45A GLY 3.4 5.4 - - - +
46A ILE* 4.4 3.4 - - + -
50A LYS* 1.3 74.0 - - - +
52A VAL* 1.3 66.3 + - - +
65A ASN* 2.8 28.2 + - - +
148A LEU* 3.7 13.2 - - + -
150A TYR* 3.7 37.5 - - + -
155A TYR* 3.6 37.0 - - + -
291A EDO 2.9 25.5 + - - -
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Residues in contact with VAL 52 (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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35A TRP* 3.8 15.9 - - + -
44A ILE* 3.4 2.5 - - - +
45A GLY 2.8 34.3 + - - +
50A LYS* 4.5 5.2 - - + +
51A VAL* 1.3 83.1 - - - +
53A GLU* 1.3 62.5 + - - +
54A VAL* 4.0 13.5 - - + -
63A ILE* 3.4 31.4 - - + -
64A TYR 3.8 5.2 - - - +
65A ASN* 4.7 0.2 - - - -
66A ILE* 3.9 14.8 - - + -
75A TRP* 3.7 38.1 - - + -
79A PHE* 5.4 0.7 - - + -
150A TYR* 5.5 0.2 - - - -
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Residues in contact with GLU 53 (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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38A GLN* 4.4 3.8 - - - +
40A ASN* 4.8 3.1 + - - +
42A ASN* 3.1 35.0 + - + +
43A TYR 3.3 10.1 - - - +
44A ILE* 3.8 18.9 - - + +
52A VAL* 1.3 74.5 - - - +
54A VAL* 1.3 64.6 + - - +
63A ILE* 3.5 2.6 - - - -
64A TYR* 2.8 53.8 + - + -
150A TYR* 2.6 39.1 + - + +
151A LYS* 3.3 19.4 - - - +
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Residues in contact with VAL 54 (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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21A PHE* 4.5 6.7 - - + -
23A LEU* 3.4 26.5 - - + +
27A PHE* 4.4 11.0 - - + -
35A TRP* 3.8 22.0 - - + -
42A ASN* 3.4 4.9 - - - -
43A TYR 2.9 29.9 + - - +
52A VAL* 4.0 7.4 - - + -
53A GLU* 1.3 80.0 - - - +
55A GLN* 1.3 64.7 + - - +
61A VAL* 3.7 26.5 - - + -
62A VAL 3.4 3.1 - - - +
63A ILE* 4.4 7.4 - - + -
79A PHE* 3.9 19.5 - - + -
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Residues in contact with GLN 55 (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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23A LEU* 4.1 2.9 - - - -
42A ASN* 3.0 33.6 + - - +
54A VAL* 1.3 77.1 - - - +
56A LYS* 1.3 65.3 + - - +
57A ILE* 3.5 32.8 + - + +
60A ASP 4.0 0.2 - - - +
61A VAL* 3.4 4.4 - - - +
62A VAL* 2.8 40.3 + - + +
64A TYR* 2.8 37.6 + - + -
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Residues in contact with LYS 56 (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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18A VAL* 4.6 12.1 + - - -
21A PHE* 3.0 31.8 + - + +
22A GLU* 3.1 16.9 + - - +
23A LEU* 3.9 14.9 - - + +
42A ASN* 5.0 0.2 + - - -
55A GLN* 1.3 76.8 - - - +
57A ILE* 1.3 65.2 + - - +
58A GLY 3.2 26.2 + - - +
59A GLU* 4.3 8.7 - - - +
60A ASP 3.5 4.7 - - - +
61A VAL* 3.4 28.3 - - + -
295A EDO 3.6 24.2 - - - +
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Residues in contact with ILE 57 (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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55A GLN* 3.5 36.8 - - + +
56A LYS* 1.3 78.5 - - - +
58A GLY* 1.3 66.1 + - - +
59A GLU 3.2 0.7 + - - -
60A ASP* 2.9 31.5 + - + +
62A VAL* 4.8 13.0 - - + -
64A TYR* 5.6 0.2 - - - +
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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