Contacts of the strand formed by residues 51 - 58 (chain A) in PDB entry 3DBD
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 ALA 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LYS* 3.4 4.7 - - - +
48A GLY 2.8 38.2 + - - +
49A GLY 4.8 0.3 - - - -
50A PHE* 1.3 79.9 - - - +
52A LYS* 1.3 62.3 + - - +
68A LYS* 5.0 10.1 - - + +
69A VAL 3.5 6.3 - - - +
70A VAL* 3.8 27.0 - - + +
313A 3FR 3.8 15.7 - - + -
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Residues in contact with LYS 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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26A ILE* 4.8 9.3 - - + +
44A PHE* 4.5 8.5 - - + -
46A GLY 3.7 4.9 - - - +
47A LYS* 4.5 17.0 - - + -
50A PHE 4.0 6.0 + - - +
51A ALA* 1.3 77.6 - - - +
53A CYS* 1.3 61.4 + - - +
54A TYR* 3.9 27.7 + - + +
67A GLY 3.7 0.9 - - - +
69A VAL* 2.9 42.9 + - + +
313A 3FR 4.2 2.0 - - - -
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Residues in contact with CYS 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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44A PHE* 3.7 2.6 - - - -
45A LEU* 3.0 48.2 + - + -
46A GLY 2.9 17.4 + - - +
52A LYS* 1.3 71.9 - - - +
54A TYR* 1.3 68.5 + - - +
66A ALA* 4.2 11.7 - - - -
67A GLY 3.5 12.6 - - - -
68A LYS* 4.7 2.0 - - + +
313A 3FR 3.5 53.5 - - + +
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Residues in contact with TYR 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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26A ILE* 3.8 26.3 - - + +
41A ARG* 3.7 48.6 + - + -
42A GLY 3.8 7.6 - - - -
43A ARG 3.7 2.7 - - - +
44A PHE* 3.5 43.0 - + + -
45A LEU* 3.7 6.1 - - - -
52A LYS* 3.9 28.7 + - + +
53A CYS* 1.3 76.6 - - - +
55A GLU* 1.3 62.4 + - - +
56A ILE* 3.3 6.5 + - + +
66A ALA 3.8 0.3 - - - -
67A GLY* 2.8 36.0 + - - +
69A VAL* 4.3 10.5 - - + -
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Residues in contact with GLU 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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40A MET 3.9 0.3 - - - +
42A GLY* 2.8 28.1 + - - -
43A ARG* 2.8 64.8 + - + +
45A LEU* 3.5 15.1 - - + +
54A TYR* 1.3 68.9 - - - +
56A ILE* 1.3 60.2 - - - +
57A THR* 4.7 4.8 + - - +
64A VAL* 3.6 34.1 - - + +
65A PHE 3.6 4.7 - - - +
118A ILE* 4.3 10.5 - - + +
120A ARG* 4.8 10.4 + - - -
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Residues in contact with ILE 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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30A LEU* 3.9 28.0 - - + -
39A TYR* 4.1 22.7 - - + -
40A MET 3.4 10.8 - - - +
41A ARG* 4.1 7.9 - - - -
54A TYR* 3.3 13.2 + - + +
55A GLU* 1.3 77.0 - - - +
57A THR* 1.3 61.7 + - - +
58A ASP 4.3 0.2 + - - -
63A GLU 3.9 0.2 - - - +
64A VAL* 3.6 2.8 - - - +
65A PHE* 2.8 54.0 + - + +
67A GLY* 3.8 22.2 - - - +
69A VAL* 6.1 0.7 - - + -
106A PHE* 6.1 0.4 - - + -
113A TYR* 6.6 0.2 - - + -
115A VAL* 3.8 36.1 - - + -
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Residues in contact with THR 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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39A TYR* 3.3 4.4 - - - -
40A MET* 2.8 50.2 + - - +
42A GLY* 5.7 1.4 + - - -
55A GLU* 4.7 6.1 + - - +
56A ILE* 1.3 76.2 + - - +
58A ASP* 1.3 68.9 + - - +
59A MET* 3.2 2.5 + - - +
62A LYS* 3.8 35.2 - - + +
63A GLU 3.5 4.5 - - - +
64A VAL* 4.7 12.1 - - + +
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Residues in contact with ASP 58 (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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37A LYS* 3.4 34.6 + - - +
38A ARG 3.5 8.3 + - - +
39A TYR* 3.4 23.8 + - + -
56A ILE 4.3 0.2 - - - -
57A THR* 1.3 70.1 - - - +
59A MET* 1.3 57.4 + - - +
60A ASP* 3.1 12.0 + - - +
61A THR* 2.9 45.2 + - - +
62A LYS* 2.7 33.3 + - - +
63A GLU* 3.0 18.9 + - + +
65A PHE* 4.9 3.2 - - + -
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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