Contacts of the strand formed by residues 49 - 58 (chain D) in PDB entry 4K81
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 49 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D THR* 4.9 12.0 + - - +
4D TYR* 4.4 7.1 + - - -
45D VAL* 3.5 1.7 - - - -
46D ILE 2.9 30.7 + - - +
47D ASP 3.1 2.4 + - - +
48D GLY* 1.3 76.2 - - - +
50D THR* 1.3 67.6 + - - +
51D CYS* 3.7 6.3 + - + -
164D ARG* 3.2 41.1 + - - +
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Residues in contact with THR 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 3.9 30.4 - - - +
2D THR* 4.0 12.6 + - - -
43D GLN* 4.0 17.9 - - + +
44D VAL 3.5 9.9 - - - +
45D VAL* 3.8 19.6 - - + +
48D GLY 3.8 3.5 + - - -
49D GLU* 1.3 75.5 - - - +
51D CYS* 1.3 64.6 + - - +
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Residues in contact with CYS 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 3.7 8.3 - - - -
2D THR* 3.0 20.4 - - - +
4D TYR* 3.6 32.5 - - + -
43D GLN* 3.4 3.3 - - - +
44D VAL* 2.9 43.8 + - - +
46D ILE* 4.2 25.6 - - - -
49D GLU* 3.7 16.6 - - - -
50D THR* 1.3 74.1 - - - +
52D LEU* 1.3 58.3 + - - +
53D LEU* 4.0 1.3 - - + -
160D VAL* 4.5 1.6 - - - -
164D ARG* 4.7 4.0 - - - -
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 3.6 25.3 - - + +
2D THR 2.9 10.0 + - - +
3D GLU* 3.2 22.3 - - + +
4D TYR* 2.7 32.6 + - - +
41D ARG* 3.1 42.4 - - + +
42D LYS* 3.7 28.9 - - - +
43D GLN* 4.0 11.0 - - + +
51D CYS* 1.3 72.7 - - - +
53D LEU* 1.3 62.5 + - - +
54D ASP* 3.6 2.3 + - + +
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D TYR* 3.6 15.0 - - + +
6D LEU* 4.5 11.9 - - + -
23D LEU* 4.5 10.1 - - + -
41D ARG* 3.3 8.0 - - - +
42D LYS* 2.8 40.6 + - + +
44D VAL* 3.8 35.0 - - + -
46D ILE* 4.5 1.1 - - + -
51D CYS* 4.6 1.8 - - - -
52D LEU* 1.3 76.5 - - - +
54D ASP* 1.3 61.2 + - - +
55D ILE* 3.6 26.6 + - + +
156D PHE* 4.9 2.2 - - + -
157D TYR* 4.5 14.4 - - + -
160D VAL* 3.6 29.2 - - + -
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Residues in contact with ASP 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLU* 4.3 14.0 - - + +
4D TYR 2.6 13.9 + - - +
5D LYS* 3.2 36.8 - - + +
6D LEU 2.9 26.3 + - - +
39D SER* 4.6 10.2 - - - -
40D TYR 3.4 11.2 - - - +
41D ARG* 4.2 25.5 + - + +
52D LEU* 3.6 3.6 + - + -
53D LEU* 1.3 73.2 - - - +
55D ILE* 1.3 62.2 + - - +
56D LEU* 4.0 2.5 + - - +
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Residues in contact with ILE 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 3.4 15.9 - - + +
8D VAL* 4.0 21.5 - - + -
20D THR* 3.7 22.7 - - + -
23D LEU* 3.6 30.7 - - + -
24D ILE* 4.3 14.6 - - + -
38D ASP 3.8 0.5 - - - +
39D SER* 3.2 5.1 - - - -
40D TYR* 2.7 46.7 + - + +
53D LEU* 4.0 27.1 - - + +
54D ASP* 1.3 78.4 + - - +
56D LEU* 1.3 66.6 + - - +
156D PHE* 4.1 11.2 - - + -
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Residues in contact with LEU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LYS* 5.1 4.7 - - - +
6D LEU 2.9 14.8 + - - +
7D VAL* 3.6 11.4 - - + +
8D VAL* 2.9 29.6 + - - +
37D GLU* 3.6 35.4 - - + +
38D ASP 3.6 4.3 - - - +
39D SER* 4.0 22.9 - - - -
54D ASP* 4.0 3.1 + - - +
55D ILE* 1.3 73.6 - - - +
57D ASP* 1.3 62.3 + - - +
58D THR* 3.8 6.3 + - + -
71D TYR* 3.5 35.2 - - + -
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Residues in contact with ASP 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D VAL* 4.5 4.4 - - - +
16D LYS* 3.5 22.9 - - - +
17D SER* 2.5 42.0 + - - -
20D THR* 4.5 8.5 + - + +
35D THR* 3.4 14.2 + - - +
37D GLU* 3.5 2.8 - - - +
38D ASP* 2.7 40.2 + - + +
40D TYR* 4.0 24.1 + - + -
55D ILE 4.0 0.6 + - - -
56D LEU* 1.3 71.6 - - - +
58D THR* 1.3 65.9 + - - +
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Residues in contact with THR 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D VAL* 3.5 26.0 - - + -
8D VAL 2.8 25.4 + - - +
9D VAL* 3.8 8.7 - - - -
10D GLY 4.9 0.5 + - - -
16D LYS* 3.3 18.1 - - - -
17D SER* 5.3 0.2 + - - -
35D THR* 3.9 9.6 - - - +
36D ILE 3.9 5.6 - - - -
37D GLU* 4.9 2.5 - - - +
56D LEU* 4.0 10.1 - - + +
57D ASP* 1.3 85.1 + - - +
59D ALA* 1.3 63.6 + - - +
60D GLY 3.8 0.2 + - - -
71D TYR* 3.5 39.0 + - + -
96D TYR* 5.6 0.7 + - - -
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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