Contacts of the strand formed by residues 57 - 66 (chain D) in PDB entry 2BME
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 57 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D ASP* 3.8 6.1 - - + +
9D PHE* 4.0 33.7 - - + -
52D ILE 3.5 0.5 - - - +
53D ASN* 3.5 0.6 - - - -
54D VAL* 2.7 63.2 + - - +
55D GLY* 3.8 19.0 + - - -
56D GLY* 1.3 80.4 - - - +
58D TYR* 1.3 63.2 + - - +
59D VAL* 3.6 1.5 + - + -
172D LEU* 4.5 17.5 - - + +
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Residues in contact with TYR 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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6D THR* 4.1 14.6 - - + +
7D TYR* 3.8 17.8 - - - -
8D ASP* 2.8 45.7 + - - +
9D PHE* 3.2 7.3 + - - -
51D ILE* 4.0 14.8 - - + -
52D ILE 3.3 5.4 - - - -
53D ASN* 3.4 39.1 + - + -
56D GLY* 3.9 14.8 - - - -
57D LYS* 1.3 70.5 - - - +
59D VAL* 1.3 62.4 + - - +
60D LYS 4.1 0.2 - - - -
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Residues in contact with VAL 59 (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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9D PHE* 3.6 17.9 - - + +
11D PHE* 3.6 31.9 - - + -
50D LYS 3.6 1.0 - - - +
51D ILE* 3.3 4.4 - - - +
52D ILE* 2.8 48.2 + - + +
54D VAL* 3.4 27.4 - - + -
57D LYS 3.9 2.9 - - - +
58D TYR* 1.3 77.4 - - - +
60D LYS* 1.3 65.3 + - - +
61D LEU* 3.8 15.7 - - + -
168D ALA* 4.5 4.3 - - + -
172D LEU* 4.0 16.6 - - + -
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Residues in contact with LYS 60 (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 TYR* 3.7 44.4 + - + +
9D PHE 2.8 16.0 + - - +
10D LEU* 3.4 18.1 - - + +
11D PHE 3.0 26.9 + - - -
49D SER* 4.2 18.6 - - - -
50D LYS 3.7 5.8 - - - +
51D ILE* 4.0 17.7 - - + -
59D VAL* 1.3 72.4 - - - +
61D LEU* 1.3 68.5 + - - +
62D GLN* 4.1 19.0 + - - -
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Residues in contact with LEU 61 (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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11D PHE* 3.6 7.4 - - + -
13D PHE* 3.5 46.9 - - + -
30D PHE* 4.0 29.2 - - + -
48D GLY 3.8 0.5 - - - +
49D SER* 3.1 28.4 - - - -
50D LYS 2.9 15.8 + - - +
52D ILE* 4.2 16.4 - - + -
59D VAL* 3.8 26.9 - - + +
60D LYS* 1.3 74.6 - - - +
62D GLN* 1.3 62.4 + - - +
63D ILE* 3.8 15.9 - - + +
164D PHE* 4.4 4.9 - - + +
168D ALA* 4.5 2.0 - - + -
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Residues in contact with GLN 62 (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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10D LEU* 3.6 39.0 - - + +
11D PHE 3.0 10.0 + - - +
12D LYS* 3.5 10.4 - - + +
13D PHE 2.9 24.4 + - - +
47D PHE* 3.9 26.9 - - + -
48D GLY 3.8 3.1 - - - -
49D SER* 4.3 6.1 - - - -
60D LYS* 4.1 15.0 + - - -
61D LEU* 1.3 74.3 - - - +
63D ILE* 1.3 60.1 + - - +
64D TRP* 4.0 10.4 - - - +
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Residues in contact with ILE 63 (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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13D PHE* 3.5 22.0 - - + +
15D VAL* 3.7 30.3 - - + -
27D LEU* 3.8 22.5 - - + +
30D PHE* 3.6 36.8 - - + -
31D ILE* 4.5 3.6 - - + -
47D PHE* 3.4 8.5 - - - -
48D GLY 2.7 40.4 + - - +
49D SER* 5.1 0.2 - - - -
61D LEU* 3.9 20.0 - - + +
62D GLN* 1.3 75.5 - - - +
64D TRP* 1.3 64.9 - - - +
65D ASP 3.8 0.3 + - - -
164D PHE* 3.8 12.3 - - + -
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Residues in contact with TRP 64 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C ILE* 4.2 6.5 - - + -
44C GLY* 5.3 1.3 - - - -
72C PHE* 4.0 14.4 - + - -
75C VAL* 4.0 27.1 - - + -
12D LYS* 3.6 36.0 - - + +
13D PHE 2.9 18.3 + - - +
14D LEU* 3.4 13.5 - - + -
15D VAL 3.0 23.2 + - - -
45D VAL* 3.9 26.5 - - + -
46D GLU 3.6 5.8 - - - -
47D PHE* 3.7 39.4 - + + -
62D GLN* 4.0 9.1 + - - +
63D ILE* 1.3 73.8 - - - +
65D ASP* 1.3 61.8 + - - +
66D THR* 3.5 5.4 + - + +
79D TYR* 3.5 36.3 - + + -
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Residues in contact with ASP 65 (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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15D VAL* 4.1 10.5 - - + +
23D LYS* 3.4 29.7 - - - +
24D SER* 2.6 37.9 + - - -
27D LEU* 3.6 26.5 - - + +
42D THR* 4.0 2.4 + - - +
45D VAL* 3.2 4.3 - - - +
46D GLU* 2.8 53.9 + - + +
63D ILE 3.8 1.0 + - - -
64D TRP* 1.3 68.1 - - - +
66D THR* 1.3 66.0 + - - +
1180D MG 4.6 0.4 - - - -
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Residues in contact with THR 66 (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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14D LEU* 5.0 8.3 - - + -
15D VAL 2.8 24.1 + - - +
16D ILE* 3.6 23.1 - - + +
17D GLY 4.8 0.7 + - - -
23D LYS* 3.0 28.8 - - - -
42D THR* 4.5 1.5 - - - -
44D GLY 4.0 4.5 - - - -
45D VAL* 4.1 9.6 - - + -
64D TRP* 4.0 9.9 - - + +
65D ASP* 1.3 79.2 - - - +
67D ALA* 1.3 63.5 + - - +
68D GLY* 5.6 0.2 - - - -
76D THR* 3.8 33.2 - - + +
79D TYR* 5.2 2.0 - - + -
80D TYR* 4.8 4.1 + - + -
104D TRP* 5.4 2.4 - - - -
1179D GNP 4.2 1.7 + - - -
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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