Contacts of the strand formed by residues 45 - 54 (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 VAL 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C ILE* 3.5 41.2 + - + +
45C VAL 5.8 0.9 + - - +
42D THR* 3.9 6.9 - - - +
43D ILE 2.9 11.0 + - - +
44D GLY* 1.3 75.1 - - - +
46D GLU* 1.3 66.9 + - - +
64D TRP* 3.9 20.9 - - + -
65D ASP 3.2 27.8 - - - +
66D THR* 4.1 9.9 - - + -
79D TYR* 3.4 41.1 - - + +
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Residues in contact with GLU 46 (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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43C ILE* 4.1 17.6 - - - +
24D SER* 4.9 3.8 + - - -
27D LEU* 4.8 5.2 - - + -
36D LYS* 5.3 11.4 - - - -
42D THR* 4.1 14.9 + - + +
45D VAL* 1.3 81.5 - - - +
47D PHE* 1.3 69.0 + - - +
64D TRP* 3.6 2.9 - - - -
65D ASP* 2.8 55.8 + - + +
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Residues in contact with PHE 47 (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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43C ILE* 3.8 23.5 - - + +
71C ARG* 5.3 10.7 + - - +
72C PHE* 4.0 21.1 - + + -
27D LEU* 4.3 5.9 - - - +
46D GLU* 1.3 83.5 + - - +
48D GLY* 1.3 76.9 + - - +
49D SER* 4.0 18.8 - - - -
62D GLN* 3.9 32.5 - - + -
63D ILE 3.4 11.9 - - - -
64D TRP* 3.7 33.2 - + + -
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Residues in contact with GLY 48 (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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27D LEU* 3.9 12.5 - - - +
31D ILE* 4.3 15.9 - - - -
47D PHE* 1.3 83.4 - - - +
49D SER* 1.3 61.6 + - - -
62D GLN* 3.8 0.3 - - - -
63D ILE* 2.7 42.1 + - - +
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Residues in contact with SER 49 (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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31D ILE* 3.7 14.9 - - - +
47D PHE* 4.0 21.5 - - - -
48D GLY* 1.3 76.3 - - - -
50D LYS* 1.3 64.5 + - - +
60D LYS* 4.2 15.9 - - - -
61D LEU 3.1 15.3 - - - -
62D GLN* 4.3 7.6 - - - -
63D ILE* 5.1 0.4 - - - -
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Residues in contact with LYS 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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30D PHE* 2.7 59.2 + - + +
31D ILE* 3.7 22.5 + - + +
33D LYS* 3.7 18.9 - - - +
49D SER* 1.3 80.6 - - - +
51D ILE* 1.3 73.7 + - - +
52D ILE* 4.0 12.4 + - + -
59D VAL 3.6 1.7 - - - +
60D LYS* 4.5 1.5 - - - +
61D LEU* 2.9 32.1 + - - +
63D ILE* 5.3 0.2 - - - +
161D GLU* 3.3 21.7 + - - -
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Residues in contact with ILE 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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4D SER 5.7 0.2 - - - -
5D GLU* 3.8 32.3 - - + +
6D THR 3.6 19.5 - - - +
7D TYR* 4.2 9.4 - - + -
50D LYS* 1.3 82.2 - - - +
52D ILE* 1.3 73.6 + - - +
58D TYR* 4.0 23.8 - - + -
59D VAL 3.3 13.7 - - - +
60D LYS* 4.0 22.2 - - + -
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Residues in contact with ILE 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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30D PHE* 3.9 27.4 - - + -
50D LYS* 4.0 16.4 - - + +
51D ILE* 1.3 81.1 - - - +
53D ASN* 1.3 60.4 + - - +
54D VAL* 4.3 10.1 - - + +
57D LYS 3.5 0.9 - - - +
58D TYR* 3.3 5.6 - - - -
59D VAL* 2.8 48.9 + - + +
61D LEU* 4.2 15.5 - - + -
161D GLU* 5.4 2.9 - - - +
165D VAL* 3.8 31.2 - - + +
168D ALA* 3.9 26.7 - - + -
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Residues in contact with ASN 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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52D ILE* 1.3 73.0 - - - +
54D VAL* 1.3 59.5 + - - +
55D GLY 3.9 1.4 + - - -
56D GLY* 3.0 31.7 + - - -
57D LYS 3.5 3.6 - - - -
58D TYR* 3.4 41.1 + - + -
165D VAL* 5.7 3.6 - - - +
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Residues in contact with VAL 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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52D ILE* 4.3 14.4 - - + -
53D ASN* 1.3 74.1 - - - +
55D GLY* 1.3 58.8 + - - +
56D GLY 3.1 1.1 - - - -
57D LYS* 2.7 49.0 + - - +
59D VAL* 3.4 33.7 - - + -
165D VAL* 4.9 8.5 - - + -
168D ALA* 4.7 5.6 - - + -
169D ARG* 4.0 29.6 - - + +
172D LEU* 3.6 21.1 - - + -
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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