Contacts of the strand formed by residues 46 - 51 (chain D) in PDB entry 5JMO
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 46 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D VAL* 3.3 4.3 - - - -
38D ARG* 2.8 87.6 + - + +
43D LYS* 6.0 2.3 - - - +
44D GLY 4.2 5.4 - - - +
45D LEU* 1.3 76.4 - - - +
47D TRP* 1.3 75.6 + - - +
48D VAL* 3.5 1.4 + - - +
61D ALA* 5.0 2.0 - - + +
63D SER* 3.5 13.2 + - - -
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Residues in contact with TRP 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B ASN* 6.4 0.7 - - - -
525B ALA* 3.7 33.7 - - + -
526B ASP* 5.4 7.0 - - - +
35D TYR* 3.9 16.6 - + - -
36D TRP 4.0 4.9 - - - -
37D VAL* 4.3 6.1 - - + -
46D GLU* 1.3 80.7 - - - +
48D VAL* 1.3 64.4 + - - +
49D SER 3.3 25.7 + - - -
50D SER* 3.6 24.0 - - - -
59D ASP* 3.8 24.0 - - + -
60D TYR* 3.3 23.8 - - - -
61D ALA* 3.3 40.5 - - + +
100D MET* 3.7 36.7 - - + +
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Residues in contact with VAL 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D TRP* 2.8 23.2 + - + +
37D VAL 3.9 1.8 - - - -
38D ARG* 3.7 44.6 - - + +
46D GLU 3.7 6.3 - - - +
47D TRP* 1.3 75.7 - - - +
49D SER* 1.3 63.2 + - - +
60D TYR* 3.5 2.3 - - - -
61D ALA* 3.0 27.4 + - - -
64D VAL* 3.6 11.6 - - + +
68D PHE* 3.6 37.2 - - + -
81D LEU* 4.3 11.0 - - + -
94D TYR* 4.2 4.7 - - + -
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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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35D TYR* 3.4 2.3 - - - -
36D TRP* 2.8 29.6 + - - +
47D TRP* 3.3 12.1 + - - +
48D VAL* 1.3 88.9 - - - +
50D SER* 1.3 63.5 + - - +
59D ASP 2.9 15.4 + - - -
60D TYR* 3.2 15.6 - - - -
68D PHE* 5.7 0.2 - - - -
70D ILE* 3.2 32.9 - - - +
81D LEU* 4.5 8.3 - - - -
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Residues in contact with SER 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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496B ASN* 5.0 3.5 - - - +
560B TYR* 2.6 29.3 + - - -
34D MET 3.3 6.7 - - - -
35D TYR* 3.6 23.3 - - - -
47D TRP* 3.6 14.6 - - - -
49D SER* 1.3 77.6 + - - +
51D ILE* 1.3 62.5 + - - +
58D THR* 3.3 3.6 - - - -
59D ASP* 3.0 37.8 + - - +
70D ILE* 3.6 8.8 - - - +
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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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560B TYR* 3.5 5.3 - - - -
33D SER* 3.2 5.5 - - - -
34D MET* 2.9 54.1 + - + +
50D SER* 1.3 77.6 - - - +
52D ASN* 1.3 74.4 + - - +
55D GLY* 3.6 26.0 - - - +
57D ASN 3.5 9.9 - - - +
58D THR* 3.8 13.0 - - + -
70D ILE* 3.8 16.2 - - + +
71D SER* 3.8 29.2 - - - +
72D ARG* 3.9 15.3 - - + +
79D LEU* 3.9 7.2 - - + -
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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