Contacts of the strand formed by residues 44 - 50 (chain F) in PDB entry 6BA5
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 LEU 44 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E PHE* 5.3 0.9 - - + -
39E GLN* 4.3 1.3 - - - +
45E PRO* 3.6 35.7 - - + -
88E TYR* 3.7 35.7 - - + -
102E PHE* 3.4 59.2 - - + +
103E GLY 4.8 1.8 + - - +
36F VAL* 4.1 14.1 - - + -
37F ARG 3.5 2.0 - - - -
38F GLN* 3.7 29.4 - - + +
43F GLY* 1.3 74.2 - - - -
45F GLU* 1.3 59.5 + - - +
91F PHE* 4.6 5.8 - - + -
106F TRP* 4.8 0.2 - - + -
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Residues in contact with GLU 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E PHE* 4.1 1.1 - - - +
36F VAL* 3.3 4.6 - - - +
37F ARG* 2.8 78.5 + - + +
43F GLY 4.8 2.7 - - - +
44F LEU* 1.3 75.0 - - - +
46F TRP* 1.4 64.9 + - - +
47F ILE* 3.6 0.7 + - - +
61F TRP* 3.3 43.0 + - + +
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Residues in contact with TRP 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E LEU* 5.0 0.7 - - + -
94E GLY* 3.6 37.0 - - - -
99E ARG* 3.9 18.4 - - + -
100E THR* 3.4 41.7 - - + +
101E SER* 5.1 1.3 - - - +
102E PHE* 3.8 21.5 - + + +
34F SER* 3.2 21.1 + - - -
35F TRP 4.0 5.4 - - - -
36F VAL* 4.0 19.7 - - + -
45F GLU* 1.4 73.0 - - - +
47F ILE* 1.3 59.9 + - - +
48F GLY* 3.4 29.8 + - - -
49F PHE* 3.7 9.2 - + + -
57F TRP 3.8 7.4 - - - -
58F TYR 4.0 0.7 - - - -
59F ALA* 3.6 32.3 - - + +
61F TRP* 3.3 21.7 + - - -
96F TYR 5.4 0.2 - - - -
103F PHE* 4.1 12.2 - + - -
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Residues in contact with ILE 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F TRP* 2.9 33.5 + - + +
36F VAL 4.2 0.4 - - - +
37F ARG* 4.1 9.6 - - + -
45F GLU 4.1 7.2 - - - +
46F TRP* 1.3 76.2 - - - +
48F GLY* 1.3 61.0 + - - +
58F TYR* 3.6 6.9 - - + +
59F ALA 2.9 23.9 + - - -
61F TRP* 3.9 20.9 - - + -
62F VAL* 3.5 14.6 - - + +
66F PHE* 3.8 31.9 - - + -
68F ILE* 5.3 0.7 - - + -
77F LEU* 4.2 13.2 - - + -
90F TYR* 3.7 37.2 - - + -
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Residues in contact with GLY 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F SER* 3.3 5.0 - - - -
35F TRP 2.9 24.4 + - - +
46F TRP* 3.4 16.9 + - - -
47F ILE* 1.3 83.1 - - - +
49F PHE* 1.3 61.2 + - - -
57F TRP 3.1 14.4 - - - -
58F TYR* 4.1 1.8 - - - -
68F ILE* 3.5 11.7 - - - +
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Residues in contact with PHE 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E GLY 3.5 24.2 - - - -
95E ASN* 3.7 5.4 - - + -
32F PRO* 4.3 3.8 - - + -
33F ILE 3.2 13.9 - - - +
34F SER* 3.3 16.4 - - - +
46F TRP* 3.8 14.4 - + + -
48F GLY* 1.3 74.4 - - - +
50F ILE* 1.3 77.0 + - - +
51F ASN* 3.7 24.0 - - + -
55F SER 4.0 0.2 - - - +
56F THR* 3.3 6.2 - - - -
57F TRP* 2.9 68.6 + + + +
68F ILE* 3.5 9.8 - - - +
96F TYR* 3.4 44.9 - + + -
380O ASN* 4.7 1.3 - - - -
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Residues in contact with ILE 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLY* 6.0 0.9 - - - -
78A GLY* 6.3 1.1 - - - -
32F PRO* 3.1 4.7 - - - +
33F ILE 3.0 37.0 + - - +
49F PHE* 1.3 80.2 - - - +
51F ASN* 1.4 70.3 + - - +
54F GLY* 3.7 28.0 - - - +
55F SER 3.4 6.5 - - - +
56F THR* 3.8 4.3 - - + -
68F ILE* 3.5 28.7 - - + +
69F SER* 3.7 33.9 - - - -
70F ARG* 3.8 22.2 - - + +
75F VAL* 3.8 15.9 - - + -
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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