Contacts of the strand formed by residues 44 - 51 (chain F) in PDB entry 43C9
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 GLY 44 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87E PHE* 6.4 1.6 - - - -
38F ARG 3.7 1.6 - - - +
39F GLN* 3.6 8.1 - - - -
40F SER 2.7 37.7 + - - -
41F PRO* 4.2 3.2 + - - -
42F GLY 3.5 2.8 + - - -
43F LYS* 1.3 80.0 - - - +
45F LEU* 1.3 60.7 + - - -
46F GLU* 4.4 1.0 - - - +
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Residues in contact with LEU 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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44E PRO* 4.5 6.1 - - + -
87E PHE* 3.5 50.5 - - + -
98E PHE* 3.3 56.8 + - + +
99E GLY 5.2 2.8 + - - +
37F VAL* 4.3 9.4 - - + -
38F ARG 3.8 1.1 - - - -
39F GLN* 3.8 32.5 - - + +
43F LYS 4.1 1.2 - - - +
44F GLY* 1.3 72.5 - - - -
46F GLU* 1.3 63.3 + - - +
91F TYR* 5.7 0.7 - - + -
103F TRP* 4.3 20.0 - - + -
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Residues in contact with GLU 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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98E PHE* 4.0 1.9 - - - -
37F VAL* 3.2 7.7 - - - +
38F ARG* 2.7 83.2 + - + +
43F LYS* 3.5 43.2 - - - +
44F GLY 4.4 2.0 - - - +
45F LEU* 1.3 78.3 - - - +
47F TRP* 1.3 63.4 + - - +
48F LEU* 3.6 3.6 + - + +
60F ASN* 5.8 2.5 - - - +
63F LEU* 6.4 0.4 - - - -
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Residues in contact with TRP 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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89E GLN* 3.5 21.5 - - - -
94E ALA* 4.2 9.9 - - + -
95E PRO* 3.4 31.0 - - + -
96E ARG* 3.4 36.6 - - + +
97E THR* 4.6 2.5 - - + +
98E PHE* 3.9 7.7 - - + -
35F HIS* 3.1 25.9 + - - -
36F TRP 4.3 1.1 - - - -
37F VAL* 4.1 12.6 - - + -
46F GLU* 1.3 72.1 - - - +
48F LEU* 1.3 58.0 + - - +
49F GLY* 3.4 38.6 + - - -
50F MET* 3.8 18.6 - - + -
58F GLU* 3.9 19.7 - - + -
59F TYR 3.9 3.8 - - - -
60F ASN* 2.7 49.5 + - - +
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Residues in contact with LEU 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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36F TRP* 2.9 26.9 + - + +
37F VAL* 4.4 5.6 - - - +
38F ARG* 4.1 16.6 - - + +
46F GLU* 4.3 7.4 - - + +
47F TRP* 1.3 78.0 - - - +
49F GLY* 1.3 56.8 + - - +
59F TYR* 3.5 0.7 - - - -
60F ASN* 2.7 32.5 + - - +
63F LEU* 3.3 28.9 - - + -
67F LEU* 3.4 17.8 - - + +
69F ILE* 5.0 0.2 - - - -
80F LEU* 3.7 32.1 - - + -
82F MET* 3.9 14.8 - - + -
90F TYR* 3.9 19.3 - - + -
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Residues in contact with GLY 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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35F HIS* 3.5 1.7 - - - -
36F TRP* 2.8 27.3 + - - +
47F TRP* 3.4 18.6 - - - -
48F LEU* 1.3 83.5 - - - +
50F MET* 1.3 59.7 + - - +
58F GLU 2.9 15.5 - - - -
69F ILE* 3.8 12.3 - - - -
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Residues in contact with MET 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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96E ARG* 3.3 29.2 - - - +
33F ASN* 3.8 17.0 - - + -
34F VAL 3.3 14.4 - - - +
35F HIS* 3.1 37.7 - - + +
36F TRP* 4.5 0.9 - - - +
47F TRP* 4.0 9.6 - - + -
49F GLY* 1.3 75.7 - - - +
51F ILE* 1.3 63.3 + - - +
52F TRP* 3.5 45.3 - - + +
57F ILE* 3.5 8.7 - - - +
58F GLU* 2.8 43.3 + - + -
69F ILE* 3.7 7.6 - - - +
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Residues in contact with ILE 51 (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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32F TYR 4.4 0.7 - - - +
33F ASN* 3.7 0.6 - - - -
34F VAL* 3.0 37.5 + - + +
50F MET* 1.3 80.8 - - - +
52F TRP* 1.3 72.5 + - - +
55F GLY* 4.1 10.3 - - - +
56F SER 3.1 11.9 - - - +
57F ILE* 4.3 16.4 - - + -
69F ILE* 4.1 11.2 - - + -
70F SER* 4.2 4.3 - - - -
71F LYS* 3.2 50.4 + - + +
78F ILE* 3.9 24.7 - - + -
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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