Contacts of the strand formed by residues 55 - 62 (chain F) in PDB entry 1I5L
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 ARG 55 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E ARG* 4.0 14.9 - - - +
26E GLU* 4.4 13.5 + - - -
25F ARG* 4.4 4.4 - - - +
46F GLU* 3.0 29.3 - - - +
47F GLU* 3.1 50.1 + - + +
53F VAL* 3.8 4.5 - - - +
54F VAL* 1.3 94.2 + - - +
56F LYS* 1.3 68.8 + - - +
57F VAL* 6.0 3.8 - - + -
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Residues in contact with LYS 56 (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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45F ALA 3.3 5.6 - - - +
46F GLU* 3.4 32.3 + - + +
53F VAL* 5.2 5.4 - - + -
55F ARG* 1.3 84.4 - - - +
57F VAL* 1.3 73.6 + - - +
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Residues in contact with VAL 57 (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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18E ILE* 5.9 4.3 - - + -
69E PHE* 6.0 2.7 - - + -
71E SER* 3.9 21.8 - - - +
72E PRO 5.1 4.3 - - - +
27F PHE* 4.4 13.7 - - + -
44F ASP* 4.6 0.4 - - - -
45F ALA* 2.8 40.2 + - + +
46F GLU* 4.9 1.3 - - - +
47F GLU* 5.3 1.6 - - + +
55F ARG* 5.7 4.3 - - + -
56F LYS* 1.3 83.9 - - - +
58F GLY* 1.3 55.0 + - - +
59F SER* 2.5 27.7 + - - +
60F VAL* 4.0 16.8 - - + -
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Residues in contact with GLY 58 (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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72E PRO* 5.5 7.8 + - - +
43F LEU* 3.4 5.0 - - - +
44F ASP* 2.6 34.5 + - - +
57F VAL* 1.3 68.6 - - - +
59F SER* 1.3 62.6 + - - +
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Residues in contact with SER 59 (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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8E VAL* 5.1 10.6 - - - +
71E SER* 3.4 13.5 - - - -
72E PRO* 3.5 23.8 - - - +
41F VAL* 5.3 4.5 - - - -
42F LEU 2.8 16.8 - - - -
43F LEU* 3.4 20.2 - - - +
57F VAL* 2.5 10.7 + - - +
58F GLY* 1.3 78.4 - - - +
60F VAL* 1.3 75.3 + - - +
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Residues in contact with VAL 60 (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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8E VAL* 6.0 0.9 - - - +
69E PHE* 4.1 16.4 - - + -
70E VAL 3.5 6.5 - - - +
71E SER* 3.5 19.5 - - - -
72E PRO* 5.3 0.4 - - - -
27F PHE* 4.4 17.9 - - + -
40F LEU 3.6 0.7 - - - +
41F VAL* 3.2 9.2 - - - +
42F LEU* 2.8 56.0 + - + +
45F ALA* 4.8 5.4 - - + -
57F VAL* 4.0 14.8 - - + -
59F SER* 1.3 85.3 - - - +
61F VAL* 1.3 67.7 + - - +
62F ILE* 4.1 8.5 - - + +
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Residues in contact with VAL 61 (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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5E PRO* 3.9 39.3 - - + +
8E VAL* 4.2 22.2 - - + -
9E LEU* 4.7 17.7 - - + -
38E MET* 4.4 21.5 - - + +
69E PHE* 3.0 5.5 - - - -
70E VAL* 2.9 43.3 + - + +
40F LEU 3.3 2.9 - - - +
41F VAL* 4.4 6.7 - - + -
60F VAL* 1.3 77.7 - - - +
62F ILE* 1.3 69.0 + - - +
63F ARG* 6.0 0.2 - - - +
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Residues in contact with ILE 62 (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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68E VAL 3.6 9.4 - - - +
69E PHE* 4.1 14.4 - - + -
19F VAL* 4.4 11.7 - - + -
21F LEU* 4.2 24.0 - - + -
27F PHE* 4.8 10.5 - - + -
39F ASN* 3.2 12.0 - - - +
40F LEU* 2.9 37.8 + - + +
42F LEU* 3.9 29.4 - - + -
60F VAL* 4.7 9.6 - - + -
61F VAL* 1.3 79.2 - - - +
63F ARG* 1.3 73.6 + - - +
66F THR* 4.3 2.2 - - + -
67F VAL* 3.9 20.4 - - + -
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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