Contacts of the strand formed by residues 35 - 43 (chain F) in PDB entry 1I81
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 35 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F ILE* 3.4 18.6 - - + +
28F ILE 3.4 10.8 - - - +
29F LYS* 3.9 20.2 + - + +
33F ASP 3.8 1.2 + - - -
34F ARG* 1.3 78.4 - - - +
36F PHE* 1.3 68.4 + - - +
37F ARG* 2.8 39.6 + - - +
56F GLU* 3.4 7.3 - - - +
57F LEU* 3.1 52.3 + - + +
64G ARG* 2.9 28.8 + - - -
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Residues in contact with PHE 36 (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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78E TYR* 3.3 33.7 - + - -
27F ILE* 4.1 0.5 - - - +
28F ILE* 2.7 43.7 + - + +
30F LEU* 3.8 21.5 - - + -
34F ARG* 3.8 11.9 - - + -
35F GLU* 1.3 76.1 - - - +
37F ARG* 1.3 68.0 + - - +
51F LEU* 4.2 5.4 - - + -
54F ALA* 4.6 10.5 - - + -
55F GLU 3.4 14.4 - - - -
56F GLU* 2.9 44.0 - - + -
66F LEU* 4.1 21.8 - - + -
69F VAL* 5.0 2.7 - - + -
71F ILE* 4.1 24.0 - - + -
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Residues in contact with ARG 37 (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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26F VAL 3.4 11.4 - - - +
27F ILE* 4.0 26.6 - - + +
35F GLU* 2.8 26.2 + - - +
36F PHE* 1.3 80.3 - - - +
38F GLY* 1.3 57.2 + - - +
51F LEU* 4.3 2.7 - - - -
53F ASP 3.8 1.7 - - - +
54F ALA* 3.2 2.6 - - - -
55F GLU* 2.6 53.5 + - + +
57F LEU* 4.0 27.8 - - + +
64G ARG* 4.8 9.1 - - - +
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Residues in contact with GLY 38 (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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25F PRO* 3.3 5.3 - - - +
26F VAL* 2.9 32.8 + - - +
37F ARG* 1.3 76.0 - - - +
39F VAL* 1.3 65.0 + - - -
51F LEU* 4.1 13.0 - - - +
52F ASN 3.6 11.0 - - - -
53F ASP 3.9 5.8 - - - -
54F ALA* 4.0 4.0 - - - -
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Residues in contact with VAL 39 (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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23F ASN* 3.3 41.5 - - - +
24F SER 3.4 3.1 - - - +
25F PRO* 4.4 19.1 - - + -
38F GLY* 1.3 72.7 - - - +
40F LEU* 1.3 65.2 + - - +
41F LYS* 3.1 17.6 + - + +
51F LEU* 3.5 3.3 - - - -
52F ASN* 3.0 36.3 + - + +
53F ASP* 4.9 10.3 - - + +
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Residues in contact with LEU 40 (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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18F LEU* 3.2 43.1 - - + +
21F SER* 3.8 24.9 - - - +
22F LEU* 3.6 10.7 - - + +
23F ASN* 2.6 34.3 + - - -
24F SER 3.1 10.4 + - - +
26F VAL* 4.1 12.8 - - + -
28F ILE* 5.8 0.2 - - + -
38F GLY 3.7 2.8 + - - -
39F VAL* 1.3 68.6 - - - +
41F LYS* 1.3 58.7 + - - +
42F SER 3.8 20.6 - - - +
43F PHE* 4.1 11.9 - - + -
49F LEU* 4.0 24.2 - - + -
50F VAL 4.2 2.5 - - - +
51F LEU* 3.8 11.9 - - + +
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Residues in contact with LYS 41 (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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9E VAL* 4.6 7.5 - - + +
11E VAL* 3.3 21.8 - - - +
22F LEU* 4.1 5.5 - - - +
23F ASN* 2.6 27.6 + - - +
39F VAL* 3.1 26.6 - - + +
40F LEU* 1.3 77.8 - - - +
42F SER* 1.3 65.5 + - - +
50F VAL* 2.8 19.1 + - + +
52F ASN* 2.9 43.1 - - + +
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Residues in contact with SER 42 (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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9E VAL* 4.1 16.2 - - - -
10E ASN 3.0 25.5 + - - -
11E VAL* 3.5 8.9 - - - +
14E PRO* 3.1 23.3 - - - +
22F LEU* 4.3 5.3 - - - +
40F LEU* 3.8 3.4 - - - +
41F LYS* 1.3 81.8 - - - +
43F PHE* 1.3 66.4 + - - +
49F LEU* 3.0 7.4 - - - +
50F VAL* 2.8 30.1 + - - -
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Residues in contact with PHE 43 (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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11E VAL 3.2 19.9 + - - +
12E GLN* 4.2 3.8 - - - -
14E PRO* 3.2 8.3 - - - +
15F LEU* 3.7 22.0 - - + -
18F LEU* 3.6 30.3 - - + -
19F GLY* 3.4 39.3 - - - -
22F LEU* 3.7 22.0 - - + -
40F LEU* 4.1 8.5 - - + -
42F SER* 1.3 83.8 + - - +
44F ASP* 1.3 72.3 + - - +
47F MET 5.1 1.3 - - - -
48F ASN 3.0 13.9 - - - +
49F LEU* 3.7 9.6 - - + -
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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