Contacts of the strand formed by residues 47 - 56 (chain F) in PDB entry 1I8F
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 47 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E LEU* 3.1 13.4 - - - +
16F LEU* 4.5 4.3 - - + -
26F VAL* 4.1 30.1 - - + -
38F LEU* 4.0 18.8 - - + -
40F SER 3.6 2.7 - - - +
41F PHE* 3.8 17.5 - - + -
45F VAL* 3.4 21.1 - - + +
46F ASN* 1.3 76.7 - - - +
48F LEU* 1.3 59.9 + - - +
49F LEU* 4.1 8.5 - - + -
66F MET 3.6 0.7 - - - +
67F VAL* 3.2 2.8 - - - -
68F VAL* 2.8 48.2 + - + +
73F VAL* 4.4 6.5 - - + -
76F ILE* 3.8 32.8 - - + -
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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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11E THR 3.9 22.0 - - - +
12E LEU* 3.4 11.0 - - + +
15E THR* 3.9 27.4 - - + +
37F ILE 3.5 0.5 - - - +
38F LEU* 3.7 4.2 - - - +
39F ARG* 3.0 46.6 + - + -
40F SER* 2.9 22.6 + - - +
47F LEU* 1.3 72.8 - - - +
49F LEU* 1.3 64.1 + - - +
65F THR* 3.8 24.7 - - + -
66F MET 3.5 11.4 - - - +
67F VAL* 4.1 7.2 - - + -
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Residues in contact with LEU 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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24F VAL* 3.9 26.5 - - + -
26F VAL* 4.6 13.0 - - + -
34F ILE* 3.6 31.0 - - + -
36F GLY* 4.0 13.0 - - - +
37F ILE 3.1 10.1 - - - +
38F LEU* 4.0 10.8 - - + -
39F ARG* 5.4 0.2 - - - -
47F LEU* 4.7 7.2 - - + -
48F LEU* 1.3 85.4 - - - +
50F GLU* 1.3 60.5 + - - +
52F ALA* 3.9 16.6 - - + -
64F GLY 4.4 0.4 - - - -
65F THR* 3.5 7.3 - - - +
66F MET* 2.9 35.6 + - + +
68F VAL* 4.1 20.0 - - + -
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Residues in contact with GLU 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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37F ILE* 2.9 35.1 + - - +
39F ARG* 5.2 4.2 - - - +
49F LEU* 1.3 74.5 - - - +
51F ASP* 1.3 75.4 + - - +
52F ALA 3.1 2.3 + - - -
64F GLY 3.9 1.3 - - - -
65F THR* 4.6 6.7 - - - +
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Residues in contact with ASP 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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23F GLN* 5.5 1.9 - - - +
35F ARG 4.3 0.3 - - - +
36F GLY* 4.2 5.2 - - - -
37F ILE* 4.6 13.4 - - + +
50F GLU* 1.3 74.3 - - - +
52F ALA* 1.3 63.2 + - - +
53F GLU* 3.9 8.7 + - - +
62F LYS* 6.1 0.9 - - - +
64F GLY* 3.1 18.3 + - - -
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Residues in contact with ALA 52 (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 ILE* 4.4 0.4 - - + -
35F ARG 3.1 12.8 - - - +
36F GLY* 3.8 1.8 - - - -
49F LEU* 3.9 25.4 - - + -
50F GLU 3.1 1.2 - - - -
51F ASP* 1.3 75.2 - - - +
53F GLU* 1.3 54.9 - - - +
62F LYS* 3.8 2.1 - - - +
63F ARG* 2.8 30.8 + - - -
64F GLY 2.7 21.1 + - - +
66F MET* 3.9 26.2 - - + -
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Residues in contact with GLU 53 (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 GLN* 4.6 5.8 - - - +
34F ILE* 3.2 7.6 - - - +
35F ARG* 2.7 83.7 + - + +
51F ASP 4.7 6.6 - - - +
52F ALA* 1.3 75.3 - - - +
54F GLU* 1.3 62.0 + - - +
55F ILE* 3.7 4.1 - - + +
60F VAL* 3.7 24.7 - - + +
61F TYR 3.2 12.3 - - - +
62F LYS* 3.9 22.0 - - + +
63F ARG* 4.3 1.6 - - - +
66F MET* 5.1 0.9 - - - -
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Residues in contact with GLU 54 (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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27E LYS* 2.8 33.3 + - - +
75E PHE* 3.5 27.5 - - + -
32F HIS* 4.4 7.8 + - - +
33F GLU 3.5 6.7 - - - +
34F ILE* 4.3 8.4 - - + +
53F GLU* 1.3 76.3 - - - +
55F ILE* 1.3 62.5 + - - +
56F ILE* 3.7 18.1 - - + +
59F ASN 3.4 1.4 - - - +
60F VAL* 3.4 2.8 - - - -
61F TYR* 2.7 41.5 + - + +
63F ARG* 2.8 43.6 + - + +
66F MET* 4.6 1.3 - - + -
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Residues in contact with ILE 55 (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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31F SER 5.5 1.4 - - - +
32F HIS* 5.6 0.2 - - - -
33F GLU* 2.9 58.2 + - + +
35F ARG* 3.5 49.6 - - + +
53F GLU* 3.7 15.7 - - + +
54F GLU* 1.3 78.8 - - - +
56F ILE* 1.3 61.2 + - - +
57F ASP 4.2 0.7 + - - -
58F GLY* 4.1 23.8 - - - +
59F ASN 3.2 8.7 - - - +
60F VAL* 4.6 6.5 - - + -
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Residues in contact with ILE 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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27E LYS* 3.7 26.2 - - - +
32F HIS* 6.0 2.9 - - - +
54F GLU* 3.7 20.9 - - + +
55F ILE* 1.3 77.0 - - - +
57F ASP* 1.3 77.5 + - - +
58F GLY 3.2 0.2 - - - -
59F ASN* 2.7 38.4 + - - +
61F TYR* 3.6 35.2 + - + +
63F ARG* 4.9 1.1 - - - +
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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