Contacts of the strand formed by residues 47 - 56 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F THR* 4.5 5.6 - - - +
12F LEU* 4.7 0.9 - - - +
16G LEU* 4.9 1.1 - - + -
26G VAL* 3.9 36.8 - - + -
38G LEU* 4.0 11.2 - - + -
40G SER 3.6 3.6 - - - +
41G PHE* 3.8 19.1 - - + -
45G VAL* 3.4 16.8 - - + +
46G ASN* 1.3 81.3 - - - +
48G LEU* 1.3 60.6 + - - +
49G LEU* 4.0 17.3 - - + -
66G MET 3.7 0.5 - - - +
67G VAL* 3.2 6.9 - - - +
68G VAL* 2.8 54.7 + - + +
73G VAL* 4.6 1.8 - - + -
76G ILE* 3.9 25.8 - - + -
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Residues in contact with LEU 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ALA 4.4 6.5 - - - +
11F THR 4.0 8.3 - - - +
15F THR* 3.5 25.8 - - - +
39G ARG* 3.0 40.1 + - + -
40G SER* 3.0 33.5 + - - +
47G LEU* 1.3 74.1 - - - +
49G LEU* 1.3 71.4 + - - +
50G GLU* 5.1 5.2 - - + +
65G THR* 3.9 17.3 - - + -
66G MET 3.6 3.8 - - - +
67G VAL* 3.6 13.0 - - + -
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Residues in contact with LEU 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G VAL* 3.8 26.2 - - + -
26G VAL* 4.5 11.4 - - + -
34G ILE* 3.9 28.5 - - + -
36G GLY* 4.3 11.9 - - - +
37G ILE 3.3 5.6 - - - +
38G LEU* 3.8 25.1 - - + +
47G LEU* 4.4 13.2 - - + -
48G LEU* 1.3 80.0 - - - +
50G GLU* 1.3 66.6 + - - +
52G ALA* 4.1 10.5 - - + -
64G GLY 4.4 0.4 - - - -
65G THR* 3.5 3.5 - - - -
66G MET* 2.9 38.0 + - - +
68G VAL* 4.3 15.7 - - + -
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Residues in contact with GLU 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G ILE* 2.8 31.2 + - + +
39G ARG* 2.5 57.0 + - + +
48G LEU* 5.1 7.4 - - + +
49G LEU* 1.3 76.9 - - - +
51G ASP* 1.3 75.6 + - - +
52G ALA 3.0 3.2 + - - -
64G GLY 3.8 3.6 - - - -
65G THR* 4.2 16.8 + - + +
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Residues in contact with ASP 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G GLN* 5.7 1.2 - - - +
35G ARG 4.1 3.3 - - - +
36G GLY* 4.1 3.8 - - - -
37G ILE* 4.0 17.9 - - + +
39G ARG* 4.9 6.6 + - - -
50G GLU* 1.3 77.3 - - - +
52G ALA* 1.3 64.9 + - - +
53G GLU* 3.8 7.4 + - - +
64G GLY* 3.2 16.2 + - - -
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Residues in contact with ALA 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G ILE* 4.6 0.2 - - + -
35G ARG 3.2 11.4 - - - +
36G GLY* 3.9 0.2 - - - -
49G LEU* 4.1 15.7 - - + -
50G GLU 3.0 2.6 - - - -
51G ASP* 1.3 76.4 - - - +
53G GLU* 1.3 54.4 + - - +
62G LYS* 3.7 2.8 - - - +
63G ARG* 2.7 31.5 + - - -
64G GLY 2.7 24.9 + - - +
66G MET* 3.8 34.8 - - + -
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Residues in contact with GLU 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G GLN* 4.1 8.5 - - - +
34G ILE* 3.2 6.4 - - - +
35G ARG* 2.6 87.4 + - + +
51G ASP 4.8 5.6 - - - +
52G ALA* 1.3 75.6 - - - +
54G GLU* 1.3 62.0 + - - +
55G ILE* 3.9 3.8 - - + +
60G VAL* 3.6 26.6 - - + +
61G TYR 3.3 13.0 - - - +
62G LYS* 4.2 6.9 - - + +
63G ARG* 4.2 1.8 - - - +
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Residues in contact with GLU 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F LEU* 4.1 0.3 - - - +
27F LYS* 2.8 37.3 + - - +
75F PHE* 3.6 22.3 - - + -
32G HIS* 4.5 6.9 + - - -
33G GLU 3.5 6.5 - - - +
34G ILE* 4.4 11.7 - - + +
53G GLU* 1.3 76.7 - - - +
55G ILE* 1.3 62.2 + - - +
56G ILE* 3.7 16.7 + - + +
59G ASN 3.4 3.1 - - - +
60G VAL* 3.5 2.6 - - - +
61G TYR* 2.9 36.6 + - + +
63G ARG* 2.7 43.1 + - + +
66G MET* 4.5 1.3 - - + -
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Residues in contact with ILE 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G SER 5.7 0.5 - - - +
33G GLU* 2.9 62.4 + - + +
35G ARG* 3.9 52.7 - - + +
53G GLU* 3.9 12.3 - - + +
54G GLU* 1.3 75.8 - - - +
56G ILE* 1.3 63.0 + - - +
57G ASP 4.3 0.3 + - - -
58G GLY* 4.4 20.9 - - - +
59G ASN 3.3 8.7 - - - +
60G VAL* 4.7 7.0 - - + -
1003G GOL 4.5 6.7 - - - +
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Residues in contact with ILE 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F LYS* 3.4 29.2 - - - +
32G HIS* 6.2 1.1 - - - +
54G GLU* 3.7 22.9 - - + +
55G ILE* 1.3 78.2 - - - +
57G ASP* 1.3 85.4 + - - +
58G GLY 3.1 0.4 - - - -
59G ASN* 2.8 30.3 + - - +
61G TYR* 3.8 27.3 + - + +
63G ARG* 5.0 2.2 - - - +
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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