Contacts of the strand formed by residues 55 - 62 (chain E) in PDB entry 1FMO
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 55 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51E THR* 4.2 1.3 + - - -
52E GLY* 3.2 28.5 + - - +
53E SER 3.7 1.2 - - - -
54E PHE* 1.3 79.5 - - - +
56E ARG* 1.3 60.1 + - - -
57E VAL* 5.7 0.7 - - - +
72E LYS* 5.9 3.7 - - - +
73E ILE 3.6 12.6 - - - -
74E LEU* 4.0 5.1 - - - +
75E ASP 5.9 0.2 - - - -
78E LYS* 4.9 3.3 - - - +
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Residues in contact with ARG 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E THR* 3.0 28.0 + - + +
50E GLY 3.7 10.8 - - - +
51E THR* 4.7 12.3 + - - +
55E GLY* 1.3 72.9 - - - -
57E VAL* 1.3 64.5 + - - +
58E MET* 3.7 30.0 - - + +
71E MET 3.7 0.5 - - - +
72E LYS* 3.7 4.1 - - - +
73E ILE* 3.0 39.6 + - + +
330E TYR* 5.1 0.2 - - - +
331E GLU 2.6 31.1 + - - -
333E GLU* 3.4 47.5 + - - +
335E ILE* 4.7 7.2 - - - -
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Residues in contact with VAL 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E THR* 3.6 3.0 - - - +
49E LEU* 2.6 34.4 + - + -
50E GLY 2.9 12.0 + - - +
51E THR* 5.9 0.2 - - - -
55E GLY 5.7 0.9 - - - +
56E ARG* 1.3 76.7 - - - +
58E MET* 1.3 58.5 + - - +
70E ALA* 3.8 29.4 - - + -
71E MET 3.6 9.9 - - - +
72E LYS* 4.4 20.6 - - + +
120E MET* 5.7 2.0 - - - -
351E ADN 3.2 56.5 - - + +
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Residues in contact with MET 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E ARG* 4.0 28.0 - - - +
46E ILE 5.6 1.3 - - - -
47E LYS 3.2 13.0 - - - +
48E THR* 4.4 11.0 - - - +
49E LEU* 3.9 4.5 - - - -
56E ARG* 3.7 28.0 - - + +
57E VAL* 1.3 77.5 - - - +
59E LEU* 1.3 67.9 + - - +
60E VAL* 3.6 6.5 + - + -
70E ALA* 3.5 2.1 - - - -
71E MET* 2.9 34.2 + - - +
73E ILE* 4.0 20.0 - - + -
332E GLU* 4.7 7.0 - - - +
333E GLU 4.1 6.7 - - - +
335E ILE* 3.9 28.5 - - + -
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Residues in contact with LEU 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E ARG* 3.9 0.7 - - - -
46E ILE* 2.8 67.8 + - + -
47E LYS 2.7 21.5 + - - +
49E LEU* 3.7 15.4 - - + +
58E MET* 1.3 71.5 - - - +
60E VAL* 1.3 73.4 + - - +
68E HIS* 3.7 15.0 - - + +
69E TYR 3.5 11.0 - - - +
122E TYR* 3.9 35.0 - - + -
322E GLY* 4.5 10.8 - - - +
324E THR* 4.2 19.7 - - + -
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Residues in contact with VAL 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E PHE* 3.0 44.6 - - + -
44E ASP 3.2 9.9 - - - +
45E ARG* 4.3 11.7 - - + -
46E ILE* 4.6 2.0 - - - +
58E MET* 4.3 3.4 - - + +
59E LEU* 1.3 79.5 - - - +
61E LYS* 1.3 66.1 + - - +
62E HIS 4.4 0.4 - - - +
68E HIS* 2.8 33.0 + - - +
69E TYR* 2.7 29.4 + - + +
71E MET* 3.9 37.2 - - + -
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Residues in contact with LYS 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E PHE* 3.3 6.1 - - - -
44E ASP* 2.7 52.3 + - + +
46E ILE* 4.4 6.7 - - + -
60E VAL* 1.3 77.6 - - - +
62E HIS* 1.3 66.7 + - - +
63E LYS* 3.5 8.1 + - - +
66E GLY* 2.5 40.4 + - - +
67E ASN 3.4 1.1 - - - +
68E HIS* 3.1 39.7 + - + +
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Residues in contact with HIS 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E GLN* 3.1 46.2 + - + +
43E PHE* 3.8 14.3 - + + -
60E VAL* 4.4 0.4 - - - +
61E LYS* 1.3 69.8 - - - +
63E LYS* 1.3 56.7 + - - +
64E GLU* 4.3 17.9 + - + +
65E SER* 2.8 27.9 + - - +
66E GLY* 2.4 37.0 + - - -
67E ASN 2.4 25.1 + - - +
69E TYR* 3.6 24.9 - + + -
108E PHE* 4.2 18.1 - + - -
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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