Contacts of the strand formed by residues 55 - 62 (chain I) in PDB entry 3E8E
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51I THR* 3.7 2.1 + - - -
52I GLY 2.9 28.7 + - - +
54I PHE* 1.3 78.5 - - - +
56I ARG* 1.3 66.8 - - - +
73I ILE 3.1 12.1 - - - -
74I LEU* 4.3 0.7 - - - -
75I ASP* 4.4 4.3 - - - -
78I LYS* 5.3 0.8 - - - +
351I G98 3.6 9.7 - - - -
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Residues in contact with ARG 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I ARG* 4.6 1.0 - - - +
48I THR* 4.0 22.3 + - + -
50I GLY 3.1 15.9 - - - +
51I THR* 4.0 8.5 - - - +
55I GLY* 1.3 78.4 - - - +
57I VAL* 1.3 61.8 + - - +
58I MET* 3.9 20.8 - - + -
71I MET 3.6 1.2 - - - +
72I LYS* 3.5 1.0 - - - +
73I ILE* 2.7 45.6 + - + +
331I GLU 5.8 1.6 - - - -
333I GLU* 3.0 40.3 + - - +
334I GLU 3.3 13.3 + - - -
335I ILE* 3.0 36.0 - - - +
351I G98 3.7 8.2 - - - -
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Residues in contact with VAL 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I THR* 3.7 0.7 - - - +
49I LEU* 2.8 25.5 + - + -
50I GLY 3.0 12.8 + - - +
56I ARG* 1.3 74.2 - - - +
58I MET* 1.3 69.3 + - - +
70I ALA* 4.1 18.2 - - + -
71I MET 3.4 9.9 - - - +
72I LYS* 4.0 14.6 - - + +
120I MET* 4.7 1.8 - - + -
351I G98 3.7 80.1 - - + +
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Residues in contact with MET 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I ARG* 3.2 41.7 - - + +
46I ILE 4.8 0.9 - - - +
47I LYS 3.4 15.3 - - - +
48I THR* 3.2 38.4 - - - +
49I LEU* 3.9 6.1 - - - +
56I ARG* 3.9 24.0 - - + +
57I VAL* 1.3 80.7 - - - +
59I LEU* 1.3 65.1 + - - +
60I VAL* 3.6 1.0 + - + -
70I ALA* 3.2 4.2 - - - -
71I MET* 2.7 42.8 + - + +
73I ILE* 4.2 16.8 - - + -
332I GLU* 3.7 8.7 - - - +
333I GLU 5.8 0.7 - - - +
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Residues in contact with LEU 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I ARG* 4.3 0.2 - - - -
46I ILE* 3.1 49.9 + - + +
47I LYS 2.7 20.5 + - - +
49I LEU* 3.6 19.1 - - + +
58I MET* 1.3 73.6 - - - +
60I VAL* 1.3 62.6 + - - +
68I HIS* 4.0 15.3 - - + +
69I TYR 3.4 16.6 - - - +
122I TYR* 3.5 31.4 - - + -
322I GLY* 3.4 28.9 - - - +
324I THR* 3.4 18.4 - - + -
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Residues in contact with VAL 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I PHE* 3.4 45.8 - - + -
44I GLU 3.1 23.6 - - - +
45I ARG* 3.8 15.3 - - + +
46I ILE* 3.8 4.0 - - - -
58I MET* 3.6 1.3 + - + -
59I LEU* 1.3 76.8 - - - +
61I LYS* 1.3 60.8 + - - +
68I HIS* 3.4 4.7 + - - -
69I TYR* 2.8 48.9 + - + +
71I MET* 3.8 27.4 - - + -
119I VAL* 4.7 0.7 - - + -
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Residues in contact with LYS 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I PHE* 3.4 2.1 - - - -
44I GLU* 2.7 62.9 + - - +
46I ILE* 3.6 15.5 - - + -
60I VAL* 1.3 75.6 - - - +
62I HIS* 1.3 67.0 + - - +
63I MET* 3.2 6.4 + - - +
66I GLY* 3.7 33.0 - - - +
67I ASN 3.5 3.6 - - - +
68I HIS* 4.0 19.6 + - + +
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Residues in contact with HIS 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I GLN* 3.7 30.8 + - + +
43I PHE* 3.7 25.4 - + + -
60I VAL 4.2 0.4 - - - -
61I LYS* 1.3 69.3 - - - +
63I MET* 1.3 57.4 + - - +
64I GLU* 3.4 19.9 + - + +
65I THR* 2.7 46.4 + - + +
66I GLY* 2.6 35.8 + - - -
67I ASN* 2.8 16.9 + - - +
69I TYR* 3.6 20.2 + + + -
108I PHE* 4.9 13.5 - + - -
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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