Contacts of the strand formed by residues 61 - 68 (chain E) in PDB entry 5FXY
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 PHE 61 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55E ARG* 4.9 1.0 - - - +
56E PRO* 3.8 19.7 - - + +
59E LYS* 3.5 40.9 - - + +
60E ASP* 1.3 94.1 - - - +
62E SER* 1.3 64.4 + - - +
63E ILE* 3.7 17.9 - - + -
85E GLN* 3.2 50.5 - - + -
86E LEU 3.3 22.0 - - - +
87E PRO* 4.0 4.5 - - + -
88E ASN* 3.5 12.5 + - - +
114E LYS* 6.1 0.7 - - - -
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Residues in contact with SER 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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53E VAL* 4.2 8.9 - - - +
55E ARG* 3.7 33.0 + - - -
56E PRO* 4.0 6.1 - - - -
61E PHE* 1.3 74.5 - - - +
63E ILE* 1.3 67.2 + - - +
64E HIS* 3.4 19.5 + - - -
84E VAL 3.5 0.2 - - - +
85E GLN* 3.8 0.2 - - - -
86E LEU* 2.9 35.9 + - - +
88E ASN* 3.4 10.5 + - - -
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Residues in contact with ILE 63 (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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52E ASP* 4.4 1.9 - - - +
53E VAL* 3.8 7.1 - - - +
54E THR* 3.4 48.3 + - + +
55E ARG 4.4 0.2 - - - +
56E PRO* 4.2 12.1 - - + +
61E PHE* 3.7 25.4 - - + -
62E SER* 1.3 70.4 - - - +
64E HIS* 1.3 72.2 + - - +
65E ARG* 4.4 10.9 - - + +
83E SER* 4.1 22.0 - - - -
84E VAL 3.5 3.6 - - - +
85E GLN* 3.8 18.4 - - + +
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Residues in contact with HIS 64 (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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49E TRP* 3.5 22.2 - + + -
50E LEU 5.8 0.9 - - - +
52E ASP 4.6 5.4 - - - +
53E VAL* 3.3 31.0 - - + +
55E ARG* 6.3 0.4 - - - -
62E SER* 3.4 33.0 + - - -
63E ILE* 1.3 74.1 - - - +
65E ARG* 1.3 60.0 - - - +
83E SER* 3.6 0.5 - - - -
84E VAL* 2.7 41.1 + - + +
86E LEU* 3.4 26.9 - - + +
383E ASN* 3.7 22.8 + - - -
385E ASN* 3.8 14.6 - - - +
386E GLU* 4.5 7.6 + - + +
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Residues in contact with ARG 65 (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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49E TRP* 3.5 3.8 - - - -
50E LEU* 3.0 46.3 + - + +
52E ASP* 3.0 47.6 + - - +
54E THR* 3.7 24.9 - - - +
63E ILE* 4.4 9.7 + - + +
64E HIS* 1.3 79.6 - - - +
66E LEU* 1.3 70.4 + - - +
81E ILE* 4.2 16.7 - - + +
82E ALA 3.4 4.5 - - - +
83E SER* 4.3 9.9 - - - +
118E GLU* 4.6 16.4 - - - -
154E TYR* 4.3 14.8 + - - -
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Residues in contact with LEU 66 (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 GLN 3.4 11.4 - - - +
49E TRP* 3.2 50.3 - - + -
50E LEU* 4.3 1.1 - - - +
65E ARG* 1.3 74.5 - - - +
67E VAL* 1.3 63.6 + - - +
68E LEU* 3.5 14.4 - - + -
81E ILE* 3.5 15.9 - - - +
82E ALA* 3.0 29.2 + - + +
84E VAL* 3.9 20.6 - - + -
391E CYS* 3.5 31.6 - - + -
399E MET* 3.7 21.1 - - + -
401E VAL* 4.6 2.9 - - + -
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Residues in contact with VAL 67 (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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46E THR* 4.1 4.2 + - - +
47E ALA* 3.5 9.7 + - - -
48E GLN* 2.8 40.2 + - + +
50E LEU* 3.5 31.6 - - + -
66E LEU* 1.3 76.8 - - - +
68E LEU* 1.3 63.7 + - - +
79E LEU* 4.4 2.9 - - + -
80E VAL 3.7 4.0 - - - +
81E ILE* 4.0 14.8 - - + -
130E ALA* 4.0 29.2 - - + +
131E ARG* 5.7 0.4 - - - -
132E TYR* 5.0 3.1 - - + -
140E ILE* 4.2 21.8 - - + -
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Residues in contact with LEU 68 (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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40E LEU* 3.9 21.5 - - + -
44E SER* 3.4 28.7 - - - +
46E THR* 3.6 12.1 - - - +
47E ALA* 5.0 4.5 - - + -
66E LEU* 3.5 31.2 - - + -
67E VAL* 1.3 81.7 - - - +
69E GLY* 1.3 60.5 + - - +
79E LEU* 3.9 4.5 - - - +
80E VAL* 2.8 48.7 + - + +
82E ALA* 4.7 7.6 - - + -
130E ALA* 5.0 1.4 - - - +
393E VAL* 3.9 13.9 - - + -
399E MET* 3.9 19.1 - - + -
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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