Contacts of the strand formed by residues 46 - 55 (chain V) in PDB entry 5FLX
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 46 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ARG* 4.8 2.7 - - - -
66A VAL* 3.3 43.5 - - + -
67A ALA* 3.6 18.4 - - - -
68A ILE 5.3 1.3 - - - -
69A GLU* 6.1 4.5 - - + -
185A MET* 3.1 32.3 + - + +
186A ARG* 5.1 1.1 - - - -
37V ALA* 3.4 26.9 - - + -
38V GLU 4.7 3.4 - - - -
39V VAL* 5.8 0.4 - - - +
44V GLY 3.9 0.4 + - - -
45V ARG* 1.3 98.2 + - + +
47V ASN* 1.3 83.6 + - - +
48V GLY* 4.0 5.6 + - - -
50V PHE* 6.5 0.2 - - + -
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Residues in contact with ASN 47 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V ALA* 4.3 4.0 - - - +
38V GLU* 3.3 57.5 + - + +
39V VAL 3.4 10.5 + - - -
40V ASP* 2.6 36.1 + - - +
45V ARG* 3.4 2.8 + - - +
46V PHE* 1.3 99.3 - - - +
48V GLY* 1.3 62.5 + - - +
49V GLN* 3.3 5.8 + - + +
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Residues in contact with GLY 48 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLU* 5.5 1.7 - - - +
37V ALA* 6.0 0.2 - - - -
45V ARG* 5.8 0.6 - - - +
46V PHE* 4.0 8.0 + - - -
47V ASN* 1.3 73.6 - - - +
49V GLN* 1.3 63.8 + - - +
50V PHE* 3.6 12.5 + - - -
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Residues in contact with GLN 49 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V ALA* 4.7 1.1 - - - -
38V GLU* 3.4 52.5 + - - +
47V ASN* 3.3 4.4 - - + +
48V GLY* 1.3 77.8 - - - +
50V PHE* 1.3 65.3 + - - +
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Residues in contact with PHE 50 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ALA* 5.5 7.4 - - + +
69A GLU* 4.7 11.0 - - - -
261C PHE 5.7 0.2 - - - -
263C LYS* 3.8 40.2 - - + -
267C GLN* 3.6 25.8 - - - +
35V ASN* 4.2 19.3 - - + -
36V VAL 3.3 13.9 - - - +
37V ALA* 3.9 8.9 - - + +
38V GLU* 5.9 0.2 - - - -
46V PHE* 6.5 0.2 - - + -
48V GLY 3.6 10.5 + - - -
49V GLN* 1.3 77.1 - - - +
51V LYS* 1.3 62.0 + - - +
52V THR* 3.6 30.4 + - + +
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Residues in contact with LYS 51 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34V MET 3.7 0.2 - - - +
35V ASN* 3.3 5.2 - - - +
36V VAL* 2.3 63.3 + - + +
38V GLU* 3.6 37.8 - - + +
49V GLN 4.1 0.2 + - - -
50V PHE 1.3 72.2 - - - +
52V THR* 1.3 61.4 + - - +
53V TYR* 4.2 10.8 - - + +
76V ASP* 2.6 40.3 + - - +
78V ILE* 3.9 26.4 - - + +
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Residues in contact with THR 52 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260C VAL 4.7 1.2 + - - -
261C PHE* 3.3 40.5 - - + +
263C LYS* 6.3 0.2 - - - -
18V SER* 5.0 0.5 + - - -
33V GLN* 3.6 24.9 - - - +
34V MET 3.5 3.6 - - - -
35V ASN* 3.5 15.5 - - - +
50V PHE* 3.6 27.1 - - + +
51V LYS* 1.3 73.7 - - - +
53V TYR* 1.3 73.2 + - - +
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Residues in contact with TYR 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C PHE* 5.1 0.7 - - - -
18V SER* 4.8 3.8 - - - -
33V GLN* 3.4 4.5 - - - +
34V MET* 2.5 55.9 + - + +
36V VAL* 3.6 37.9 - - + -
51V LYS* 4.2 8.7 - - + +
52V THR* 1.3 85.2 - - - +
54V ALA* 1.3 58.3 + - - +
55V ILE* 5.0 4.0 - - + -
69V ILE* 4.9 15.3 - - + -
72V LEU* 3.7 33.2 - - + -
73V ALA* 3.9 25.6 - - + +
76V ASP* 2.9 36.5 + - + +
78V ILE* 4.3 2.1 - - + +
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Residues in contact with ALA 54 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C PHE* 3.5 28.6 - - + -
15V ARG* 5.5 3.4 - - + -
16V LYS 4.0 12.3 - - - +
17V CYS* 3.2 19.9 - - - -
18V SER* 3.3 16.5 + - - +
19V ALA 4.3 0.2 + - - -
24V ILE* 4.5 13.7 - - + -
32V ILE 4.1 3.8 - - - +
33V GLN* 4.5 7.2 - - + +
53V TYR* 1.3 72.5 - - - +
55V ILE* 1.3 70.1 + - - +
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Residues in contact with ILE 55 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ASP* 4.8 4.7 - - - +
17V CYS* 3.8 1.3 - - - -
19V ALA* 4.8 5.6 - - + -
24V ILE* 4.7 2.6 - - - +
30V ALA 4.8 0.2 - - - +
31V SER* 3.4 3.3 - - - -
32V ILE* 3.2 40.9 + - + +
34V MET* 5.0 5.4 - - + -
53V TYR* 4.9 5.2 - - + +
54V ALA* 1.3 84.6 - - - +
56V CYS* 1.3 73.8 + - - +
59V ILE* 4.3 10.5 - - + -
60V ARG* 4.5 6.3 - - + +
65V SER* 3.9 24.0 - - - +
68V SER* 4.1 18.8 - - - +
69V ILE* 3.9 35.2 - - + +
72V LEU* 5.1 9.2 - - + -
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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