Contacts of the helix formed by residues 52 - 64 (chain C) in PDB entry 1FBA
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 GLU 52 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C THR* 1.3 75.9 + - - +
53C ASP* 1.3 57.3 + - - +
55C ARG* 3.5 23.9 + - - +
56C ARG* 2.9 26.0 + - + +
81C GLU* 3.9 19.2 - - - +
85C GLN* 3.7 22.2 - - - +
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Residues in contact with ASP 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C THR* 3.0 9.4 + - + +
52C GLU* 1.3 77.5 - - - +
54C ASN* 1.3 59.5 + - - +
56C ARG* 2.8 40.2 + - - +
57C ALA* 2.7 34.7 + - - +
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Residues in contact with ASN 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU* 4.5 7.0 - - + -
48C VAL* 3.0 28.4 - - + +
49C GLU* 2.5 39.1 + - - +
51C THR* 2.8 25.6 + - + +
53C ASP* 1.3 80.3 - - - +
55C ARG* 1.3 61.5 + - - +
57C ALA* 3.2 8.6 + - - +
58C TYR* 2.9 24.3 + - - +
313C TRP* 4.2 4.8 - - - -
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Residues in contact with ARG 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLY* 3.9 19.8 - - - -
39C MET* 3.9 29.2 - - + -
43C LEU* 4.2 7.4 - - + -
50C ASN* 2.8 41.5 + - - +
51C THR 2.9 12.9 + - - +
52C GLU* 3.6 33.6 - - - +
54C ASN* 1.3 76.1 - - - +
56C ARG* 1.3 63.1 + - - +
58C TYR* 3.2 4.5 + - - -
59C ARG* 2.9 45.7 + - - +
81C GLU* 2.7 44.9 + - - +
85C GLN* 4.9 0.7 - - - +
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Residues in contact with ARG 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C GLU* 2.9 18.8 + - - +
53C ASP* 2.8 41.7 + - - +
55C ARG* 1.3 75.9 - - - +
57C ALA* 1.3 63.6 - - - +
59C ARG* 3.3 1.0 + - - -
60C GLN* 2.9 40.7 + - - +
85C GLN* 3.7 35.4 - - + +
86C LYS 3.0 26.5 + - - +
87C ALA 3.8 0.8 - - - -
88C ASP* 2.7 32.8 + - - +
93C PHE* 3.3 20.1 - - + -
317C LYS* 5.8 1.8 - - - +
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Residues in contact with ALA 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C ASP* 2.7 25.2 + - - +
54C ASN* 3.2 11.0 - - - +
55C ARG 3.2 0.2 - - - -
56C ARG* 1.3 82.2 - - - +
58C TYR* 1.3 63.1 + - - +
60C GLN* 3.0 19.5 + - - +
61C LEU* 3.1 12.8 + - - +
313C TRP* 4.5 15.2 - - + -
317C LYS* 4.9 15.5 + - - +
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Residues in contact with TYR 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C MET* 3.3 31.2 - - + -
43C LEU* 4.6 4.9 - - + -
54C ASN 2.9 12.7 + - - +
55C ARG* 3.2 5.1 + - - +
57C ALA* 1.3 75.5 - - - +
59C ARG* 1.3 73.3 + - - +
61C LEU* 3.4 8.5 - - + +
62C LEU* 3.4 32.9 + - + +
306C GLN* 3.0 46.0 + - - +
309C VAL* 3.8 24.7 - - + +
310C LEU* 3.6 23.0 - - + +
313C TRP* 3.5 42.1 - + + -
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Residues in contact with ARG 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ALA* 3.4 18.9 + - + +
34C GLU* 3.1 46.5 + - - -
39C MET* 3.6 22.8 - - - +
55C ARG* 2.9 40.5 + - - +
56C ARG* 3.7 4.7 - - - +
58C TYR* 1.3 91.2 - - - +
60C GLN* 1.3 66.2 + - - +
62C LEU* 3.4 8.4 + - + +
63C PHE* 3.0 50.9 + - + -
79C PHE* 5.7 0.8 - - - +
81C GLU* 4.4 6.5 + - - -
82C THR* 3.7 31.3 + - + -
85C GLN* 5.0 1.6 - - - +
93C PHE* 4.0 9.0 - - + -
306C GLN* 5.6 0.2 + - - -
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Residues in contact with GLN 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ARG* 2.9 20.9 + - - +
57C ALA* 3.0 13.0 + - - +
59C ARG* 1.3 75.5 - - - +
61C LEU* 1.3 53.7 - - - +
63C PHE* 3.4 1.5 + - - +
64C SER* 2.6 52.6 + - - +
87C ALA* 3.1 15.4 - - + -
88C ASP* 2.8 53.8 + - - +
93C PHE* 3.7 17.4 - - + -
96C ILE* 6.5 0.2 - - - -
317C LYS* 4.1 14.3 - - - +
320C ILE* 5.8 2.2 - - - +
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Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ALA 3.1 11.0 + - - +
58C TYR* 3.4 12.6 - - + +
59C ARG 3.2 0.2 - - - -
60C GLN* 1.3 78.4 - - - +
62C LEU* 1.3 73.0 + - + +
64C SER* 3.1 6.1 + - - -
65C THR* 3.2 2.8 + - - -
309C VAL* 3.8 26.7 - - + -
313C TRP* 3.4 50.0 - - + +
320C ILE* 4.1 25.1 - - + +
323C GLY* 5.0 1.1 - - - -
324C GLN* 2.9 46.9 + - + +
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU* 4.7 10.9 - - + +
32C ALA* 4.5 17.5 - - + -
58C TYR* 3.4 47.4 + - + +
59C ARG* 3.4 12.8 + - - +
61C LEU* 1.3 78.9 - - + +
63C PHE* 1.3 71.3 + - + +
65C THR* 2.7 25.8 + - - -
69C LEU* 4.2 7.1 - - - +
306C GLN* 3.8 20.4 - - + +
309C VAL* 3.9 17.5 - - + -
327C LEU* 3.7 28.9 - - + +
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Residues in contact with PHE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU* 5.1 2.7 - - + -
32C ALA* 4.6 9.9 - - + -
59C ARG* 3.0 28.9 + - + +
60C GLN 4.2 2.0 - - - +
62C LEU* 1.3 87.7 - - + +
64C SER* 1.3 57.6 + - - +
65C THR* 3.2 3.4 - - - -
69C LEU* 5.9 1.1 - - - -
76C VAL* 3.8 22.9 - - + -
78C LEU* 3.6 25.6 - - + -
82C THR* 3.6 26.7 - - + -
93C PHE* 3.6 35.7 - + + -
96C ILE* 3.3 19.8 - - + +
97C LEU* 3.9 31.6 - - + +
100C LYS* 3.0 20.7 + - - +
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Residues in contact with SER 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C GLN* 2.6 35.5 + - - +
61C LEU* 3.1 1.8 + - - -
63C PHE* 1.3 75.7 - - - +
65C THR* 1.3 68.5 + - - +
66C ASP* 3.7 0.5 + - - -
67C PRO* 5.5 0.3 - - - +
96C ILE* 4.9 9.6 - - - -
100C LYS* 3.5 6.1 + - - +
320C ILE* 5.3 1.6 - - - +
324C GLN* 3.1 22.2 + - - +
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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