Contacts of the helix formed by residues 52 - 63 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A THR* 1.3 74.3 - - - +
53A ASP* 1.3 58.6 + - - +
55A ARG* 3.3 33.2 + - - +
56A ARG* 2.9 28.0 + - + +
81A GLU* 4.2 7.4 - - - +
85A GLN* 3.1 29.9 + - - +
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Residues in contact with ASP 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A THR* 3.0 7.2 - - - +
52A GLU* 1.3 78.8 - - - +
54A ASN* 1.3 61.8 + - - +
56A ARG* 3.3 34.5 + - - +
57A ALA* 2.9 28.9 + - - +
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Residues in contact with ASN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 4.3 5.1 - - + +
48A VAL* 3.3 24.2 - - + +
49A GLU* 2.9 36.6 + - - +
51A THR* 3.0 22.4 + - - +
53A ASP* 1.3 79.0 - - - +
55A ARG* 1.3 61.3 + - - +
57A ALA* 3.4 8.5 + - - +
58A TYR* 3.0 28.4 + - - +
313A TRP* 4.3 5.5 - - + -
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A SER 5.3 0.2 - - - -
36A GLY* 4.1 18.3 - - - +
39A MET* 3.8 30.3 - - + -
43A LEU* 4.0 7.4 - - + -
50A ASN* 2.9 37.9 + - - +
51A THR 3.0 21.7 + - - +
52A GLU* 3.4 28.6 - - - +
54A ASN* 1.3 75.3 - - - +
56A ARG* 1.3 59.1 + - - +
58A TYR* 3.4 3.9 + - - +
59A ARG* 2.9 45.6 + - - +
81A GLU* 2.9 44.5 + - - +
85A GLN* 5.0 0.9 - - - -
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLU* 2.9 17.2 + - - +
53A ASP* 3.3 36.5 + - - +
55A ARG* 1.3 77.6 - - - +
57A ALA* 1.3 58.9 + - - +
59A ARG* 3.2 2.2 + - - -
60A GLN* 2.7 53.1 + - - +
85A GLN* 3.8 34.5 + - + +
86A LYS 3.0 30.8 + - - +
87A ALA* 3.8 0.6 - - - +
88A ASP* 2.8 33.7 + - - +
93A PHE* 3.6 8.2 - - + -
317A LYS* 5.8 1.0 - - - +
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASP* 2.9 19.5 + - - +
54A ASN* 3.6 12.6 - - - +
55A ARG 3.3 0.2 - - - -
56A ARG* 1.3 86.8 - - - +
58A TYR* 1.3 62.7 + - - +
60A GLN* 3.1 12.0 + - - +
61A LEU* 3.1 21.8 + - - +
313A TRP* 4.7 13.2 - - + -
317A LYS* 5.4 9.6 - - - +
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Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 5.7 0.2 - - - -
39A MET* 4.1 25.6 - - + -
43A LEU* 4.6 4.5 - - + -
54A ASN 3.0 17.1 + - - +
55A ARG* 3.9 4.3 - - - +
57A ALA* 1.3 75.2 - - - +
59A ARG* 1.3 76.6 + - - +
61A LEU* 3.2 24.2 + - + +
62A LEU* 3.3 28.0 + - + +
306A GLN* 2.5 45.7 + - - +
309A VAL* 4.1 18.0 - - + +
310A LEU* 3.6 28.3 - - + +
313A TRP* 3.7 37.4 - + + -
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Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ALA* 3.1 20.8 + - + +
34A GLU* 2.9 54.4 + - - +
39A MET* 3.8 16.4 - - - +
55A ARG* 2.9 38.7 + - - +
56A ARG* 3.8 4.3 - - - +
58A TYR* 1.3 90.5 - - - +
60A GLN* 1.3 65.2 + - - +
62A LEU* 3.5 7.2 + - + -
63A PHE* 3.1 50.7 + - + -
79A PHE* 4.9 1.2 - - - +
81A GLU* 4.3 5.5 + - - -
82A THR* 3.6 34.4 + - + -
85A GLN* 5.0 1.3 + - - +
93A PHE* 4.0 10.5 - - + -
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ARG* 2.7 22.6 + - - +
57A ALA* 3.1 10.2 + - - +
59A ARG* 1.3 75.5 - - - +
61A LEU* 1.3 65.7 + - - +
63A PHE* 3.3 2.1 + - - +
64A SER* 3.0 35.6 + - - +
87A ALA* 3.0 15.6 - - + +
88A ASP* 2.6 57.3 + - - -
93A PHE* 3.8 18.8 - - + -
96A ILE* 6.1 0.9 - - + -
317A LYS* 4.1 11.3 - - - +
320A ILE* 5.8 2.8 - - - +
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Residues in contact with LEU 61 (chain A).
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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57A ALA 3.1 10.7 + - - +
58A TYR* 3.2 13.7 - - + +
60A GLN* 1.3 78.4 - - - +
62A LEU* 1.3 70.1 + - + +
64A SER* 3.4 2.4 + - - -
65A THR* 3.3 3.8 + - - -
309A VAL* 3.9 26.0 - - + -
313A TRP* 3.3 51.1 - - + +
320A ILE* 4.1 31.9 - - + +
323A GLY* 5.0 0.4 - - - -
324A GLN* 2.6 45.5 + - + +
327A LEU* 6.0 0.2 - - + -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 4.9 8.7 - - + +
32A ALA* 4.6 17.3 - - + -
58A TYR* 3.3 53.7 + - + +
59A ARG* 3.9 12.6 - - - +
60A GLN 3.3 0.2 - - - -
61A LEU* 1.3 77.4 - - + +
63A PHE* 1.3 72.4 + - + +
65A THR* 3.0 22.5 + - - -
69A LEU* 4.0 7.6 - - - +
97A LEU* 5.6 0.2 - - - +
306A GLN* 3.7 18.6 - - + +
309A VAL* 4.0 18.8 - - + -
327A LEU* 4.0 25.5 - - + +
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Residues in contact with PHE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 5.2 3.4 - - + -
32A ALA* 4.5 9.6 - - + -
59A ARG* 3.1 32.1 + - + +
60A GLN* 4.2 3.4 - - - +
62A LEU* 1.3 91.1 - - + +
64A SER* 1.3 57.7 + - - +
65A THR 3.3 3.4 - - - -
69A LEU* 5.9 0.9 - - - -
76A VAL* 3.8 22.9 - - + -
78A LEU* 3.6 24.7 - - + -
82A THR* 3.7 24.5 - - + -
93A PHE* 3.8 26.0 - + + +
96A ILE* 3.1 19.3 - - + +
97A LEU* 3.8 36.6 - - + +
100A LYS* 2.8 19.9 + - - +
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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