Contacts of the helix formed by residues 42 - 49 (chain A) in PDB entry 3FTC
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 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A GLY 3.9 7.9 + - - -
41A THR* 1.3 76.9 + - - +
43A ASN* 1.3 60.2 + - - -
44A LEU 3.4 1.3 - - - -
45A THR* 3.5 20.6 - - - -
46A LYS* 2.9 35.2 + - - +
68A ASN* 5.1 9.3 - - - +
69A LEU* 4.6 7.6 - - - -
72A ILE* 4.5 4.9 - - - +
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Residues in contact with ASN 43 (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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13A LEU* 4.6 13.1 - - - +
14A VAL 5.2 4.6 + - - -
16A GLU* 4.4 11.9 + - - +
19A LEU* 3.7 18.3 - - + +
41A THR* 2.8 33.2 + - + +
42A GLY* 1.3 73.1 - - - +
44A LEU* 1.3 63.7 + - - +
46A LYS* 3.4 12.6 + - - +
47A VAL* 3.1 28.6 + - - +
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Residues in contact with LEU 44 (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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19A LEU* 3.9 36.3 - - + +
22A ILE* 3.9 23.3 - - + -
23A ALA* 5.1 0.7 - - + +
36A GLU* 3.3 31.2 - - + +
41A THR 3.6 7.0 + - - +
43A ASN* 1.3 74.7 - - - +
45A THR* 1.3 66.9 + - - +
47A VAL* 3.1 4.1 + - + -
48A LEU* 2.9 44.0 + - + +
99A VAL* 4.2 14.4 - - + -
100A GLY* 4.3 0.7 - - - -
101A ASN* 4.2 28.3 - - + +
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Residues in contact with THR 45 (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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36A GLU* 2.6 27.9 + - - +
39A GLY* 4.8 1.6 - - - -
42A GLY* 3.5 18.4 + - - -
43A ASN 3.3 0.2 - - - -
44A LEU* 1.3 79.3 - - - +
46A LYS* 1.3 63.0 + - - +
48A LEU* 3.3 6.2 + - - +
49A LEU* 3.1 26.8 + - + +
56A LEU* 4.0 7.0 - - + -
58A VAL* 4.8 0.5 - - - +
69A LEU* 3.5 29.2 - - + +
72A ILE* 3.8 14.6 - - + -
77A LEU* 3.9 20.6 - - + -
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Residues in contact with LYS 46 (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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42A GLY 2.9 22.7 + - - +
43A ASN* 3.7 12.1 - - - +
44A LEU 3.2 0.4 - - - -
45A THR* 1.3 76.5 - - - +
47A VAL* 1.3 63.8 + - + +
49A LEU* 3.2 17.2 + - - +
50A GLN* 3.3 19.2 + - - +
72A ILE* 4.2 24.0 - - + -
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Residues in contact with VAL 47 (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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16A GLU* 3.8 22.0 - - - +
19A LEU* 3.9 26.2 - - + +
20A LYS* 4.1 18.6 - - + +
23A ALA* 3.8 21.5 - - + -
43A ASN 3.1 15.1 + - - +
44A LEU* 3.1 10.1 + - + +
46A LYS* 1.3 75.7 - - + +
48A LEU* 1.3 64.7 + - - +
50A GLN* 3.0 36.4 + - - +
51A HIS* 3.5 9.3 - - - +
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Residues in contact with LEU 48 (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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23A ALA* 4.1 14.8 - - + -
26A LEU* 3.6 30.1 - - + -
28A ILE* 4.3 6.4 - - + +
34A VAL* 4.6 2.0 - - + -
36A GLU* 3.8 22.0 - - - +
44A LEU* 2.9 35.7 + - + +
45A THR 3.6 4.3 - - - +
47A VAL* 1.3 74.3 - - - +
49A LEU* 1.3 57.0 + - - +
50A GLN 3.1 0.2 - - - -
51A HIS* 3.0 25.3 + - - +
53A LEU* 3.5 20.1 - - + +
56A LEU* 4.1 22.4 - - + -
99A VAL* 3.8 22.2 - - + -
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Residues in contact with LEU 49 (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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45A THR* 3.1 34.1 + - + +
46A LYS* 3.6 9.0 - - - +
47A VAL 3.2 0.6 - - - -
48A LEU* 1.3 72.4 - - - +
50A GLN* 1.3 57.7 + - - +
51A HIS 3.1 7.2 + - - +
53A LEU* 4.1 12.3 - - + -
56A LEU* 3.9 20.6 - - + -
72A ILE* 3.7 29.4 - - + -
74A ASP* 4.0 20.1 - - + +
76A ARG* 2.9 46.6 + - + +
77A LEU* 4.4 8.3 - - + -
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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