Contacts of the helix formed by residues 59 - 71 (chain C) in PDB entry 4NFT
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 THR 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C ASN* 4.7 2.5 - - - +
57C THR* 3.8 23.8 - - + +
58C ILE* 1.3 77.4 - - - +
60C SER* 1.3 61.0 + - - +
61C ARG* 3.0 18.7 + - - +
62C GLU* 2.5 39.8 + - - +
63C ILE* 3.1 17.9 + - - +
127C GLY* 4.8 7.9 - - - -
130C ALA* 4.3 4.5 - - - -
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Residues in contact with SER 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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59C THR* 1.3 71.6 - - - +
61C ARG* 1.3 58.9 + - - +
63C ILE* 3.6 10.9 - - - +
64C GLN* 2.7 36.4 + - - +
129C THR* 3.4 17.9 + - - -
130C ALA* 4.4 6.5 - - - +
133C TYR* 3.3 44.3 - - - -
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Residues in contact with ARG 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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59C THR* 3.0 15.2 + - - +
60C SER* 1.3 83.0 + - - +
62C GLU* 1.3 69.0 + - - +
64C GLN* 3.7 19.4 + - - +
65C THR* 3.3 25.3 + - - +
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Residues in contact with GLU 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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46C ALA* 3.7 21.0 - - + +
49C LEU* 3.8 17.5 - - + +
50C ALA* 3.8 24.9 - - + +
53C ASN* 2.9 27.6 + - - +
58C ILE* 4.8 0.7 - - + -
59C THR* 2.5 47.4 + - - +
61C ARG* 1.3 80.9 - - - +
63C ILE* 1.3 61.4 + - - +
65C THR* 3.4 4.3 + - - -
66C ALA* 2.9 29.3 + - - +
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Residues in contact with ILE 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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42C ILE* 4.3 12.1 - - + +
46C ALA* 4.0 20.2 - - + -
58C ILE* 4.1 12.6 - - + -
59C THR 3.1 16.1 + - - +
60C SER* 3.6 13.0 - - - +
62C GLU* 1.3 75.1 - - - +
64C GLN* 1.3 66.4 - - - +
66C ALA* 3.1 3.1 + - - +
67C VAL* 2.8 41.9 + - + +
116C LEU* 4.1 13.7 - - + -
130C ALA* 4.4 7.9 - - + +
133C TYR* 4.8 7.6 - - + -
134C SER* 3.4 28.7 - - - +
137C ILE* 4.3 13.2 - - + -
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Residues in contact with GLN 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 SER 2.7 21.9 + - - +
61C ARG* 3.7 21.4 + - - +
63C ILE* 1.3 75.4 - - - +
65C THR* 1.3 59.8 + - - +
67C VAL* 3.2 3.6 + - - +
68C ARG* 2.9 47.0 + - + +
80C VAL* 3.8 43.8 - - + +
133C TYR* 6.3 3.7 - - + -
137C ILE* 5.8 0.2 - - - -
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Residues in contact with THR 65 (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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49C LEU* 3.6 26.9 - - + -
61C ARG* 3.3 13.9 + - - +
62C GLU* 3.9 3.1 - - - -
63C ILE 3.3 0.4 - - - -
64C GLN* 1.3 78.6 + - - +
66C ALA* 1.3 63.9 - - - +
68C ARG* 3.1 22.5 + - + +
69C LEU* 3.0 31.0 + - + +
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Residues in contact with ALA 66 (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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42C ILE* 3.6 33.1 - - + +
45C GLU* 3.8 19.2 - - + +
46C ALA* 3.7 14.8 - - + +
49C LEU* 4.0 1.1 - - + +
62C GLU 2.9 17.0 + - - +
63C ILE 3.1 4.5 + - - +
65C THR* 1.3 77.3 - - - +
67C VAL* 1.3 62.8 + - - +
69C LEU* 3.0 13.8 + - - +
70C LEU* 3.2 13.0 + - - +
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Residues in contact with VAL 67 (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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42C ILE* 3.9 27.1 - - + -
63C ILE* 2.8 23.3 + - + +
64C GLN* 3.5 8.5 - - - +
66C ALA* 1.3 75.0 - - - +
68C ARG* 1.3 58.3 + - - +
70C LEU* 3.1 2.5 + - - +
71C LEU* 2.9 55.3 + - + +
76C ALA* 4.3 13.2 - - + +
79C ALA* 4.8 1.1 - - + -
80C VAL* 4.5 11.0 - - + -
137C ILE* 3.7 30.7 - - + -
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Residues in contact with ARG 68 (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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64C GLN* 2.9 36.1 + - + +
65C THR* 3.1 22.6 + - + +
67C VAL* 1.3 76.6 - - + +
69C LEU* 1.3 60.0 + - + +
71C LEU 3.6 11.6 - - - +
76C ALA* 4.5 18.4 - - + -
77C LYS* 4.8 19.5 - - - +
80C VAL* 5.7 2.2 - - + -
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Residues in contact with LEU 69 (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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41C ARG* 4.6 9.9 + - - +
45C GLU* 3.8 36.6 - - + +
49C LEU* 4.7 6.5 - - + -
65C THR* 3.0 28.8 + - + +
66C ALA* 3.0 10.1 + - - +
68C ARG* 1.3 81.3 - - + +
70C LEU* 1.3 57.3 + - - +
182C ALA* 5.9 0.7 - - - +
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Residues in contact with LEU 70 (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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38C ILE* 4.0 25.4 - - + +
41C ARG* 4.3 28.3 - - + +
42C ILE* 4.5 10.8 - - + -
66C ALA 3.2 9.2 + - - +
67C VAL* 3.1 5.6 + - - +
69C LEU* 1.3 80.5 - - - +
71C LEU* 1.3 83.7 + - + +
72C PRO* 3.9 3.5 - - - +
178C SER 5.6 0.2 - - - -
179C LEU* 3.9 13.8 - - + +
182C ALA* 3.6 40.1 - - + +
183C THR* 3.9 16.4 - - - +
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ILE* 5.3 2.9 - - + -
67C VAL* 2.9 36.1 + - + +
68C ARG 3.6 14.7 - - - +
70C LEU* 1.3 106.6 - - + +
72C PRO* 1.3 81.1 - - + +
73C GLY* 3.6 1.9 + - - -
75C LEU* 4.0 18.4 - - + -
76C ALA* 4.0 18.4 - - + +
79C ALA* 4.2 8.7 - - + -
137C ILE* 5.3 0.2 - - + -
141C LEU* 4.0 26.7 - - + -
179C LEU* 3.7 15.7 - - + -
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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