Contacts of the helix formed by residues 62 - 71 (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 ASP 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLU* 2.8 22.0 + - - +
61A LEU* 1.3 69.6 - - - +
63A ARG* 1.3 60.9 + - - +
64A GLU* 3.3 11.5 + - - +
65A MET* 3.1 47.4 + - + +
66A VAL* 2.9 31.4 + - - +
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Residues in contact with ARG 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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61A LEU 3.3 5.7 + - - +
62A ASP* 1.3 75.1 + - - +
64A GLU* 1.3 62.7 + - - +
66A VAL* 4.0 5.8 - - + +
67A GLU* 3.1 55.4 + - + +
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Residues in contact with GLU 64 (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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62A ASP* 3.3 9.9 + - - +
63A ARG* 1.3 78.9 - - - +
65A MET* 1.3 64.4 + - + +
67A GLU* 3.2 18.3 + - + +
68A ASN* 3.2 23.0 + - - +
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Residues in contact with MET 65 (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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39A GLY 3.4 16.2 - - - +
40A GLY* 3.6 22.4 - - - +
41A THR* 5.7 0.2 - - - -
60A GLU* 3.3 33.7 - - + +
62A ASP* 3.1 27.8 + - - +
64A GLU* 1.3 77.8 - - + +
66A VAL* 1.3 60.6 + - - +
68A ASN* 3.5 15.6 + - - +
69A LEU* 3.3 27.2 + - - +
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Residues in contact with VAL 66 (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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60A GLU* 3.6 34.1 - - + +
61A LEU 4.3 2.2 - - - +
62A ASP 2.9 22.4 + - - +
63A ARG* 4.0 6.7 - - - +
65A MET* 1.3 73.2 - - - +
67A GLU* 1.3 68.1 + - - +
69A LEU* 3.4 7.8 + - - +
70A LYS* 3.1 41.7 + - + +
79A VAL* 4.0 13.0 - - + -
81A ASN* 3.8 17.5 - - - +
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Residues in contact with GLU 67 (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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63A ARG* 3.1 50.3 + - - +
64A GLU* 3.2 12.5 + - + +
66A VAL* 1.3 78.2 - - - +
68A ASN* 1.3 65.7 + - - +
70A LYS* 3.1 28.8 + - - +
71A SER* 3.6 6.8 + - - -
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Residues in contact with ASN 68 (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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39A GLY 5.3 1.0 + - - -
41A THR* 4.3 19.4 + - - +
42A GLY* 5.1 9.2 - - - +
64A GLU* 3.2 23.0 + - - +
65A MET* 3.6 17.7 - - - +
67A GLU* 1.3 78.9 - - - +
69A LEU* 1.3 59.0 + - + +
71A SER* 2.7 24.4 + - - -
72A ILE* 4.1 9.3 - - - +
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Residues in contact with LEU 69 (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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39A GLY* 4.4 11.2 - - - +
42A GLY* 4.6 8.1 - - - -
45A THR* 3.5 40.4 - - + +
58A VAL* 3.7 26.7 - - + -
60A GLU* 4.4 3.8 - - + -
65A MET 3.3 16.6 + - - +
66A VAL* 3.7 9.9 - - - +
67A GLU 3.2 0.8 - - - -
68A ASN* 1.3 74.8 - - + +
70A LYS* 1.3 65.9 + - - +
72A ILE* 3.2 29.0 + - + +
77A LEU* 3.8 9.8 - - + +
79A VAL* 3.7 36.3 - - + -
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Residues in contact with LYS 70 (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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66A VAL* 3.1 34.4 + - + +
67A GLU* 3.1 23.8 + - - +
69A LEU* 1.3 79.4 - - - +
71A SER* 1.3 60.8 + - - +
72A ILE 3.3 9.4 + - - +
73A GLY* 5.1 0.7 - - - -
79A VAL* 4.0 28.3 + - + +
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Residues in contact with SER 71 (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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67A GLU 3.6 5.2 + - - -
68A ASN* 2.7 26.2 + - - -
70A LYS* 1.3 73.9 - - - +
72A ILE* 1.3 63.3 + - - +
73A GLY 3.5 3.3 + - - -
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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