Contacts of the helix formed by residues 71 - 77 (chain A) in PDB entry 1TVK
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 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ASP* 3.4 17.1 - - - +
70A LEU* 1.3 79.3 - - - +
72A PRO* 1.3 72.7 - - - +
73A THR* 3.8 13.7 - - - -
74A VAL* 3.2 22.6 + - - +
95A GLY 3.3 1.4 + - - -
99A ALA* 3.3 22.9 - - + -
9500A GTP 4.9 4.4 + - - +
2B ARG* 2.6 44.2 + - - +
247B ASN* 3.1 20.7 - - - +
249B ASP* 4.5 4.0 - - - +
252B LYS* 5.9 2.5 - - + +
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Residues in contact with PRO 72 (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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70A LEU 4.4 0.2 - - - -
71A GLU* 1.3 85.5 - - + +
73A THR* 1.3 54.5 + - - +
74A VAL 2.3 21.3 + - - -
75A ILE* 2.8 15.8 + - - +
76A ASP* 3.4 13.9 + - + +
94A THR* 4.3 22.0 - - + +
95A GLY 3.0 19.6 - - - +
96A LYS* 4.2 11.9 - - + -
97A GLU 4.5 4.7 - - - +
2B ARG* 4.8 8.7 - - - +
46B ARG* 3.5 22.4 - - - +
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Residues in contact with THR 73 (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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71A GLU* 3.8 13.2 - - - -
72A PRO* 1.3 74.7 - - - +
74A VAL* 1.3 59.0 + - - +
75A ILE 3.5 0.2 - - - -
76A ASP* 3.5 11.0 - - - +
77A GLU* 2.7 60.3 + - - +
2B ARG* 5.4 0.2 + - - -
46B ARG* 2.7 37.1 + - - +
241B ARG* 5.1 1.4 - - - -
242B PHE 3.2 27.3 + - - +
243B PRO* 3.7 1.8 - - + -
247B ASN* 3.6 13.7 - - - +
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Residues in contact with VAL 74 (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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11A GLN* 3.3 56.5 - - + +
14A VAL* 4.6 9.6 - - + -
15A GLN* 4.7 4.9 - - + -
69A ASP* 3.7 11.7 - - - +
71A GLU* 3.2 18.6 - - - +
72A PRO 2.3 11.9 + - - -
73A THR* 1.3 66.1 - - - +
75A ILE* 1.3 69.0 + - - +
77A GLU* 2.7 23.0 + - + +
78A VAL* 3.6 5.7 + - - +
9500A GTP 5.9 0.9 - - - +
244B GLY 5.2 0.2 - - - +
247B ASN* 3.7 19.7 - - - +
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Residues in contact with ILE 75 (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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14A VAL* 3.2 37.9 - - + -
67A PHE* 4.5 2.7 - - + -
68A VAL 3.8 4.7 - - - +
69A ASP* 3.2 42.6 - - + +
71A GLU 4.7 0.4 - - - +
72A PRO 2.8 11.4 + - - +
74A VAL* 1.3 75.7 - - - +
76A ASP* 1.3 58.7 + - - +
78A VAL* 2.9 29.2 + - + +
79A ARG* 3.3 10.6 - - - +
92A LEU* 4.1 31.0 - - + -
93A ILE 4.4 4.5 - - - +
94A THR* 3.0 29.8 - - + +
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Residues in contact with ASP 76 (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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72A PRO* 3.4 9.3 + - - +
73A THR* 3.5 23.1 - - - +
74A VAL 3.0 0.2 - - - -
75A ILE* 1.3 75.6 - - - +
77A GLU* 1.3 53.1 + - - +
78A VAL 3.0 7.2 + - - -
79A ARG* 3.2 42.8 + - - +
80A THR* 2.7 37.9 - - - +
94A THR* 5.7 0.3 - - - +
45B GLU* 5.2 6.1 - - - +
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Residues in contact with GLU 77 (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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73A THR* 2.7 48.3 + - + +
74A VAL* 2.7 17.5 + - + +
76A ASP* 1.3 76.2 - - - +
78A VAL* 1.3 60.1 + - - +
80A THR* 3.4 21.8 - - + +
81A GLY* 4.5 3.8 + - - -
42B LEU* 5.8 1.6 - - - +
243B PRO* 3.1 38.7 - - + +
244B GLY 5.4 0.9 - - - +
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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