Contacts of the helix formed by residues 86 - 95 (chain A) in PDB entry 1TQN
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A LYS* 3.7 30.9 + - - +
84A ILE* 3.9 1.8 - - - +
85A THR* 1.3 78.4 + - - +
87A PRO* 1.3 73.8 - - - +
88A ASP* 3.0 32.7 + - - +
89A MET* 3.0 19.0 + - + +
90A ILE* 2.9 22.2 + - - +
384A ASN* 4.9 1.7 - - - +
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Residues in contact with PRO 87 (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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85A THR 3.4 6.2 - - - +
86A ASP* 1.3 90.3 - - - +
88A ASP* 1.3 65.5 + - - +
90A ILE* 3.4 6.9 + - + +
91A LYS* 3.0 22.7 + - - +
407A TYR* 3.3 25.4 - - + +
428A ASP* 3.4 29.2 - - - +
430A TYR* 3.7 14.6 - - + +
431A ILE* 3.5 14.1 - - + -
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Residues in contact with ASP 88 (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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86A ASP* 3.0 13.6 + - - +
87A PRO* 1.3 76.8 - - - +
89A MET* 1.3 65.4 + - - +
91A LYS* 3.2 11.3 + - - +
92A THR* 2.8 28.4 + - - -
96A LYS* 4.9 10.7 + - - +
384A ASN* 4.0 9.6 - - + +
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Residues in contact with MET 89 (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 LYS* 2.9 32.1 - - - +
71A VAL* 4.6 0.2 - - - -
84A ILE* 3.6 36.1 - - + -
86A ASP* 3.0 18.6 + - + +
88A ASP* 1.3 77.6 - - - +
90A ILE* 1.3 58.4 + - - +
92A THR* 3.1 4.3 + - - -
93A VAL* 2.9 28.2 + - - +
383A ILE* 3.5 27.6 - - + +
384A ASN* 3.1 40.7 - - - +
386A MET* 4.0 21.8 - - + +
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Residues in contact with ILE 90 (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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84A ILE* 3.9 24.7 - - + +
85A THR* 3.8 20.6 - - - +
86A ASP 2.9 19.8 + - - +
87A PRO* 3.6 8.3 - - + +
89A MET* 1.3 76.5 - - - +
91A LYS* 1.3 52.8 + - - +
93A VAL* 3.3 1.4 + - - -
94A LEU* 2.8 59.8 + - + +
396A ILE* 3.8 16.4 - - + -
401A LEU* 3.8 18.4 - - + -
430A TYR* 3.4 33.9 - - + +
431A ILE* 5.0 0.4 - - + -
433A THR* 5.3 0.2 - - + -
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Residues in contact with LYS 91 (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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87A PRO 3.0 14.7 + - - +
88A ASP* 3.2 13.4 + - - +
90A ILE* 1.3 74.2 - - - +
92A THR* 1.3 59.8 + - - +
95A VAL* 2.6 41.8 + - + +
96A LYS* 2.9 38.1 + - - +
430A TYR* 3.5 47.6 - - + +
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Residues in contact with THR 92 (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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88A ASP 2.8 17.8 + - - -
89A MET* 3.2 9.0 - - - -
91A LYS* 1.3 77.8 - - - +
93A VAL* 1.3 58.1 + - - +
96A LYS* 3.5 26.0 + - + +
97A GLU* 2.6 46.7 + - + +
383A ILE* 3.6 34.5 - - + -
384A ASN* 3.1 17.0 + - - +
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Residues in contact with VAL 93 (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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84A ILE* 4.1 6.7 - - + -
89A MET 2.9 17.6 + - - +
90A ILE 3.7 3.8 - - - +
92A THR* 1.3 79.3 - - - +
94A LEU* 1.3 68.3 + - + +
95A VAL 3.6 0.2 + - - -
97A GLU 3.9 7.6 - - - -
98A CYS* 4.0 2.8 + - - -
102A PHE* 3.6 49.1 - - + +
375A ARG* 4.0 19.0 - - + +
383A ILE* 3.8 24.2 - - + -
394A VAL* 3.8 26.0 - - + +
396A ILE* 4.6 3.8 - - + -
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Residues in contact with LEU 94 (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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90A ILE* 2.8 43.8 + - + +
91A LYS* 4.9 0.2 - - - -
93A VAL* 1.3 78.0 - - + +
95A VAL* 1.3 63.7 + - + +
98A CYS* 3.8 7.9 - - - +
373A LEU* 4.4 16.6 - - + -
375A ARG* 3.8 35.3 + - + +
396A ILE* 3.3 25.4 - - + -
430A TYR* 4.6 2.2 - - + -
433A THR* 5.0 2.9 - - + -
437A SER* 3.6 36.4 - - - +
438A GLY* 3.2 16.3 - - - -
439A PRO* 3.4 8.3 - - - +
440A ARG 5.1 0.3 + - - -
508A HEM 4.9 0.7 - - - +
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Residues in contact with VAL 95 (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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91A LYS* 2.6 30.4 + - + +
94A LEU* 1.3 78.1 - - + +
96A LYS* 1.3 70.5 + - + +
97A GLU 3.2 2.4 + - - -
98A CYS* 3.3 16.1 + - - +
99A TYR* 5.9 1.0 - - - -
430A TYR* 3.4 39.5 - - + +
437A SER* 4.3 0.4 - - - +
438A GLY* 3.8 19.7 - - - +
439A PRO* 4.2 9.4 - - + +
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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