Contacts of the helix formed by residues 81 - 89 (chain A) in PDB entry 1TQ6
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A GLY 3.3 2.8 - - - -
80A SER* 1.3 78.7 - - - +
82A LYS* 1.3 58.7 + - - +
83A SER 3.2 0.3 + - - -
84A SER 3.4 0.2 + - - -
85A PHE* 2.9 32.8 + - - +
155A ILE* 4.7 3.8 - - - -
183A THR* 4.5 0.4 - - - -
232A ASN* 3.6 6.8 + - - -
500A GNP 2.7 42.3 + - - -
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Residues in contact with LYS 82 (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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74A VAL* 3.5 33.9 - - + +
75A THR 4.6 2.9 - - - +
76A GLY 3.0 33.3 + - - +
80A SER* 3.4 7.1 + - - +
81A GLY* 1.3 77.9 - - - +
83A SER* 1.3 58.3 + - - +
85A PHE* 3.6 2.1 - - - +
86A ILE* 3.2 29.5 + - - +
105A VAL* 4.3 0.2 - - - +
106A GLU* 3.1 19.6 + - - -
126A ASP* 2.9 29.0 + - - +
127A LEU 2.7 22.8 + - - -
129A GLY 3.8 1.2 - - - +
155A ILE* 4.1 11.4 - - + +
500A GNP 2.8 26.4 + - - +
501A MG 4.3 0.9 - - - -
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 1.3 68.9 - - - +
84A SER* 1.3 56.2 + - - +
85A PHE 3.0 2.0 + - - -
86A ILE* 3.2 2.4 + - - +
87A ASN* 2.8 43.9 + - - +
94A ASN* 5.4 1.1 - - - -
100A ALA* 3.7 23.0 + - - -
101A LYS 3.3 15.9 + - - -
102A THR 3.9 0.2 + - - -
500A GNP 2.5 32.8 + - - -
501A MG 2.3 30.3 - - - -
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Residues in contact with SER 84 (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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81A GLY 3.9 1.6 - - - -
83A SER* 1.3 77.0 - - - +
85A PHE* 1.3 50.9 + - - +
87A ASN* 3.7 0.9 - - - +
88A THR* 2.7 43.3 + - - -
94A ASN* 2.7 35.6 + - - +
232A ASN* 3.8 24.0 - - - -
233A LYS* 4.9 2.0 + - - -
500A GNP 2.9 32.3 + - - -
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Residues in contact with PHE 85 (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 VAL* 5.7 2.9 - - + -
74A VAL* 4.0 26.5 - - + -
81A GLY 2.9 19.1 + - - +
82A LYS 3.6 4.3 - - - +
84A SER* 1.3 73.1 - - - +
86A ILE* 1.3 63.1 + - - +
88A THR* 3.0 3.6 + - - -
89A LEU* 2.9 59.2 + - + +
124A PHE* 5.9 1.8 - + - -
153A ILE* 4.6 12.1 - - + -
155A ILE* 3.4 24.5 - - + -
181A VAL* 4.1 24.2 - - + -
183A THR* 5.6 0.7 - - + -
230A LEU* 5.2 2.9 - - + -
232A ASN* 3.8 14.3 + - - +
240A PHE* 4.4 12.3 - + - -
243A LEU* 4.0 27.4 - - + -
247A LEU* 6.1 2.9 - - + -
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Residues in contact with ILE 86 (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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74A VAL* 3.9 30.1 - - + -
82A LYS 3.2 14.3 + - - +
83A SER* 3.2 5.2 + - - +
85A PHE* 1.3 81.0 - - + +
87A ASN* 1.3 66.3 + - - +
89A LEU* 3.4 6.0 + - - +
90A ARG* 2.9 47.7 + - - +
100A ALA* 4.5 4.3 - - + -
114A TYR* 4.4 13.7 - - + -
124A PHE* 4.1 18.2 - - + -
125A TRP 4.6 0.9 - - - -
126A ASP* 3.6 49.1 - - + +
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Residues in contact with ASN 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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83A SER* 2.8 30.1 + - - +
84A SER 3.8 3.3 - - - +
86A ILE* 1.3 76.8 - - - +
88A THR* 1.3 65.0 + - - +
90A ARG* 3.0 18.7 + - - +
91A GLY 3.0 10.7 + - - -
92A ILE* 3.0 30.0 + - + +
93A GLY 4.2 1.6 - - - +
94A ASN* 3.8 24.1 + - - +
99A ALA* 3.6 12.2 - - - +
100A ALA* 3.0 42.3 + - - +
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Residues in contact with THR 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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84A SER* 2.7 29.2 + - - -
85A PHE* 3.4 7.2 - - - -
87A ASN* 1.3 74.0 - - - +
89A LEU* 1.3 60.9 + - - +
90A ARG 3.1 1.4 + - - -
91A GLY* 3.2 10.8 + - - +
92A ILE 4.7 2.2 - - - -
94A ASN* 5.2 2.3 + - - -
232A ASN* 3.8 11.4 + - - +
235A VAL* 4.0 22.5 - - + +
240A PHE* 3.9 25.8 - - + -
264A PRO* 3.5 20.6 - - + +
266A ILE* 5.4 1.1 - - + -
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Residues in contact with LEU 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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85A PHE* 2.9 67.4 + - + +
86A ILE* 3.8 4.9 - - - +
87A ASN 3.2 0.2 - - - -
88A THR* 1.3 76.6 - - - +
90A ARG* 1.3 58.8 + - - +
91A GLY 3.5 0.4 - - - -
116A HIS* 3.8 14.7 + - - -
124A PHE* 3.8 32.9 - - + -
240A PHE* 4.1 19.1 - - + -
243A LEU* 6.3 0.9 - - + -
244A MET* 4.9 3.8 - - + -
247A LEU* 5.9 4.3 - - + -
259A PHE* 5.2 4.0 - - + -
262A SER 4.0 2.6 - - - +
263A LEU* 4.3 15.8 - - + +
264A PRO* 3.9 33.5 - - + +
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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