Contacts of the helix formed by residues 85 - 98 (chain A) in PDB entry 1TE6
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A LEU* 4.5 9.9 - - + -
82A SER* 2.9 26.6 + - - +
84A VAL* 1.3 90.0 - - + +
86A GLN* 1.3 64.2 + - - +
87A GLU 3.3 3.1 - - - +
88A LYS* 3.1 47.2 + - + +
89A LEU* 3.0 26.0 + - - +
125A ARG* 5.1 4.2 + - - -
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Residues in contact with GLN 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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83A VAL 4.2 3.8 + - - +
84A VAL 2.9 10.2 + - - +
85A GLU* 1.3 71.2 - - - +
87A GLU* 1.3 57.3 + - - +
89A LEU* 3.9 3.7 - - - +
90A ASP* 2.8 61.9 + - - +
114A SER* 3.2 27.5 + - - -
117A VAL* 3.8 10.6 - - - +
118A CYS* 3.0 39.3 + - - +
132A HIS* 4.9 1.0 + - - +
136A LEU* 3.7 33.6 - - + +
349A VAL* 3.8 12.9 - - + +
350A THR* 3.6 7.0 - - - +
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Residues in contact with GLU 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 GLU 3.3 0.6 - - - -
86A GLN* 1.3 79.1 - - - +
88A LYS* 1.3 60.4 + - + +
90A ASP* 3.9 0.3 - - - +
91A ASN* 2.8 54.2 + - - +
136A LEU* 5.6 1.0 - - - +
350A THR* 3.3 26.7 + - + +
354A GLN* 4.2 12.7 + - - -
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Residues in contact with LYS 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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81A LEU* 3.9 34.5 - - + +
85A GLU* 3.1 38.4 + - + +
87A GLU* 1.3 79.0 - - + +
89A LEU* 1.3 62.4 + - - +
91A ASN* 3.6 6.3 + - - +
92A LEU* 3.1 23.6 + - - +
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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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2A ILE* 5.3 4.5 - - + -
76A LEU* 4.2 30.9 - - + +
79A SER* 4.1 8.1 - - - +
81A LEU* 3.9 31.4 - - + +
82A SER 3.6 22.2 - - - +
83A VAL* 3.8 10.5 - - + -
85A GLU 3.0 16.4 + - - +
86A GLN 3.9 2.0 - - - +
88A LYS* 1.3 74.4 - - - +
90A ASP* 1.3 68.0 + - - +
92A LEU* 3.2 7.1 - - - +
93A MET* 3.2 26.6 + - + +
117A VAL* 3.5 37.7 - - + -
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Residues in contact with ASP 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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86A GLN* 2.8 35.3 + - - +
87A GLU 3.9 0.9 - - - +
89A LEU* 1.3 74.7 - - - +
91A ASN* 1.3 67.5 + - - +
93A MET* 3.0 18.3 + - - +
94A LEU* 2.9 26.6 + - + +
110A ILE* 5.5 0.3 - - - +
114A SER* 2.6 30.9 + - - -
348A SER* 4.0 14.3 - - - +
350A THR* 2.7 41.3 + - + +
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Residues in contact with ASN 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 GLU* 2.8 48.0 + - - +
88A LYS* 4.0 6.2 - - - +
90A ASP* 1.3 76.2 - - - +
92A LEU* 1.3 57.3 + - - +
94A LEU* 3.4 22.3 - - - +
95A GLU* 2.9 38.6 + - + +
350A THR* 4.9 7.0 - - - +
354A GLN* 5.9 0.9 + - - -
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Residues in contact with LEU 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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75A ALA* 4.5 6.5 - - + +
76A LEU* 3.8 17.7 - - + -
79A SER* 3.7 30.7 - - - +
81A LEU* 4.1 11.4 - - + -
88A LYS 3.1 13.1 + - - +
89A LEU* 3.2 11.9 - - + +
90A ASP 3.0 0.4 - - - -
91A ASN* 1.3 78.0 - - - +
93A MET* 1.3 57.4 + - - +
95A GLU* 3.3 8.0 + - + +
96A LEU* 2.9 59.6 + - + +
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Residues in contact with MET 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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72A ILE* 3.8 24.7 - - + -
76A LEU* 4.1 11.7 - - + -
89A LEU 3.2 14.1 + - - +
90A ASP* 3.0 31.1 + - - +
92A LEU* 1.3 73.4 - - - +
94A LEU* 1.3 61.6 + - - +
96A LEU* 3.1 9.7 + - + +
97A ASP* 2.8 32.3 + - - +
105A PHE* 4.7 1.7 - - - -
110A ILE* 3.8 44.2 - - + +
113A VAL* 3.7 28.7 - - + -
114A SER* 3.8 12.1 - - - +
117A VAL* 5.3 2.7 - - + -
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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 ASP* 2.9 18.6 + - + +
91A ASN* 3.4 31.6 - - - +
92A LEU 3.2 0.2 - - - -
93A MET* 1.3 78.0 - - - +
95A GLU* 1.3 61.3 + - - +
97A ASP* 3.4 6.3 + - - +
98A GLY* 2.9 25.8 + - - -
99A THR 4.6 2.9 + - - +
102A LYS* 3.4 41.1 - - + +
110A ILE* 4.8 7.4 - - + -
348A SER* 4.8 3.8 - - - +
350A THR* 6.3 0.7 - - + -
351A GLU* 3.6 26.5 - - + +
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Residues in contact with GLU 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 ASN* 2.9 24.4 + - + +
92A LEU* 3.6 7.9 - - + +
94A LEU* 1.3 77.2 - - - +
96A LEU* 1.3 67.8 + - + +
98A GLY* 3.1 15.5 + - - +
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Residues in contact with LEU 96 (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 THR* 5.2 3.6 - - + +
72A ILE* 4.8 10.5 - - + -
75A ALA* 3.6 27.1 - - + -
76A LEU* 4.6 3.1 - - + -
92A LEU* 2.9 45.9 + - + +
93A MET* 3.1 21.3 + - + +
95A GLU* 1.3 78.5 - - + +
97A ASP* 1.3 60.9 + - - +
98A GLY* 4.6 0.2 - - - -
104A LYS* 3.1 19.6 + - - -
105A PHE* 3.8 19.0 - - + -
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Residues in contact with ASP 97 (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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93A MET 2.8 15.5 + - - +
94A LEU* 3.6 4.3 - - - +
96A LEU* 1.3 75.7 - - - +
98A GLY* 1.3 57.7 + - - +
99A THR* 2.5 52.1 + - - +
102A LYS* 3.3 18.1 - - + +
104A LYS* 3.0 36.8 + - - +
105A PHE* 3.0 36.8 + - + +
110A ILE* 3.9 14.7 - - + +
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Residues in contact with GLY 98 (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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94A LEU 2.9 14.3 + - - -
95A GLU* 3.1 13.5 + - - -
97A ASP* 1.3 75.6 - - - +
99A THR* 1.3 60.8 + - - +
104A LYS* 5.2 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