Contacts of the helix formed by residues 80 - 97 (chain C) in PDB entry 1T5A
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 THR 80 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C GLY* 1.3 78.4 - - - -
81C HIS* 1.3 58.0 + - - +
82C GLU* 3.3 11.5 + - - +
83C TYR* 2.6 43.0 + - + +
84C HIS* 3.0 12.9 + - - -
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Residues in contact with HIS 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C PHE* 4.1 11.9 - + - -
79C GLY 5.5 0.7 - - - -
80C THR* 1.3 73.8 - - - +
82C GLU* 1.3 61.6 + - - +
84C HIS* 4.6 3.4 - - - +
85C ALA* 2.9 27.9 + - - +
224C LYS* 4.6 4.8 + - - -
227C GLN* 3.8 22.1 - - + +
228C ASP* 2.8 30.4 + - - -
231C PHE* 3.5 47.4 - + + +
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Residues in contact with GLU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C THR* 3.0 9.9 + - - +
81C HIS* 1.3 79.1 - - - +
83C TYR* 1.3 63.0 + - - +
85C ALA* 4.2 4.8 - - - +
86C GLU* 3.5 20.4 + - - +
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Residues in contact with TYR 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ILE 5.7 3.8 - - - -
52C GLY* 4.4 0.9 - - - -
53C PRO* 3.7 27.0 - - - +
56C ARG* 3.1 64.7 + - - +
79C GLY* 4.7 8.1 - - - -
80C THR* 2.6 34.7 + - + +
82C GLU* 1.3 69.8 - - - +
84C HIS* 1.3 79.6 + + - +
86C GLU* 3.1 4.6 + - - +
87C THR* 3.0 29.5 + - + -
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Residues in contact with HIS 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LEU* 4.0 23.1 - - + -
75C ASN 3.6 12.9 + - - -
76C PHE* 3.2 54.0 - + + -
78C HIS 2.8 31.9 + - - -
79C GLY* 3.9 8.5 + - - -
80C THR 3.0 11.1 + - - +
81C HIS 4.0 4.9 - - - +
83C TYR* 1.3 93.7 - + - +
85C ALA* 1.3 56.7 + - - +
86C GLU 3.0 1.8 - - - -
87C THR* 2.7 7.9 + - - -
88C ILE* 2.6 39.3 + - - +
231C PHE* 4.3 3.4 - - + -
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Residues in contact with ALA 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C HIS 2.9 18.5 + - - +
82C GLU* 4.2 5.8 - - - +
84C HIS* 1.3 76.4 - - - +
86C GLU* 1.3 53.5 + - - +
88C ILE* 3.6 3.5 - - - +
89C LYS* 2.8 33.3 + - - +
231C PHE* 3.8 16.7 - - + -
235C GLN* 4.0 23.2 - - - +
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Residues in contact with GLU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ARG* 3.7 21.6 + - - +
82C GLU 3.5 12.3 + - - +
83C TYR* 3.1 10.8 + - - +
84C HIS 3.0 0.8 - - - -
85C ALA* 1.3 76.2 - - - +
87C THR* 1.3 64.5 + - - +
89C LYS* 3.3 12.8 + - + +
90C ASN* 2.8 43.5 + - - +
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Residues in contact with THR 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ILE* 3.6 33.0 - - + +
56C ARG* 2.9 32.8 + - + +
61C LEU* 5.7 0.4 - - + -
74C LEU* 3.5 26.1 - - + +
83C TYR* 3.0 18.9 + - + -
84C HIS* 2.7 10.0 + - - -
86C GLU* 1.3 76.3 - - - +
88C ILE* 1.3 62.6 + - - -
90C ASN* 2.9 8.0 + - - +
91C VAL* 2.9 29.2 + - + +
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Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LEU* 3.4 27.6 - - + -
76C PHE* 5.8 0.2 - - + -
84C HIS 2.6 19.8 + - - +
85C ALA 3.6 6.5 - - - +
87C THR* 1.3 72.3 - - - +
89C LYS* 1.3 63.8 + - - +
91C VAL* 3.2 9.2 + - - +
92C ARG* 3.1 61.2 + - + +
110C VAL* 4.2 11.0 - - + -
231C PHE* 4.4 8.1 - - + -
235C GLN* 3.4 40.2 - - + +
237C VAL* 4.3 11.0 - - + -
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Residues in contact with LYS 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ALA 2.8 22.4 + - - +
86C GLU* 3.5 14.6 - - + +
87C THR 3.2 0.2 - - - -
88C ILE* 1.3 74.4 - - - +
90C ASN* 1.3 57.8 + - - +
92C ARG* 3.8 7.0 + - - +
93C THR* 2.6 45.6 + - - +
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Residues in contact with ASN 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ARG* 2.9 30.9 + - - +
57C SER* 4.3 1.4 - - - +
58C VAL* 2.9 34.6 - - + +
61C LEU* 3.6 5.3 - - + +
86C GLU* 2.8 36.3 + - - +
87C THR* 2.9 10.5 + - - +
89C LYS* 1.3 80.6 + - - +
91C VAL* 1.3 68.0 + - - +
93C THR* 3.2 2.6 + - - -
94C ALA* 2.9 25.3 + - - +
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Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ILE* 4.8 2.0 - - + -
61C LEU* 3.5 24.2 - - + -
65C ILE* 4.8 0.6 - - + +
69C MET* 5.3 4.3 - - + -
72C ALA* 4.2 24.5 - - + -
74C LEU* 6.0 1.8 - - + -
87C THR* 2.9 28.8 + - + +
88C ILE* 3.5 9.9 - - - +
90C ASN* 1.3 77.5 - - - +
92C ARG* 1.3 55.9 + - + +
94C ALA* 3.0 2.1 + - - +
95C THR* 2.7 39.4 + - - +
108C VAL* 4.2 26.5 - - + +
110C VAL* 4.3 15.3 - - + -
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Residues in contact with ARG 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ILE* 3.1 38.5 + - + +
89C LYS* 4.0 6.5 - - - +
91C VAL* 1.3 79.8 - - + +
93C THR* 1.3 57.7 + - - +
95C THR* 4.0 7.9 - - - -
96C GLU* 2.9 42.0 + - + +
110C VAL* 4.6 16.5 - - + +
235C GLN* 2.9 23.4 + - - -
236C ASP* 2.9 37.2 + - - +
237C VAL* 4.8 0.4 - - - +
238C ASP* 5.6 1.0 + - - -
461C ARG* 5.3 6.7 - - - +
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Residues in contact with THR 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C VAL* 4.0 24.6 - - + +
62C LYS* 5.3 1.1 - - - -
89C LYS* 2.6 36.2 + - - +
90C ASN* 3.5 5.5 - - - -
91C VAL 3.1 0.4 - - - -
92C ARG* 1.3 76.6 - - - +
94C ALA* 1.3 63.3 + - - +
96C GLU* 4.0 2.7 - - - +
97C SER* 3.3 21.5 + - - -
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Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C VAL* 3.8 15.0 - - + +
61C LEU* 3.9 22.2 - - + +
62C LYS* 3.7 26.2 - - + +
65C ILE* 3.9 4.7 - - + -
90C ASN 2.9 12.6 + - - +
91C VAL 3.5 7.0 - - - +
93C THR* 1.3 76.2 - - - +
95C THR* 1.3 61.2 - - - +
97C SER* 2.8 23.7 + - - -
98C PHE* 3.2 10.7 - - - -
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Residues in contact with THR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ILE* 3.4 15.2 - - - +
91C VAL* 2.7 20.0 + - - +
92C ARG* 3.7 8.1 - - - -
94C ALA* 1.3 79.3 - - - +
96C GLU* 1.3 69.5 + - - +
97C SER 3.3 1.0 + - - -
98C PHE* 3.3 14.6 + - - -
105C TYR* 3.5 37.4 - - + +
106C ARG 4.4 10.0 - - - +
108C VAL* 3.3 33.4 - - + +
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Residues in contact with GLU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ARG* 2.9 25.4 + - + +
93C THR* 4.2 3.6 - - - +
95C THR* 1.3 77.1 - - - +
97C SER* 1.3 54.6 + - - +
98C PHE 2.7 16.3 + - - -
99C ALA* 2.8 37.8 + - + +
100C SER 4.4 1.0 + - - -
105C TYR* 3.3 23.5 + - - -
475C LYS* 5.4 1.4 + - - -
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Residues in contact with SER 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C LYS* 3.8 24.3 - - - +
93C THR 3.3 13.0 + - - -
94C ALA 2.8 18.7 + - - -
95C THR 3.2 0.6 - - - -
96C GLU* 1.3 75.3 - - - +
98C PHE* 1.3 75.1 + - - +
99C ALA 3.6 0.2 - - - -
100C SER* 4.2 9.5 + - - -
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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
------------------------------------------------------------
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