Contacts of the helix formed by residues 81 - 104 (chain S) in PDB entry 3TDD
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 LEU 81 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R PHE* 4.2 22.2 - - + -
19R GLY 5.3 4.0 - - - +
20R ARG* 6.5 0.2 - - - -
21R LEU* 4.5 10.1 - - + -
121R LEU* 5.0 4.7 - - + -
156R THR* 6.0 3.4 - - + -
30S ALA* 4.9 10.1 - - + -
80S GLY* 1.3 70.4 - - - -
82S ALA* 1.3 67.9 + - - +
83S PRO* 4.2 8.3 - - + -
84S ASP* 3.3 31.9 + - - +
85S ALA 3.3 7.6 + - - -
130S ARG* 4.1 14.6 - - - +
133S GLY* 2.7 21.8 + - - +
134S VAL* 3.6 10.4 - - - +
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Residues in contact with ALA 82 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156R THR* 4.4 11.3 - - + +
64S GLN* 3.2 32.3 - - - +
65S LYS 6.0 0.4 - - - +
78S LEU* 4.5 16.7 - - + +
80S GLY 3.2 5.8 + - - -
81S LEU* 1.3 70.5 - - - +
83S PRO* 1.3 74.5 - - + +
85S ALA* 2.9 15.6 + - - +
86S ARG* 3.0 11.8 + - - +
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Residues in contact with PRO 83 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121R LEU* 3.6 24.2 - - + -
154R SER 3.2 24.7 - - - +
155R GLY* 3.8 15.0 - - - +
156R THR* 3.5 15.9 - - + -
81S LEU* 3.5 9.2 - - + -
82S ALA* 1.3 93.2 - - + +
84S ASP* 1.3 62.6 + - - +
86S ARG* 3.0 22.5 + - + +
87S VAL* 3.0 18.1 + - - +
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Residues in contact with ASP 84 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121R LEU* 4.0 6.2 - - - +
81S LEU* 3.3 17.1 + - - +
82S ALA 3.1 0.8 + - - -
83S PRO* 1.3 76.5 - - - +
85S ALA* 1.3 57.8 + - - +
87S VAL* 3.3 11.2 + - - +
88S LEU* 2.9 32.4 + - - +
130S ARG* 2.8 37.9 + - - -
132S TYR* 3.3 16.3 - - + -
133S GLY* 2.7 27.4 + - - -
134S VAL* 3.8 17.3 - - + -
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Residues in contact with ALA 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68S ILE* 4.5 4.3 - - + -
78S LEU* 3.6 41.5 - - + -
81S LEU 3.3 7.3 + - - +
82S ALA 2.9 10.3 + - - +
84S ASP* 1.3 77.8 - - - +
86S ARG* 1.3 55.1 + - - +
88S LEU* 3.9 2.0 - - - +
89S SER* 2.7 40.1 + - - -
134S VAL* 3.9 10.7 - - + +
136S LEU* 4.1 9.7 - - + +
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Residues in contact with ARG 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114R GLN* 3.2 45.2 - - - +
115R SER* 5.8 0.2 - - - +
118R ASP* 2.7 40.3 + - - -
65S LYS* 6.2 0.2 - - - +
68S ILE* 4.7 5.8 - - + +
82S ALA 3.0 8.7 + - - +
83S PRO* 3.0 16.7 + - + +
85S ALA* 1.3 76.9 - - - +
87S VAL* 1.3 57.6 + - + +
89S SER* 3.1 7.3 + - - -
90S ASN* 3.0 46.5 + - + +
93S ARG* 5.3 7.5 - - - +
69Z ASP* 5.3 7.9 + - - -
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Residues in contact with VAL 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126R ARG* 6.1 6.1 - - - +
83S PRO* 3.0 18.8 + - + +
84S ASP* 3.5 12.3 - - - +
85S ALA 3.2 0.2 - - - -
86S ARG* 1.3 79.7 - - + +
88S LEU* 1.3 58.6 + - - +
90S ASN* 3.6 4.8 - - - +
91S TYR* 3.1 25.3 + - - +
119S LYS* 5.0 8.3 - - - +
132S TYR* 3.8 26.9 - - + +
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Residues in contact with LEU 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76S LEU* 5.4 0.2 - - - -
84S ASP 2.9 16.9 + - - +
85S ALA 3.9 2.0 - - - +
87S VAL* 1.3 76.0 - - - +
89S SER* 1.3 60.0 + - - +
91S TYR* 3.3 6.4 + - - +
92S LEU* 3.0 25.5 + - - +
116S LEU* 3.8 26.9 - - + +
119S LYS* 3.8 22.4 - - + -
120S ALA 5.3 0.7 - - - +
132S TYR* 3.6 39.9 - - + -
134S VAL* 4.0 8.7 - - + -
136S LEU* 4.0 18.8 - - + -
151S PHE* 3.5 35.9 - - + -
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Residues in contact with SER 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68S ILE* 3.8 34.6 - - - +
70S CYS* 4.1 3.4 - - - -
76S LEU* 4.1 20.1 - - - +
85S ALA 2.7 26.5 + - - -
86S ARG* 3.1 11.3 + - - -
88S LEU* 1.3 70.5 - - - +
90S ASN* 1.3 58.0 + - - +
92S LEU* 3.0 8.4 + - - +
93S ARG* 2.7 42.3 + - - +
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Residues in contact with ASN 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86S ARG* 3.0 32.3 + - + +
87S VAL* 3.6 6.7 - - - +
89S SER* 1.3 83.7 + - - +
91S TYR* 1.3 60.7 + - - +
93S ARG* 3.2 18.5 + - - +
94S GLN* 3.1 46.3 + - - +
65Z TRP* 3.8 23.9 - - - -
69Z ASP* 5.0 4.4 + - - -
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Residues in contact with TYR 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87S VAL 3.1 14.3 + - - +
88S LEU 3.5 10.5 - - - +
89S SER 3.2 0.2 - - - -
90S ASN* 1.3 76.7 - - - +
92S LEU* 1.3 60.4 + - + +
94S GLN* 3.4 16.7 + - - +
95S GLN* 3.1 65.1 + - + +
115S LEU* 4.0 40.0 + - + +
116S LEU* 4.4 9.9 - - + -
119S LYS* 3.5 43.8 - - + +
122S LYS* 5.9 0.7 + - - -
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Residues in contact with LEU 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70S CYS* 3.5 27.6 - - + -
74S MET* 4.1 18.4 - - - -
76S LEU* 4.4 10.1 - - + -
88S LEU 3.0 13.3 + - - +
89S SER* 3.0 8.3 + - - +
91S TYR* 1.3 79.3 - - + +
93S ARG* 1.3 64.4 + - - +
95S GLN* 3.3 6.0 + - + -
96S CYS* 2.9 24.4 + - - -
107S LEU* 4.4 7.9 - - + -
112S ALA* 3.5 36.6 - - + +
115S LEU* 5.3 2.2 - - + -
116S LEU* 4.4 22.7 - - + -
138S ILE* 4.6 8.3 - - + -
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Residues in contact with ARG 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68S ILE* 3.4 22.7 - - - +
69S LYS* 2.8 26.6 + - - +
70S CYS* 3.5 29.8 - - + +
86S ARG* 5.3 7.3 - - - +
89S SER* 2.7 23.8 + - - +
90S ASN* 3.2 25.0 + - - +
92S LEU* 1.3 74.8 - - - +
94S GLN* 1.3 56.5 + - - +
96S CYS* 3.7 2.1 - - - +
97S ASN* 3.0 28.9 + - - +
64Z LYS* 5.4 0.9 + - - -
65Z TRP* 3.6 19.4 - - + -
68Z PHE* 3.4 60.4 + - + +
69Z ASP* 4.8 2.6 + - - -
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Residues in contact with GLN 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90S ASN* 3.1 27.7 + - - +
91S TYR* 3.7 22.2 - - - +
92S LEU 3.2 0.2 - - - -
93S ARG* 1.3 74.8 - - - +
95S GLN* 1.3 61.7 + - - +
97S ASN* 3.1 7.6 + - - +
98S TYR* 2.6 37.4 + - - +
65Z TRP* 4.1 17.4 - - + -
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Residues in contact with GLN 95 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91S TYR* 3.1 54.4 + - + +
92S LEU* 3.3 7.6 + - + +
94S GLN* 1.3 82.4 + - - +
96S CYS* 1.3 60.2 + - - +
98S TYR* 3.5 15.4 + - - +
99S SER* 3.2 22.5 + - - -
107S LEU* 3.9 10.5 - - + +
111S ARG* 5.3 2.8 + - - -
115S LEU* 3.7 35.7 - - + +
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Residues in contact with CYS 96 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70S CYS* 4.3 7.0 - - - +
71S ASP* 3.4 39.6 - - + +
73S HIS* 4.4 3.4 - - - -
74S MET* 4.0 26.7 - - - -
92S LEU* 2.9 22.5 + - - +
93S ARG 3.7 4.7 - - - +
95S GLN* 1.3 75.7 - - - +
97S ASN* 1.3 65.8 + - - +
99S SER* 3.2 6.1 + - - -
100S SER* 3.1 23.2 + - - -
105S ARG 4.8 0.2 - - - +
107S LEU* 4.0 22.6 + - + +
64Z LYS* 5.4 0.2 - - - +
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Residues in contact with ASN 97 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93S ARG 3.0 18.9 + - - +
94S GLN* 3.4 8.7 - - - +
96S CYS* 1.3 78.0 - - - +
98S TYR* 1.3 62.3 + - - +
100S SER* 3.3 4.7 + - - -
101S LEU* 3.0 39.6 + - + +
61Z ASN* 2.8 44.7 - - - +
64Z LYS* 3.2 24.7 - - - +
65Z TRP* 2.9 21.0 + - + +
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Residues in contact with TYR 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821 TYR* 6.2 0.2 - - - -
94S GLN 2.6 19.9 + - - +
95S GLN* 3.7 20.4 - - - +
97S ASN* 1.3 73.9 - - - +
99S SER* 1.3 67.2 + - - +
101S LEU* 4.9 4.5 - - - -
102S VAL* 3.0 55.8 + - + +
103S PHE* 4.0 21.7 - + - -
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Residues in contact with SER 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95S GLN 3.2 10.2 + - - -
96S CYS 3.2 9.1 + - - -
98S TYR* 1.3 83.4 - - - +
100S SER* 1.3 57.8 + - - +
103S PHE* 3.0 32.7 + - - +
104S ASN 3.2 4.2 + - - -
105S ARG* 2.6 39.1 + - - +
107S LEU* 3.8 27.4 + - - +
111S ARG* 5.6 1.3 + - - -
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Residues in contact with SER 100 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811 GLU* 4.7 0.5 - - - +
71S ASP* 4.1 12.0 + - - -
96S CYS 3.1 12.1 + - - -
97S ASN* 3.6 14.0 - - - -
98S TYR 3.2 0.2 - - - -
99S SER* 1.3 73.2 - - - +
101S LEU* 1.3 63.5 + - - +
104S ASN* 2.7 32.0 + - - +
105S ARG 3.6 16.8 + - - +
106S LYS* 4.6 7.3 - - - +
57Z LYS* 5.4 0.2 - - - -
64Z LYS* 4.9 3.8 + - - -
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Residues in contact with LEU 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811 GLU* 3.5 6.2 - - - +
851 THR* 4.1 1.8 + - - -
97S ASN* 3.0 41.7 + - - +
98S TYR* 4.1 3.4 - - - +
100S SER* 1.3 80.0 - - - +
102S VAL* 1.3 65.7 + - + +
57Z LYS* 2.9 56.0 + - + +
61Z ASN* 3.9 28.5 - - + +
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Residues in contact with VAL 102 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811 GLU* 3.0 30.5 - - - +
821 TYR* 3.3 15.6 + - + -
851 THR* 3.8 26.0 - - + +
891 GLN* 5.8 0.7 - - - +
98S TYR* 3.0 48.4 + - + +
101S LEU* 1.3 80.9 - - + +
103S PHE* 1.3 87.0 + - + +
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Residues in contact with PHE 103 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621 LEU* 3.6 30.7 - - + -
741 LEU* 5.9 0.7 - - + -
781 TYR* 3.1 36.9 - - + -
811 GLU* 3.7 4.0 - - - -
821 TYR* 3.6 38.8 - + + -
98S TYR* 4.0 19.1 - + - -
99S SER* 3.0 23.4 + - - +
102S VAL* 1.3 93.2 - - + +
104S ASN* 1.3 72.4 + - - +
105S ARG* 3.2 20.8 + - + -
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Residues in contact with ASN 104 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771 SER* 4.3 18.7 + - - +
781 TYR* 3.6 12.0 - - - -
811 GLU* 3.6 28.5 - - + +
100S SER* 2.7 27.9 + - - +
102S VAL 3.7 0.8 - - - -
103S PHE* 1.3 75.0 - - - +
105S ARG* 1.3 55.9 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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