Contacts of the helix formed by residues 50 - 71 (chain X) 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 GLY 50 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48X GLU 3.5 0.4 - - - -
49X ALA* 1.3 78.6 - - - +
51X ASP* 1.3 66.2 + - - +
52X THR 3.1 3.2 + - - -
53X VAL* 3.5 5.0 + - - +
54X GLN* 3.2 23.7 + - - +
88Y TYR* 3.7 9.4 - - - -
91Y LYS* 3.9 3.2 - - - +
116Y ASP 3.3 21.2 + - - -
117Y GLY* 3.9 19.0 - - - +
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Residues in contact with ASP 51 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48X GLU* 3.1 32.3 + - + +
50X GLY* 1.3 74.3 - - - +
52X THR* 1.3 56.2 + - - +
54X GLN* 3.8 0.4 - - - +
55X PHE* 2.8 37.6 + - - +
93X ARG* 3.0 26.0 + - - -
94X PRO 3.9 2.4 - - - +
95X TYR* 3.8 11.4 - - + -
96X GLN* 3.4 16.1 + - - +
97X VAL* 3.5 14.8 - - + -
88Y TYR* 2.7 29.8 + - - -
91Y LYS* 3.2 6.8 - - - -
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Residues in contact with THR 52 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45X PHE* 3.8 25.1 - - + -
46X ALA* 3.6 7.6 + - - -
47X GLY* 3.4 25.4 + - - -
48X GLU 3.1 15.0 + - - -
49X ALA 3.8 12.6 - - - +
51X ASP* 1.3 81.3 - - - +
53X VAL* 1.3 87.8 + - + +
55X PHE* 3.9 2.1 - - - +
56X ALA* 3.3 20.1 + - - +
97X VAL* 3.5 12.4 - - - +
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Residues in contact with VAL 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35X ARG* 3.9 15.3 - - - +
45X PHE* 4.2 13.0 - - + -
50X GLY 3.5 4.9 + - - +
52X THR* 1.3 92.9 - - + +
54X GLN* 1.3 67.6 + - - +
56X ALA* 4.4 4.9 - - - -
57X GLU* 2.9 52.4 + - + +
119Y ARG 5.8 3.8 - - - +
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Residues in contact with GLN 54 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X GLY 3.2 18.4 + - - +
51X ASP 3.8 2.7 - - - +
53X VAL* 1.3 76.6 - - - +
55X PHE* 1.3 57.1 - - - +
57X GLU* 3.9 4.7 - - - +
58X TYR* 3.0 30.4 + - - +
95X TYR* 4.5 7.8 + - + +
84Y SER* 4.9 3.3 + - - -
85Y ASN* 2.9 31.4 + - - +
88Y TYR* 3.6 49.9 - - + +
117Y GLY 5.4 4.0 - - - +
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Residues in contact with PHE 55 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43X MET* 4.6 3.1 - - + -
51X ASP 2.8 18.4 + - - +
52X THR 3.9 2.2 - - - +
54X GLN* 1.3 75.1 - - - +
56X ALA* 1.3 70.2 + - - +
58X TYR* 3.0 11.9 + + - +
59X ILE* 2.9 56.3 + - + +
83X VAL* 4.1 17.3 - - + -
86X GLU* 4.2 12.3 - - + -
87X LEU* 3.5 38.4 - - + -
95X TYR* 3.7 40.1 - + + -
97X VAL* 4.1 20.9 - - + -
99X VAL* 4.3 14.8 - - + -
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Residues in contact with ALA 56 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X ARG* 3.8 13.6 - - + +
37X LEU* 4.5 0.5 - - - +
43X MET* 3.7 18.8 - - + +
45X PHE* 3.3 42.8 - - + -
52X THR 3.3 11.4 + - - +
53X VAL* 3.8 3.8 - - - +
55X PHE* 1.3 79.9 - - + +
57X GLU* 1.3 57.2 + - - +
59X ILE* 3.3 2.6 + - - +
60X GLN* 2.9 28.6 + - - +
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Residues in contact with GLU 57 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101Q LEU* 3.7 21.8 - - + +
104Q GLU* 4.4 4.7 - - - +
35X ARG* 2.7 38.1 + - + +
53X VAL* 2.9 34.4 + - + +
54X GLN* 4.1 5.0 - - - +
56X ALA* 1.3 72.2 - - - +
58X TYR* 1.3 60.5 + - - +
60X GLN* 3.6 13.6 - - - +
61X ALA* 3.0 30.0 + - - +
81Y LYS* 2.8 37.5 + - - -
119Y ARG* 5.1 2.4 + - - -
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Residues in contact with TYR 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101Q LEU* 4.7 11.2 - - + +
54X GLN* 3.0 19.9 + - - +
55X PHE* 3.3 15.9 - + - +
57X GLU* 1.3 78.9 - - - +
59X ILE* 1.3 72.1 + - + +
61X ALA* 3.4 5.1 + - + +
62X ASN* 3.1 51.9 + - - +
82X PHE* 5.4 0.6 - + - -
86X GLU* 3.0 38.1 + - + -
95X TYR* 4.7 16.6 - + - +
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Residues in contact with ILE 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37X LEU* 3.9 21.5 - - + -
43X MET* 4.1 7.2 - - + -
55X PHE* 2.9 53.1 + - + +
56X ALA 3.6 6.3 - - - +
58X TYR* 1.3 79.3 - - + +
60X GLN* 1.3 68.0 + - - +
62X ASN* 3.0 5.8 + - - +
63X ILE* 3.0 27.8 + - + +
82X PHE* 3.8 22.2 - - + -
83X VAL* 3.7 27.4 - - + -
86X GLU* 4.1 10.3 - - + -
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Residues in contact with GLN 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101Q LEU* 6.1 0.5 - - - +
35X ARG* 4.0 23.3 + - + +
36X GLN* 2.9 38.4 + - - +
37X LEU* 3.8 17.6 - - + +
56X ALA 2.9 17.4 + - - +
57X GLU* 3.6 12.4 - - - +
58X TYR 3.3 0.2 - - - -
59X ILE* 1.3 77.5 - - - +
61X ALA* 1.3 63.5 + - - +
63X ILE* 3.2 1.8 + - - +
64X GLN* 2.9 51.3 + - + +
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Residues in contact with ALA 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Q GLN* 4.1 25.3 + - + +
101Q LEU* 3.8 27.8 - - + -
57X GLU 3.0 18.2 + - - +
58X TYR* 3.6 4.5 - - + +
60X GLN* 1.3 75.8 - - - +
62X ASN* 1.3 60.5 + - - +
64X GLN* 3.3 5.1 + - - +
65X LEU* 2.9 29.7 + - - +
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Residues in contact with ASN 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X TYR* 3.1 46.0 + - - +
59X ILE 3.0 8.7 + - - +
61X ALA* 1.3 80.4 - - - +
63X ILE* 1.3 63.3 + - - +
65X LEU* 3.4 15.1 + - - +
66X TYR* 3.1 21.8 + - - +
82X PHE* 3.8 34.7 - - + -
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Residues in contact with ILE 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103P TYR* 5.7 0.4 - - + -
37X LEU* 3.4 34.5 - - + +
38X SER* 4.3 11.2 - - - -
59X ILE* 3.0 23.1 + - + +
60X GLN 3.8 2.7 - - - +
62X ASN* 1.3 74.7 - - - +
64X GLN* 1.3 61.6 + - - +
66X TYR* 3.1 7.1 + - + +
67X SER* 2.9 34.1 + - - +
74X LEU* 4.7 17.5 - - + +
79X VAL* 4.1 33.2 - - + -
82X PHE* 4.0 29.4 - - + -
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Residues in contact with GLN 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97Q GLN* 3.1 32.0 + - - +
100Q ARG* 3.8 21.4 + - - +
36X GLN 4.4 3.6 + - - -
37X LEU 4.1 11.4 + - - +
60X GLN* 2.9 48.6 + - - +
61X ALA* 3.7 2.1 - - - +
63X ILE* 1.3 75.8 - - - +
65X LEU* 1.3 63.1 + - - +
67X SER* 3.2 10.0 + - - -
68X ILE* 3.0 25.2 + - + +
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Residues in contact with LEU 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90Q GLU* 4.9 0.4 - - - +
93Q ARG* 3.8 41.3 - - + +
94Q VAL* 4.0 21.3 - - + +
97Q GLN* 3.8 15.6 + - + -
61X ALA 2.9 17.2 + - - +
62X ASN* 3.6 15.3 - - - +
64X GLN* 1.3 76.3 - - - +
66X TYR* 1.3 63.3 + - - +
68X ILE* 3.3 4.5 + - + -
69X ARG* 2.9 52.2 + - + +
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Residues in contact with TYR 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P TYR* 2.5 35.5 + + - -
103P TYR* 3.6 29.6 - + - +
108P PRO* 4.8 2.1 - - - +
111P ILE* 3.5 14.1 - - + +
62X ASN 3.1 14.7 + - - +
63X ILE* 3.4 11.9 - - + +
65X LEU* 1.3 76.6 - - - +
67X SER* 1.3 66.1 + - - +
69X ARG* 3.8 20.6 - - - +
70X GLU* 3.0 50.1 + - + +
72X TYR* 4.4 16.2 - + + -
74X LEU* 3.4 36.6 - - + +
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Residues in contact with SER 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X LEU 5.1 0.2 + - - -
38X SER* 4.7 8.1 - - - -
39X PRO* 5.7 1.9 - - - +
63X ILE* 2.9 24.1 + - - +
64X GLN* 3.4 13.0 - - - -
66X TYR* 1.3 76.4 - - - +
68X ILE* 1.3 55.7 + - - +
71X ASP* 2.7 35.9 + - - -
72X TYR 3.3 21.6 + - - -
73X GLU* 4.7 6.5 - - - +
74X LEU 5.3 0.7 + - - -
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Residues in contact with ILE 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69Q LYS* 3.8 16.0 - - + +
70Q ILE 3.4 13.9 - - - +
71Q ASP* 3.2 47.1 - - - +
72Q SER* 4.1 2.9 - - - +
93Q ARG* 3.5 39.0 + - + +
96Q ALA* 6.0 0.2 - - + -
97Q GLN* 3.8 15.7 - - + +
64X GLN 3.0 13.8 + - - +
65X LEU* 3.9 5.2 - - + +
67X SER* 1.3 77.2 - - - +
69X ARG* 1.3 68.0 + - - +
70X GLU 3.5 0.2 + - - -
71X ASP* 3.6 8.8 + - - +
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Residues in contact with ARG 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114P ARG* 3.7 28.2 + - - +
90Q GLU* 2.9 41.3 + - - +
93Q ARG* 3.6 28.6 + - - +
65X LEU* 2.9 49.4 + - + +
66X TYR* 3.8 26.1 - - - +
68X ILE* 1.3 80.0 - - - +
70X GLU* 1.3 78.4 + - - +
71X ASP* 5.2 0.3 - - - +
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Residues in contact with GLU 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108P PRO* 6.1 0.2 - - + -
110P GLU* 4.9 1.0 - - - +
111P ILE* 3.3 36.4 - - + +
114P ARG* 2.5 39.6 + - - -
144P ARG* 2.9 29.8 + - - +
66X TYR* 3.0 39.4 + - + +
69X ARG* 1.3 99.2 + - - +
71X ASP* 1.3 74.0 + - - +
72X TYR* 4.1 8.1 - - + -
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Residues in contact with ASP 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144P ARG* 3.1 16.4 + - - +
69Q LYS* 5.3 11.7 + - - -
67X SER 2.7 19.8 + - - -
68X ILE* 3.6 6.1 + - - +
69X ARG 3.5 3.0 - - - +
70X GLU* 1.3 75.9 - - - +
72X TYR* 1.3 57.8 + - - +
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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