Contacts of the helix formed by residues 81 - 104 (chain G) 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 PRO 81 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ALA* 3.5 20.0 - - + +
33G GLN* 3.3 28.5 - - + +
34G THR* 4.1 8.2 - - + -
80G GLY* 1.3 86.7 - - - +
82G ILE* 1.3 64.0 + - - +
83G PRO* 3.8 16.2 - - + -
84G ASP* 3.6 11.2 + - + +
85G ALA* 3.1 18.7 + - - +
133G GLY* 3.1 18.6 - - - +
134G VAL* 4.0 2.0 - - + +
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Residues in contact with ILE 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156F SER* 3.3 29.4 - - - +
158F TRP* 3.6 28.9 - - + -
65G SER 3.6 23.3 - - - +
66G TYR* 3.9 20.8 + - + +
68G PHE* 4.4 3.8 - - + -
80G GLY 3.5 0.8 + - - -
81G PRO* 1.3 70.7 - - - +
83G PRO* 1.4 81.9 - - + +
85G ALA* 3.1 7.5 + - + +
86G ARG* 2.9 65.3 + - + +
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Residues in contact with PRO 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F GLN* 5.0 0.5 - - - +
121F GLN* 3.4 26.7 - - + +
154F SER* 3.4 33.9 - - - +
155F GLY 3.8 15.0 - - - +
156F SER* 4.1 9.0 - - - +
81G PRO* 3.4 13.7 - - + -
82G ILE* 1.4 102.6 - - + +
84G ASP* 1.3 64.8 + - - +
86G ARG* 3.5 6.8 + - + +
87G ASN 3.2 16.1 + - - -
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Residues in contact with ASP 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F PHE* 4.7 1.4 - - - -
121F GLN* 2.9 15.1 - - - +
81G PRO* 3.6 13.6 + - + +
82G ILE 3.2 0.4 - - - -
83G PRO* 1.3 79.1 - - - +
85G ALA* 1.3 65.3 + - - +
87G ASN* 3.1 4.4 + - - +
88G ALA* 3.0 23.6 + - - +
130G ARG* 2.7 44.5 + - - -
132G LEU* 3.6 15.9 - - + +
133G GLY* 3.0 18.1 + - - +
134G VAL* 3.6 19.5 - - + +
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Residues in contact with ALA 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G TYR* 4.8 1.6 - - + -
68G PHE* 4.2 11.8 - - + -
76G MET* 4.1 4.2 - - - +
78G VAL* 3.3 39.9 - - + -
80G GLY 4.6 1.8 - - - +
81G PRO 3.1 16.7 + - - +
82G ILE* 3.1 13.0 + - + +
84G ASP* 1.3 79.2 - - - +
86G ARG* 1.3 58.1 + - - +
88G ALA* 3.4 4.9 + - - +
89G ALA* 2.9 27.5 + - - +
134G VAL* 3.8 1.7 - - - +
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Residues in contact with ARG 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F ASP* 4.0 4.7 - - - +
118F GLN* 3.1 23.8 + - - +
155F GLY 4.8 1.0 + - - -
157F TYR* 2.8 85.1 + - - +
158F TRP* 3.5 23.8 - - - +
63G THR 4.1 5.9 + - - -
65G SER 5.4 0.6 + - - -
68G PHE* 4.1 18.4 - - + -
82G ILE* 2.9 41.0 + - + +
83G PRO* 3.9 6.1 - - + +
85G ALA* 1.3 73.2 - - - +
87G ASN* 1.3 67.0 + - - +
89G ALA* 3.6 7.3 - - - +
90G LEU* 3.0 19.1 + - - +
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Residues in contact with ASN 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F GLN* 3.6 14.3 + - - +
121F GLN* 3.3 32.0 + - - +
125F LEU* 4.0 12.0 - - - +
83G PRO 3.2 13.2 + - - +
84G ASP* 3.1 10.0 + - - +
86G ARG* 1.3 78.9 - - - +
88G ALA* 1.3 68.3 + - - +
90G LEU* 3.3 2.8 + - - +
91G ARG* 3.1 23.9 + - - +
123G TYR* 5.8 1.8 + - - -
132G LEU* 3.9 19.1 - - + +
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Residues in contact with ALA 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G MET* 4.3 2.4 - - + +
84G ASP 3.0 11.3 + - - +
85G ALA* 3.6 8.7 - - - +
87G ASN* 1.3 84.5 - - - +
89G ALA* 1.3 55.3 + - - +
91G ARG* 3.4 0.6 + - - -
92G ALA* 2.9 31.7 + - - +
116G MET* 3.5 13.0 - - + +
132G LEU* 4.4 13.2 - - + +
134G VAL* 4.7 2.5 - - + -
136G LEU* 4.0 35.0 - - + -
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Residues in contact with ALA 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G PHE* 3.6 35.2 - - + -
70G ILE* 3.8 3.9 - - + +
76G MET* 3.5 16.1 - - + +
85G ALA 2.9 17.7 + - - +
86G ARG* 3.6 5.4 - - - +
88G ALA* 1.3 76.3 - - - +
90G LEU* 1.3 64.4 + - - +
92G ALA* 3.3 2.6 + - - +
93G LYS* 2.9 34.8 + - - +
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Residues in contact with LEU 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F ASP* 4.5 6.1 - - - +
118F GLN* 3.6 35.2 - - + +
86G ARG 3.0 16.5 + - - +
87G ASN* 3.7 4.3 - - - +
89G ALA* 1.3 74.7 - - - +
91G ARG* 1.3 63.9 + - - +
93G LYS* 3.2 10.4 + - + +
94G ALA* 3.0 26.6 + - + +
65N LEU* 5.9 1.3 - - + -
69N GLN* 3.5 34.5 - - + +
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Residues in contact with ARG 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G ASN* 3.1 16.0 + - - +
88G ALA* 3.7 8.1 - - - +
90G LEU* 1.3 78.5 - - - +
92G ALA* 1.3 58.6 + - - +
94G ALA* 3.1 10.9 + - - +
95G GLU* 2.7 62.3 + - + +
115G ARG* 3.3 17.0 - - - +
116G MET* 4.0 9.9 - - + -
119G LEU* 3.7 33.5 - - + +
123G TYR* 4.8 6.6 + - - +
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Residues in contact with ALA 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ILE* 3.6 25.3 - - + +
76G MET* 4.7 0.9 - - - -
88G ALA 2.9 19.2 + - - +
89G ALA* 3.5 4.3 - - - +
91G ARG* 1.3 77.5 - - - +
93G LYS* 1.3 55.6 + - - +
95G GLU* 3.3 2.3 + - - +
96G ALA* 2.9 31.0 + - - +
112G LEU* 4.1 17.8 - - + +
116G MET* 4.0 15.9 - - + +
138G PHE* 4.4 7.9 - - + -
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Residues in contact with LYS 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G PHE* 4.8 11.3 - - - -
69G CYS 3.2 21.2 + - - +
70G ILE* 3.6 35.0 - - - +
89G ALA* 2.9 29.2 + - - +
90G LEU* 3.5 9.4 - - + +
92G ALA* 1.3 75.6 - - - +
94G ALA* 1.3 57.9 + - - +
96G ALA* 3.4 2.3 + - - +
97G ALA* 3.0 24.1 + - - +
65N LEU* 3.4 14.1 - - + +
68N SER* 2.8 43.3 + - - +
69N GLN* 4.2 15.4 + - + +
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Residues in contact with ALA 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G LEU* 3.0 16.5 + - + +
91G ARG* 3.4 15.7 - - - +
93G LYS* 1.3 75.7 - - - +
95G GLU* 1.3 59.6 + - + +
97G ALA* 3.3 2.3 + - - +
98G GLU* 2.9 31.4 + - - +
61N TYR* 4.8 3.3 + - - +
65N LEU* 3.6 21.0 - - + +
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Residues in contact with GLU 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G ARG* 2.7 64.9 + - + +
92G ALA* 3.6 7.2 - - - +
94G ALA* 1.3 77.4 - - - +
96G ALA* 1.3 57.3 + - - +
98G GLU* 4.0 17.0 - - - +
99G PHE* 3.0 31.0 + - - +
107G MET* 3.5 12.6 - - + +
112G LEU* 4.4 4.3 - - + -
115G ARG* 3.0 39.8 + - + +
116G MET* 4.6 3.4 - - - -
119G LEU* 4.7 0.2 - - - -
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Residues in contact with ALA 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ILE* 4.1 16.2 - - + +
71G SER* 4.3 17.0 - - - +
74G ILE* 5.5 1.3 - - + -
92G ALA 2.9 17.7 + - - +
93G LYS* 3.7 4.5 - - - +
95G GLU* 1.3 77.8 - - - +
97G ALA* 1.3 61.9 + - - +
99G PHE* 3.7 2.3 + - - +
100G ARG* 3.4 20.8 + - - +
107G MET* 3.0 29.5 + - + +
112G LEU* 4.8 1.6 - - + -
64N GLU* 4.1 4.0 - - - +
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Residues in contact with ALA 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G LYS 3.0 17.2 + - - +
94G ALA 3.7 2.9 - - - +
96G ALA* 1.3 75.2 - - - +
98G GLU* 1.3 65.3 + - - +
100G ARG* 3.3 6.1 + - - +
101G TYR 3.2 15.9 + - - -
61N TYR* 3.4 26.5 - - + -
64N GLU* 4.0 23.5 - - + -
65N LEU* 3.8 23.8 - - + +
68N SER* 5.7 0.7 - - - +
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Residues in contact with GLU 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G ALA 2.9 17.3 + - - +
95G GLU* 4.0 16.4 - - - +
97G ALA* 1.3 77.7 - - - +
99G PHE* 1.3 57.8 + - - +
101G TYR* 3.1 6.9 + - + +
102G LYS* 2.9 63.6 + - + +
103G TYR* 6.1 0.2 - - - -
61N TYR* 3.5 17.4 - - + +
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Residues in contact with PHE 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G GLU 3.0 19.0 + - - +
96G ALA 3.8 3.8 - - - +
98G GLU* 1.3 79.5 - - - +
100G ARG* 1.3 56.2 + - - +
102G LYS* 4.7 0.4 - - - -
103G TYR* 2.8 49.1 + + + +
105G TYR* 3.2 59.9 - + - -
107G MET* 3.6 38.4 - - + -
108G PRO* 3.9 7.6 - - + -
111G VAL* 4.2 19.5 - - + -
66H HIS* 3.5 20.9 - + - -
70H THR* 4.5 2.0 - - + -
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Residues in contact with ARG 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2081 THR* 3.1 36.0 + - - -
2091 GLN* 5.6 0.8 - - - +
96G ALA 3.4 10.3 + - - +
97G ALA 3.3 9.1 + - - +
98G GLU 3.2 0.4 - - - -
99G PHE* 1.3 78.6 - - - +
101G TYR* 1.3 60.4 + - - +
104G GLY* 2.9 35.8 + - - -
105G TYR* 3.4 31.6 - - - +
106G ASP* 3.6 18.4 + - - +
81H GLN* 4.4 7.3 - - - +
60N GLN* 4.2 22.9 + - + +
64N GLU* 3.9 26.0 - - - +
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Residues in contact with TYR 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G ALA 3.2 9.7 + - - +
98G GLU* 3.1 11.1 + - + +
100G ARG* 1.3 83.0 - - - +
102G LYS* 1.3 71.9 + - + +
81H GLN* 2.9 29.9 + - - +
85H GLN* 3.2 38.6 + - - +
54N ALA* 5.0 1.4 + - - +
57N ASP* 3.7 39.4 - - + +
58N ILE* 3.5 26.9 - - + +
61N TYR* 3.8 25.6 - + + -
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Residues in contact with LYS 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G GLU* 2.9 51.2 + - + +
99G PHE 4.0 2.2 - - - +
101G TYR* 1.3 91.1 - - + +
103G TYR* 1.3 96.7 + - + +
81H GLN* 3.5 16.7 - - - +
82H MET* 4.0 10.4 - - - +
85H GLN* 4.0 13.3 - - - +
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Residues in contact with TYR 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G GLU* 6.1 0.2 - - - -
99G PHE* 2.8 53.6 + + + +
102G LYS* 1.3 111.2 + - + +
104G GLY* 1.3 61.2 + - - +
105G TYR* 3.3 16.4 - - + -
66H HIS* 3.5 38.6 - + + -
78H SER* 2.5 45.2 + - - +
81H GLN* 4.3 1.8 - - - -
82H MET* 4.2 31.6 - - + -
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Residues in contact with GLY 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2081 THR* 3.4 38.5 - - - +
100G ARG* 2.9 27.7 + - - -
102G LYS 3.7 1.6 - - - -
103G TYR* 1.3 74.2 - - - +
105G TYR* 1.3 61.4 + - - +
77H VAL* 3.9 11.7 - - - +
81H GLN* 4.2 7.3 - - - +
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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) + - + + + + + -
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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