Contacts of the helix formed by residues 81 - 104 (chain K) in PDB entry 5T0G
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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J PHE* 5.8 4.5 - - + -
14J GLY 5.7 1.6 - - - +
16J LEU* 5.3 11.0 - - + -
19J VAL* 6.0 1.6 - - + -
20J GLU* 5.2 11.0 - - - +
150J SER* 4.4 22.4 - - - +
152J THR* 6.1 2.0 - - + -
30K ALA* 5.0 11.9 - - + -
33K LEU* 4.3 20.4 - - + -
66K LYS* 4.9 0.2 + - - -
78K MET* 4.7 2.1 - - - +
79K SER 3.3 11.7 + - - +
80K GLY* 1.3 77.1 - - - -
82K ILE* 1.3 64.0 + - - +
83K ALA* 5.0 0.7 - - + +
84K ASP* 3.1 37.2 - - + +
85K ALA* 4.1 8.1 + - - +
138K GLY 5.7 1.2 + - - -
139K VAL* 4.1 7.8 - - - +
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Residues in contact with ILE 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152J THR* 4.3 19.5 - - + +
153J TYR* 6.1 5.6 - - + -
64K ILE* 4.6 24.2 - - + -
65K GLU 5.1 4.3 - - - +
66K LYS* 3.9 28.7 - - + +
78K MET* 3.8 28.9 - - + +
80K GLY 4.6 3.1 - - - +
81K LEU* 1.3 74.2 - - - +
83K ALA* 1.3 64.7 + - - +
84K ASP 3.0 1.1 - - - -
85K ALA* 2.8 23.9 + - - +
86K LYS* 3.0 10.4 + - + -
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Residues in contact with ALA 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J ALA 5.3 0.2 - - - +
113J SER* 6.5 0.2 - - - -
116J GLN* 3.4 36.9 - - + +
150J SER* 3.4 6.3 - - - +
151J GLY* 3.1 30.3 - - - +
152J THR* 4.0 8.4 - - + +
81K LEU* 5.0 0.6 - - + +
82K ILE* 1.3 80.6 - - - +
84K ASP* 1.3 63.6 + - - +
86K LYS* 3.3 25.0 + - + +
87K THR 3.9 1.7 + - - -
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Residues in contact with ASP 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J PHE* 4.8 9.0 - - - -
16J LEU* 5.4 0.7 - - - +
116J GLN* 3.1 27.5 + - - +
150J SER* 5.6 0.2 - - - -
81K LEU* 3.1 47.2 - - + +
82K ILE 3.0 0.6 + - - -
83K ALA* 1.3 78.5 - - - +
85K ALA* 1.3 60.1 + - - +
87K THR* 4.0 2.6 + - - -
88K LEU 4.5 0.3 + - - -
135K ARG* 3.9 16.9 + - - -
137K PHE* 3.5 42.4 - - + -
138K GLY* 5.1 3.8 + - - +
139K VAL* 4.3 12.5 + - + -
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Residues in contact with ALA 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K MET* 4.0 18.6 - - + -
81K LEU 4.1 0.8 + - - +
82K ILE 2.8 9.5 + - - +
84K ASP* 1.3 74.9 - - - +
86K LYS* 1.3 67.5 + - - +
87K THR 3.1 2.9 - - - -
88K LEU* 2.7 19.7 + - + +
89K ILE* 2.8 25.2 + - + +
139K VAL* 3.6 34.0 - - + +
141K LEU* 4.8 4.0 - - + -
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Residues in contact with LYS 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J SER* 6.1 6.3 - - - -
116J GLN* 5.9 0.2 - - + -
153J TYR* 6.3 2.7 - - + -
78K MET* 5.2 1.7 - - - +
82K ILE* 3.0 7.7 + - + +
83K ALA* 3.3 24.4 + - + +
85K ALA* 1.3 74.6 - - - +
87K THR* 1.3 64.6 + - - +
89K ILE* 3.4 8.8 - - - +
90K ASP* 3.1 28.4 + - - +
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Residues in contact with THR 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J SER* 5.6 0.7 + - - -
116J GLN* 4.0 21.3 - - - +
117J ARG* 5.1 20.3 + - + +
83K ALA 3.9 1.3 + - - -
84K ASP 4.2 0.7 - - - -
85K ALA 3.1 0.4 - - - -
86K LYS* 1.3 77.1 - - - +
88K LEU* 1.3 64.4 + - + +
90K ASP* 5.0 1.1 - - - +
91K LYS* 3.4 27.9 + - + +
137K PHE* 4.0 28.8 - - + -
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Residues in contact with LEU 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84K ASP 4.5 1.1 - - - +
85K ALA* 2.7 16.6 + - + +
87K THR* 1.3 75.3 - - + +
89K ILE* 1.3 65.7 + - + +
91K LYS* 3.3 8.5 + - - +
92K ALA* 2.9 27.0 + - - +
116K VAL* 4.6 7.6 - - + -
119K LEU* 3.7 35.1 - - + +
137K PHE* 3.8 38.4 - - + -
139K VAL* 4.6 15.3 - - + +
141K LEU* 4.5 23.8 - - + -
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Residues in contact with ILE 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K VAL* 3.7 25.8 - - + -
70K ILE* 3.5 32.2 - - + +
76K CYS* 4.4 18.8 - - - -
77K ALA 6.2 0.2 - - - -
78K MET* 4.0 20.6 - - + -
85K ALA* 2.8 28.0 + - + +
86K LYS* 3.4 9.6 - - - +
88K LEU* 1.3 77.8 - - + +
90K ASP* 1.3 70.6 + - + +
91K LYS 3.0 0.2 + - - -
92K ALA* 3.0 8.1 + - - +
93K ARG* 3.0 22.5 + - - +
141K LEU* 4.7 7.0 - - + -
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Residues in contact with ASP 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J ARG* 5.9 1.2 + - - -
86K LYS 3.1 11.2 + - - +
87K THR* 5.0 1.6 - - - +
89K ILE* 1.3 81.9 - - + +
91K LYS* 1.3 60.2 + - - +
93K ARG* 3.7 21.4 + - - +
94K VAL* 3.4 24.2 + - - +
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Residues in contact with LYS 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87K THR* 3.4 25.8 + - + +
88K LEU* 3.3 7.4 + - - +
89K ILE 3.1 1.2 - - - -
90K ASP* 1.3 77.1 - - - +
92K ALA* 1.3 65.2 + - - +
94K VAL* 3.1 13.8 + - + +
95K GLU* 3.0 40.9 + - + +
119K LEU* 3.3 36.7 - - - +
122K GLN* 6.3 0.7 - - - +
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Residues in contact with ALA 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70K ILE* 3.7 17.5 - - + -
88K LEU 2.9 17.5 + - - +
89K ILE* 3.6 4.3 - - - +
91K LYS* 1.3 73.8 - - - +
93K ARG* 1.3 67.7 + - - +
95K GLU* 2.9 32.8 + - - +
96K THR* 3.0 16.6 + - - +
112K VAL* 5.0 7.9 - - + -
116K VAL* 4.8 15.3 - - + -
119K LEU* 6.4 0.4 - - + -
143K PHE* 6.5 0.4 - - + -
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Residues in contact with ARG 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K VAL* 5.4 6.0 - - - +
69K GLU* 2.3 38.8 + - - +
70K ILE* 3.2 34.9 + - + +
89K ILE* 3.0 27.5 - - - +
90K ASP* 3.7 24.2 + - - +
92K ALA* 1.3 74.2 - - - +
94K VAL* 1.3 61.2 + - + +
96K THR* 2.9 17.3 + - - -
97K GLN* 3.0 18.1 + - - +
228K MET* 6.1 1.6 - - - +
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Residues in contact with VAL 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90K ASP* 3.4 20.0 - - - +
91K LYS* 3.1 13.6 + - + +
92K ALA 3.1 0.4 - - - -
93K ARG* 1.3 75.0 - - + +
95K GLU* 1.3 63.2 + - - +
97K GLN* 3.2 7.4 + - + +
98K ASN* 2.5 49.8 + - - +
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Residues in contact with GLU 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91K LYS* 3.0 38.5 + - - +
92K ALA* 2.9 24.1 + - - +
94K VAL* 1.3 79.5 - - + +
96K THR* 1.3 66.6 + - + +
98K ASN* 3.1 7.3 + - - +
99K HIS* 3.0 19.1 + - - +
107K MET* 4.7 8.2 - - + +
112K VAL* 5.7 0.3 - - - +
115K ALA* 3.2 36.4 - - + +
116K VAL* 4.6 1.0 + - - +
119K LEU* 3.4 14.6 - - - +
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Residues in contact with THR 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K ILE* 4.8 4.0 - - + +
71K ASP* 4.0 32.6 + - + +
92K ALA 3.0 10.9 + - - +
93K ARG* 2.9 20.6 + - - -
95K GLU* 1.3 76.4 - - + +
97K GLN* 1.3 63.5 + - - +
99K HIS* 3.1 5.1 + - - +
100K TRP* 2.9 20.8 + - - +
107K MET* 3.5 43.6 + - + +
112K VAL* 4.3 19.3 - - + -
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Residues in contact with GLN 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71K ASP* 5.3 6.2 + - - -
93K ARG* 3.0 13.2 + - - +
94K VAL* 3.4 13.2 - - + +
96K THR* 1.3 82.9 + - - +
98K ASN* 1.3 60.0 + - - +
100K TRP* 2.9 37.2 + - - +
101K PHE* 3.0 41.0 + - + -
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Residues in contact with ASN 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94K VAL* 2.5 51.5 + - - +
95K GLU* 3.1 7.1 + - - +
97K GLN* 1.3 74.8 - - - +
99K HIS* 1.3 63.9 + - - +
101K PHE* 3.0 22.9 + - + +
102K THR* 2.9 30.2 + - + +
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Residues in contact with HIS 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K GLU 3.0 7.3 + - - +
96K THR 3.2 10.1 - - - +
98K ASN* 1.3 76.7 - - - +
100K TRP* 1.3 62.2 + - - +
102K THR* 3.1 6.6 + - - -
103K TYR* 3.0 58.2 + + - +
105K GLU* 3.1 37.8 + - + -
106K THR 3.8 11.9 - - - -
107K MET* 3.7 49.1 + - + +
108K THR* 5.3 1.8 - - + -
111K SER* 6.0 0.4 - - - -
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Residues in contact with TRP 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96K THR 2.9 9.3 + - - +
97K GLN* 2.9 28.3 + - - +
99K HIS* 1.3 72.8 - - - +
101K PHE* 1.3 95.6 + + - +
104K ASN* 3.0 49.7 + - - +
105K GLU* 3.3 33.7 + - - +
106K THR* 3.7 20.9 - - + +
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Residues in contact with PHE 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97K GLN* 3.0 45.2 + - + -
98K ASN* 3.0 24.4 + - + +
100K TRP* 1.3 112.9 - + - +
102K THR* 1.3 68.7 + - + +
104K ASN* 4.0 9.5 + - - +
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Residues in contact with THR 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98K ASN* 2.9 16.4 + - + +
99K HIS* 3.1 12.3 + - - -
101K PHE* 1.3 79.8 - - + +
103K TYR* 1.3 88.8 + - - +
104K ASN* 3.8 1.9 + - - +
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Residues in contact with TYR 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K HIS* 3.0 43.8 + + - +
102K THR* 1.3 97.9 - - - +
104K ASN* 1.3 70.4 + - - +
105K GLU* 3.0 31.9 + - + +
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Residues in contact with ASN 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K TRP* 3.0 41.4 + - - +
101K PHE* 4.0 6.9 + - - +
102K THR 3.5 3.0 + - - -
103K TYR* 1.3 78.3 - - - +
105K GLU* 1.3 58.3 + - - +
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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
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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