Contacts of the helix formed by residues 94 - 117 (chain K) in PDB entry 2I2X
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 ASN 94 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90K GLN* 3.0 36.2 + - - +
91K MET 3.3 8.7 - - - +
93K ASN* 1.3 88.6 - - - +
95K PRO* 1.3 69.1 - - - +
96K SER* 3.1 3.8 - - - +
97K TRP* 2.8 51.1 + - + +
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Residues in contact with PRO 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 MET 3.9 6.7 - - - +
92K SER 3.9 2.2 - - - +
93K ASN 3.5 10.5 - - - +
94K ASN* 1.3 82.9 - - - +
96K SER* 1.3 56.2 + - - +
98K GLY* 3.4 4.4 + - - -
99K ALA 3.2 19.9 + - - -
145K VAL* 3.8 20.4 - - + +
148K GLU* 3.8 25.6 - - + +
149K ALA* 3.7 21.5 - - - +
152K GLN* 3.8 25.5 - - + +
153K CYS* 4.7 2.8 - - - -
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Residues in contact with SER 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55K LYS* 5.4 1.0 + - - -
94K ASN* 2.8 6.3 + - - +
95K PRO* 1.3 74.9 - - - +
97K TRP* 1.3 69.4 + - - -
99K ALA* 3.7 8.8 - - - +
100K GLU* 3.0 44.9 + - - +
152K GLN* 4.4 11.7 - - - -
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Residues in contact with TRP 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52K GLY 4.9 4.0 - - - -
53K ALA 4.8 6.5 - - - -
54K SER* 4.4 3.8 - - - -
55K LYS* 3.5 62.5 - - + +
58K LEU* 4.0 15.5 - - + -
59K ILE* 5.3 0.3 - - - +
90K GLN* 3.7 41.3 - - + -
91K MET* 4.0 10.8 - - + -
94K ASN* 2.8 41.2 + - + +
96K SER* 1.3 76.2 - - - +
98K GLY* 1.3 66.5 + - - +
100K GLU* 3.0 3.8 + - - +
101K VAL* 3.0 30.0 + - + +
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Residues in contact with GLY 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87K HIS* 3.8 18.2 - - - -
91K MET* 3.4 30.9 + - - +
95K PRO 3.4 3.0 + - - -
97K TRP* 1.3 77.8 - - - +
99K ALA* 1.3 56.9 + - - +
101K VAL* 3.4 3.5 + - - +
102K ALA* 3.0 24.8 + - - +
124K HIS* 3.5 8.0 + - - -
153K CYS* 3.6 6.7 - - - -
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Residues in contact with ALA 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 PRO 3.2 12.1 + - - +
96K SER* 3.8 10.5 - - - +
97K TRP 3.1 0.6 - - - -
98K GLY* 1.3 76.0 - - - +
100K GLU* 1.3 59.6 + - + +
102K ALA* 3.3 1.4 + - - +
103K HIS* 3.0 22.3 + - - +
152K GLN* 3.4 39.0 - - + +
153K CYS* 3.8 9.3 - - - +
156K ASN* 3.4 24.1 - - - +
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Residues in contact with GLU 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55K LYS* 2.8 38.3 + - + -
59K ILE* 4.0 20.2 - - + +
96K SER* 3.0 31.5 + - - +
97K TRP* 3.0 4.2 + - - +
99K ALA* 1.3 75.8 - - + +
101K VAL* 1.3 66.8 + - - +
103K HIS* 3.1 7.5 + - + +
104K ALA* 2.9 25.3 + - - +
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Residues in contact with VAL 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55K LYS* 6.1 1.1 - - + -
58K LEU* 4.8 4.3 - - + -
59K ILE* 4.1 24.2 - - + +
62K TYR* 3.5 39.0 - - + -
91K MET* 3.9 24.2 - - + -
97K TRP* 3.0 17.5 + - + +
98K GLY 3.5 7.6 - - - +
100K GLU* 1.3 76.7 - - - +
102K ALA* 1.3 62.0 + - - +
104K ALA* 3.5 4.1 + - - +
105K GLN* 3.0 46.9 + - - +
124K HIS* 4.1 1.6 - - - +
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Residues in contact with ALA 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 GLY 3.0 9.6 + - - +
99K ALA* 3.4 13.2 - - - +
100K GLU 3.2 0.2 - - - -
101K VAL* 1.3 75.7 - - - +
103K HIS* 1.3 56.7 + - - +
105K GLN* 3.6 1.7 - - - +
106K LYS* 2.9 31.7 + - - +
122K LEU* 3.6 5.1 - - + +
124K HIS* 3.4 32.1 - - + +
153K CYS* 4.3 5.4 - - - +
156K ASN 3.3 14.5 - - - +
158K ALA 4.2 12.3 - - - +
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Residues in contact with HIS 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 ALA 3.0 12.1 + - - +
100K GLU* 3.1 10.5 + - + +
102K ALA* 1.3 74.0 - - - +
104K ALA* 1.3 61.3 + - - +
106K LYS* 3.2 4.6 + - + +
107K THR* 2.9 51.1 + - - -
156K ASN* 3.0 38.9 + - + +
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Residues in contact with ALA 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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59K ILE* 3.8 19.7 - - + +
62K TYR* 6.3 0.7 - - + -
63K GLU* 3.6 28.3 - - + +
100K GLU 2.9 15.4 + - - +
101K VAL* 3.8 3.8 - - - +
103K HIS* 1.3 77.4 + - - +
105K GLN* 1.3 64.3 + - + +
107K THR* 3.5 6.2 + - - -
108K ILE* 3.3 29.4 + - - +
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Residues in contact with GLN 105 (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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45K TYR* 3.1 21.8 + - - -
62K TYR* 4.3 14.7 - - + +
66K THR* 3.1 28.9 + - - +
83K LEU* 4.2 4.0 - - - +
85K THR* 2.6 24.6 + - - +
101K VAL* 3.0 31.4 + - + +
102K ALA 3.6 3.6 - - - +
104K ALA* 1.3 73.3 - - + +
106K LYS* 1.3 65.6 + - - +
108K ILE* 3.2 6.5 + - - +
109K MET* 2.9 38.0 + - + +
122K LEU* 3.9 7.6 - - + +
124K HIS* 3.2 22.6 - - - -
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Residues in contact with LYS 106 (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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29K GLY* 5.1 0.4 - - - -
30K LEU* 3.9 31.4 - - + +
102K ALA 2.9 21.5 + - - +
103K HIS* 3.8 5.6 - - + +
105K GLN* 1.3 72.2 - - - +
107K THR* 1.3 53.3 + - - +
109K MET* 2.9 22.1 + - + +
110K GLU* 2.8 49.8 + - - +
120K CYS* 6.0 0.2 - - - -
121K ALA* 5.6 1.3 - - - +
122K LEU* 4.6 1.5 - - + +
157K GLY* 2.5 46.3 + - - +
159K ASP* 2.8 32.2 + - - -
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Residues in contact with THR 107 (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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103K HIS* 2.9 44.9 + - - -
104K ALA* 3.7 7.1 - - - -
106K LYS* 1.3 76.6 - - - +
108K ILE* 1.3 66.0 + - + +
110K GLU* 3.3 18.3 + - - +
111K LYS* 3.1 21.2 + - + +
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Residues in contact with ILE 108 (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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63K GLU* 3.6 37.7 - - + +
66K THR* 3.8 19.5 - - + +
67K THR* 3.6 30.1 - - - +
70K MET* 4.6 0.7 - - + -
104K ALA 3.3 13.8 + - - +
105K GLN 3.2 7.4 + - - +
107K THR* 1.3 80.6 - - + +
109K MET* 1.3 64.2 + - - +
111K LYS* 3.2 20.3 + - + +
112K TYR* 3.3 31.5 + - + -
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Residues in contact with MET 109 (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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30K LEU* 4.1 2.4 - - + +
66K THR* 3.9 16.4 - - + -
70K MET* 4.6 13.5 - - - -
83K LEU* 4.0 21.1 - - + -
105K GLN* 2.9 39.5 + - + +
106K LYS* 2.9 18.4 + - + +
108K ILE* 1.3 76.6 - - - +
110K GLU* 1.3 56.8 + - - +
112K TYR* 3.3 4.4 + - - +
113K HIS* 2.9 28.9 + - - +
120K CYS* 4.0 22.0 - - - -
121K ALA 4.5 8.1 - - - +
122K LEU* 3.6 46.4 - - + -
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Residues in contact with GLU 110 (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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30K LEU* 4.0 28.1 - - + +
106K LYS* 2.8 36.0 + - + +
107K THR* 3.6 19.6 + - - +
109K MET* 1.3 71.8 - - - +
111K LYS* 1.3 57.6 + - - +
113K HIS* 3.6 1.7 - - - +
114K ASP* 2.8 44.9 + - - +
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Residues in contact with LYS 111 (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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107K THR* 3.1 12.7 + - + +
108K ILE* 3.2 14.1 + - + +
110K GLU* 1.3 76.3 - - - +
112K TYR* 1.3 89.3 + - + +
114K ASP* 3.3 6.7 + - - +
115K GLU* 3.1 41.5 + - - +
116K TYR* 5.9 1.0 - - - -
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Residues in contact with TYR 112 (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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67K THR* 4.0 18.2 - - + +
70K MET* 3.4 41.3 - - + -
71K GLU* 2.9 51.1 + - - +
74K VAL* 4.2 3.8 - - + -
108K ILE* 3.3 29.0 + - + +
109K MET 3.8 5.8 - - - +
111K LYS* 1.3 102.5 + - + +
113K HIS* 1.3 58.0 + - - +
115K GLU* 3.4 0.6 + - - -
116K TYR* 2.9 66.4 + + - +
118K ILE* 4.0 4.9 - - + +
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Residues in contact with HIS 113 (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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30K LEU* 3.8 50.5 + - + +
31K ASP* 3.8 16.9 + - + +
109K MET 2.9 17.9 + - - +
110K GLU* 3.6 4.2 - - - +
112K TYR* 1.3 76.6 - - - +
114K ASP* 1.3 68.7 + - - +
117K GLY* 2.9 33.8 + - - -
118K ILE* 2.9 36.2 - - - +
120K CYS* 4.8 1.3 - - - -
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Residues in contact with ASP 114 (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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110K GLU* 2.8 29.5 + - - +
111K LYS* 3.3 6.4 + - - +
113K HIS* 1.3 90.7 + - - +
115K GLU* 1.3 58.7 + - - +
117K GLY 4.9 0.2 + - - -
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Residues in contact with GLU 115 (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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20J LEU* 3.8 29.1 - - + +
111K LYS* 3.1 40.2 + - - +
112K TYR* 5.5 0.2 - - - -
114K ASP* 1.3 78.2 - - - +
116K TYR* 1.3 96.4 + - + +
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Residues in contact with TYR 116 (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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234I LEU* 3.6 28.1 - - + +
14J THR* 5.4 1.0 - - - +
16J TYR* 3.3 45.5 - + + -
20J LEU* 3.5 32.7 - - + +
71K GLU* 4.8 5.7 + - - -
74K VAL* 3.9 14.0 - - + +
111K LYS* 5.9 0.9 - - - -
112K TYR* 2.9 54.5 + + - +
115K GLU* 1.3 106.6 + - + +
117K GLY* 1.3 64.7 + - - +
118K ILE* 4.2 2.0 - - + +
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Residues in contact with GLY 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J TYR* 4.7 1.8 - - - -
31K ASP* 5.2 2.1 - - - +
79K PRO 4.9 0.7 - - - +
113K HIS* 2.9 26.2 + - - -
114K ASP 4.9 0.2 + - - -
115K GLU 3.8 0.4 - - - -
116K TYR* 1.3 78.5 - - - +
118K ILE* 1.3 64.3 + - - +
119K LYS* 3.4 9.4 + - - +
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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