Contacts of the helix formed by residues 100 - 121 (chain F) in PDB entry 3IKM
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 100 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127E PRO 4.2 1.8 - - - -
196E CYS* 6.1 0.9 - - - -
77F HIS* 2.8 24.7 - - - -
78F PHE 2.8 16.8 + - - -
80F SER* 3.3 7.6 - - - +
99F PHE* 1.3 77.4 - - - +
101F PRO* 1.3 64.6 - - - +
102F LEU 2.9 2.2 - - - -
103F GLY 2.7 15.5 + - - -
104F VAL* 3.1 10.0 + - - +
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Residues in contact with PRO 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E PHE* 3.8 19.5 - - + -
127E PRO* 2.8 59.8 - - + +
196E CYS* 4.5 17.9 - - - -
199E LEU* 5.8 3.4 - - + -
208E LEU* 5.8 0.2 - - + -
77F HIS* 3.4 24.5 - - + +
100F GLY* 1.3 82.9 - - - +
102F LEU* 1.3 64.9 + - + +
104F VAL 3.3 1.2 + - - -
105F GLU* 3.0 16.4 + - - +
381F ILE* 6.4 0.2 - - - -
414F TRP* 6.2 2.5 - - + -
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Residues in contact with LEU 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F ARG 2.8 28.9 - - - +
77F HIS* 3.0 10.5 - - + +
78F PHE* 2.9 37.2 - - + -
101F PRO* 1.3 79.8 - - + +
103F GLY* 1.3 65.2 - - - +
105F GLU* 3.3 4.4 + - - +
106F LEU* 3.1 21.6 + - + +
374F LEU* 6.0 1.6 - - + -
380F PRO* 3.6 33.0 - - + +
381F ILE* 5.4 5.6 - - + -
431F LYS* 5.6 0.2 - - - +
435F MET* 2.9 37.7 - - + -
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Residues in contact with GLY 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F PHE* 2.8 32.9 - - - -
99F PHE* 3.5 17.3 - - - -
100F GLY 2.7 11.4 + - - -
102F LEU* 1.3 83.0 - - - +
104F VAL* 1.3 61.8 + - - -
106F LEU 3.3 0.2 + - - -
107F ARG* 3.1 22.0 + - - +
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Residues in contact with VAL 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E TRP* 4.7 10.3 - - + -
127E PRO* 3.7 23.3 - - + +
128E VAL 3.8 23.6 - - - +
129E ASP* 4.8 2.5 - - - +
210E GLN* 5.5 5.6 - - + +
99F PHE* 4.3 6.5 - - + +
100F GLY 3.3 14.8 - - - +
101F PRO 3.5 6.1 - - - +
103F GLY* 1.3 74.4 - - - +
105F GLU* 1.3 53.1 + - - +
107F ARG* 3.2 28.5 + - - +
108F LYS* 2.5 45.3 + - + +
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Residues in contact with GLU 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E TRP* 4.5 9.0 + - - -
127E PRO* 4.1 14.4 - - + -
101F PRO 3.0 12.7 + - - +
102F LEU 3.6 2.9 - - - +
104F VAL* 1.3 78.6 - - - +
106F LEU* 1.3 52.6 + - - +
108F LYS* 3.3 33.9 + - - +
109F ASN* 2.5 45.5 + - - +
380F PRO* 3.6 36.5 - - + +
381F ILE* 5.0 7.5 - - + +
412F SER* 4.4 11.4 - - - -
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F PHE* 4.2 9.9 - - + -
102F LEU* 3.1 11.5 + - + +
103F GLY 3.6 6.7 - - - +
105F GLU* 1.3 75.3 - - - +
107F ARG* 1.3 71.3 + - - +
109F ASN* 2.6 24.1 + - + +
110F LEU* 2.6 25.6 + - + +
346F MET* 3.3 38.8 - - + +
349F TYR* 5.5 4.3 - - + -
350F LEU* 4.5 13.0 - - + +
374F LEU* 4.9 14.6 - - + -
378F LEU* 3.5 29.6 - - + +
380F PRO* 4.1 8.7 - - + +
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Residues in contact with ARG 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E GLN* 5.6 4.0 + - - -
99F PHE* 4.2 25.0 - - + -
103F GLY 3.1 9.9 + - - +
104F VAL* 3.7 28.0 + - - +
106F LEU* 1.3 80.7 - - - +
108F LYS* 1.3 63.3 + - - +
110F LEU* 3.0 10.5 + - + +
111F ALA* 2.7 36.6 + - + +
235F THR* 4.8 23.4 + - + +
343F ASP* 3.9 35.2 + - - +
346F MET* 4.4 13.6 - - + +
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Residues in contact with LYS 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E TRP* 3.5 33.7 - - + +
104F VAL* 2.5 29.3 + - + +
105F GLU* 3.3 29.0 + - - +
106F LEU 2.8 0.6 + - - -
107F ARG* 1.3 75.0 - - - +
109F ASN* 1.3 73.5 + - - +
111F ALA* 4.8 4.0 - - + -
112F ALA* 2.8 33.9 + - + +
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Residues in contact with ASN 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F GLU* 2.5 32.0 + - - +
106F LEU* 2.6 7.2 + - + +
108F LYS* 1.3 77.5 - - - +
110F LEU* 1.3 51.6 + - + +
112F ALA* 3.4 5.1 - - - +
113F GLU* 2.5 41.8 + - + +
377F CYS 3.7 17.3 - - - +
378F LEU* 3.0 11.6 + - - +
379F ALA 2.9 30.7 + - - -
380F PRO* 3.7 10.0 + - - +
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Residues in contact with LEU 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU* 2.6 23.1 + - + +
107F ARG* 3.2 12.6 - - + +
108F LYS 2.9 0.4 + - - -
109F ASN* 1.3 70.2 - - + +
111F ALA* 1.3 69.2 + - - +
112F ALA 3.0 0.9 - - - -
113F GLU* 2.7 6.9 + - + +
114F TRP* 2.6 27.7 + - + +
262F TRP* 4.4 21.5 - - + -
263F TRP* 5.5 1.6 - - + -
266F PHE* 5.5 2.9 - - + -
342F LEU* 6.4 0.7 - - + -
343F ASP 5.0 0.7 - - - +
345F GLY* 4.5 1.8 - - - -
346F MET* 3.4 43.7 - - + +
349F TYR* 4.1 26.9 - - + -
378F LEU* 5.3 10.1 - - + -
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Residues in contact with ALA 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F ARG* 2.7 24.2 + - + +
108F LYS* 4.0 4.3 - - + +
110F LEU* 1.3 71.1 - - - +
112F ALA* 1.3 50.9 + - - +
114F TRP* 3.9 5.2 - - - +
115F TRP* 2.6 44.4 + - - +
211F ILE* 3.9 28.9 - - + -
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Residues in contact with ALA 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F LYS* 2.8 26.9 + - + +
109F ASN* 3.4 5.8 - - - +
111F ALA* 1.3 78.6 - - - +
113F GLU* 1.3 55.2 + - - +
115F TRP* 3.4 7.1 - - - +
116F THR* 3.0 28.5 + - - +
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Residues in contact with GLU 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F ASN* 2.5 24.9 + - + +
110F LEU* 2.7 9.1 + - + +
112F ALA* 1.3 70.1 - - - +
114F TRP* 1.3 60.0 + - - +
116F THR* 2.7 29.6 + - - +
117F SER* 3.3 8.0 + - - -
262F TRP* 4.0 4.3 + - + +
266F PHE* 3.3 42.3 - - + -
377F CYS* 4.9 11.3 - - + +
483F LYS* 3.8 23.0 - - - +
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Residues in contact with TRP 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F LEU* 2.6 19.0 + - + +
111F ALA* 3.9 2.2 - - - +
113F GLU* 1.3 73.2 - - - +
115F TRP* 1.3 94.3 + + - +
117F SER* 2.8 15.6 + - - -
118F VAL* 3.3 36.0 + - + +
209F ALA* 6.2 1.3 - - + -
210F GLN 5.6 0.9 - - - -
211F ILE* 3.7 32.1 - - + -
237F ALA* 3.8 27.8 - - + -
238F SER 5.2 1.8 - - - -
239F LEU* 5.2 7.2 - - + -
259F ARG* 2.4 55.2 - - - +
262F TRP* 2.9 39.7 - + + +
338F VAL* 5.3 5.2 - - + -
339F ASN* 4.3 9.4 - - - -
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Residues in contact with TRP 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E VAL* 6.1 0.2 - - + -
108E LYS* 4.8 25.2 - - + +
111F ALA 2.6 26.2 + - - +
112F ALA* 3.4 8.7 - - - +
114F TRP* 1.3 90.6 - + + +
116F THR* 1.3 69.1 + - - +
118F VAL* 2.8 31.9 + - + +
119F VAL* 2.7 37.7 + - + +
125F VAL 5.0 0.4 - - - -
126F PHE* 3.8 23.6 - + - -
209F ALA 3.8 7.0 - - - -
210F GLN* 3.2 63.3 - - + -
211F ILE* 3.6 19.5 - - + -
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Residues in contact with THR 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F ALA 3.0 14.8 + - - +
113F GLU* 2.7 42.1 + - - +
115F TRP* 1.3 80.3 - - - +
117F SER* 1.3 54.4 + - - +
119F VAL* 3.2 6.2 + - - +
120F VAL* 2.7 39.8 + - - +
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Residues in contact with SER 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F GLU 3.3 11.6 + - - -
114F TRP 2.8 15.1 + - - -
116F THR* 1.3 80.3 + - - +
118F VAL* 1.3 62.1 + - - +
120F VAL* 3.4 26.6 - - - +
258F HIS* 4.2 29.0 + - - -
259F ARG* 5.7 0.4 - - - -
262F TRP* 3.4 15.5 + - - -
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Residues in contact with VAL 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F TRP* 3.3 40.4 + - + +
115F TRP* 2.8 30.4 + - + +
117F SER* 1.3 81.4 - - - +
119F VAL* 1.3 75.5 + - + +
120F VAL* 3.6 0.5 + - - -
121F PHE* 4.6 3.1 + - - +
123F GLU 4.4 4.5 - - - +
124F GLN* 4.2 9.4 - - + +
125F VAL 5.9 2.7 - - - +
209F ALA* 6.3 1.1 - - + -
239F LEU* 4.6 24.2 - - + -
255F TRP* 5.6 9.2 - - + -
258F HIS* 5.6 1.1 - - - -
259F ARG* 6.0 0.4 - - - +
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Residues in contact with VAL 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412E SER* 5.9 2.7 - - - +
115F TRP* 2.7 53.3 + - + +
116F THR* 3.2 7.6 + - - +
118F VAL* 1.3 85.5 - - + +
120F VAL* 1.3 64.1 + - - +
124F GLN* 3.2 39.3 + - + +
126F PHE* 5.5 7.2 - - + -
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Residues in contact with VAL 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403E PHE* 3.6 23.4 - - - -
404E ASN* 5.3 7.1 + - - +
407E LEU* 4.3 15.6 - - + +
116F THR* 2.7 34.8 - - - +
117F SER* 3.4 18.4 - - - +
118F VAL 3.5 0.2 - - - -
119F VAL* 1.3 76.4 - - - +
121F PHE* 1.3 85.9 + - + +
122F ARG 4.1 0.2 - - - -
124F GLN* 5.1 2.3 + - - -
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Residues in contact with PHE 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400E GLN* 4.5 21.1 - - - +
403E PHE* 4.2 11.8 - - - -
404E ASN* 5.8 1.1 + - - +
417E TYR* 5.4 2.1 + - - -
118F VAL 4.6 2.9 + - - +
119F VAL 3.6 3.0 + - - -
120F VAL* 1.3 90.3 - - + +
122F ARG* 1.3 94.2 + - + +
123F GLU* 4.4 21.2 + - + +
251F TRP* 5.3 15.5 - + - -
254F PHE* 6.2 5.6 - + + -
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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