Contacts of the helix formed by residues 100 - 115 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77E HIS 3.5 1.8 - - - -
79E LEU* 2.6 33.4 - - - +
80E SER* 3.5 1.6 - - - -
99E PHE* 1.3 75.7 - - - +
101E PRO* 1.3 59.1 - - - -
102E LEU 3.3 2.5 - - - -
103E GLY* 2.6 9.9 + - - -
104E VAL* 2.5 31.3 + - - -
128F VAL* 3.2 6.7 - - - -
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Residues in contact with PRO 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ARG 5.1 1.1 - - - +
77E HIS* 3.3 31.2 - - + +
79E LEU 4.2 0.2 - - - +
80E SER* 5.3 0.9 - - - -
100E GLY* 1.3 77.5 - - - -
102E LEU* 1.3 67.4 + - - +
104E VAL* 3.9 1.0 - - - +
105E GLU* 3.0 24.3 + - - +
125F VAL* 5.8 4.7 - - + -
126F PHE* 3.9 26.4 - - + +
128F VAL* 2.7 25.9 - - + -
192F HIS* 5.6 1.3 - - + -
196F CYS* 6.3 3.8 - - - -
199F LEU* 4.9 14.6 - - + -
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ARG 3.7 9.1 + - - +
77E HIS 2.4 34.8 + - - +
78E PHE* 2.9 47.1 - - + -
101E PRO* 1.3 70.9 - - - +
103E GLY* 1.3 55.9 + - - +
105E GLU* 3.2 18.0 + - - +
106E LEU* 2.9 29.5 + - + -
383E VAL* 4.5 19.7 - - + -
435E MET* 5.3 14.1 - - + -
436E SER* 5.6 14.1 - - - +
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Residues in contact with GLY 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E PHE* 3.6 5.1 - - - +
79E LEU* 3.9 9.4 - - - -
99E PHE* 4.9 1.8 - - - -
100E GLY 2.6 16.2 + - - -
102E LEU* 1.3 80.3 - - - +
104E VAL* 1.3 56.1 + - - -
106E LEU* 3.1 8.4 + - - +
107E ARG* 3.0 41.5 + - - -
346E MET* 4.7 11.7 - - - -
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Residues in contact with VAL 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E PHE* 4.2 11.2 - - + -
100E GLY 2.5 20.3 + - - +
101E PRO* 3.9 2.9 - - + +
102E LEU 3.2 0.2 - - - -
103E GLY* 1.3 68.7 - - - +
105E GLU* 1.3 67.9 + - - +
106E LEU 3.0 1.3 - - - -
107E ARG* 3.5 17.2 + - - +
108E LYS* 3.8 11.5 + - + +
115F TRP* 5.8 0.2 - - + -
126F PHE* 4.1 11.4 - - + -
128F VAL* 2.7 56.1 - - + +
129F ASP* 4.0 0.4 - - - +
210F GLN* 3.9 28.9 + - + +
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Residues in contact with GLU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E PRO 3.0 16.7 + - - +
102E LEU* 3.4 13.2 - - - +
104E VAL* 1.3 78.4 - - - +
106E LEU* 1.3 51.8 + - - +
108E LYS* 2.8 33.3 - - + +
109E ASN* 2.3 24.3 - - - +
381E ILE 5.2 2.2 - - - +
382E LYS* 1.7 37.7 - - - +
383E VAL* 3.5 16.3 - - + +
126F PHE* 5.2 14.6 - - + -
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Residues in contact with LEU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E PHE* 3.8 20.0 - - + -
102E LEU* 2.9 18.7 + - + +
103E GLY 3.2 10.1 - - - +
105E GLU* 1.3 72.5 - - - +
107E ARG* 1.3 58.6 + - - +
109E ASN* 2.2 45.8 - - - +
110E LEU* 2.8 27.2 + - + +
346E MET* 3.3 41.7 - - + +
349E TYR* 6.4 3.1 - - + -
350E LEU* 6.0 0.9 - - + -
374E LEU* 6.6 0.4 - - + -
378E LEU* 4.9 4.7 - - + -
379E ALA* 5.9 1.1 - - + -
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Residues in contact with ARG 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E PHE* 2.8 68.9 - - - +
103E GLY 3.0 25.2 + - - +
104E VAL* 3.5 12.5 + - - +
105E GLU 3.5 0.4 - - - -
106E LEU* 1.3 75.0 - - - +
108E LYS* 1.3 54.8 + - - +
110E LEU* 3.2 7.9 + - + +
111E ALA* 2.7 41.8 + - + +
235E THR* 5.2 7.9 - - - +
342E LEU* 5.5 5.3 + - + +
343E ASP* 3.9 22.0 + - - +
346E MET* 4.1 30.7 - - - +
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Residues in contact with LYS 108 (chain E).
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 3.8 6.1 + - - +
105E GLU* 2.8 40.8 - - + +
107E ARG* 1.3 79.1 - - - +
109E ASN* 1.3 74.6 + - + +
111E ALA* 4.6 3.1 - - - -
112E ALA* 3.2 23.4 + - - +
381E ILE* 5.7 6.7 - - - +
115F TRP* 4.8 27.6 - - + +
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Residues in contact with ASN 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E GLU* 2.3 27.2 - - - +
106E LEU* 2.2 48.6 - - - +
108E LYS* 1.3 82.3 - - + +
110E LEU* 1.3 58.3 + - - +
112E ALA* 3.9 3.8 + - - +
113E GLU* 3.6 13.2 + - - +
378E LEU* 2.7 66.8 + - - +
379E ALA* 3.3 6.1 - - - +
381E ILE* 3.2 14.6 - - + +
383E VAL* 6.3 0.4 - - - +
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Residues in contact with LEU 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU* 2.8 26.1 + - + +
107E ARG* 3.5 7.6 - - + +
109E ASN* 1.3 74.9 - - - +
111E ALA* 1.3 59.8 + - - +
113E GLU* 4.0 6.2 - - - +
114E TRP* 3.8 12.0 + - - +
262E TRP* 4.0 15.7 - - + -
263E TRP* 5.9 3.8 - - + -
266E PHE* 6.1 0.2 - - + -
342E LEU* 3.8 39.2 - - + +
345E GLY 4.4 4.3 - - - +
346E MET* 4.1 23.1 - - + +
349E TYR* 4.0 28.0 - - + -
378E LEU* 3.2 23.8 - - + -
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Residues in contact with ALA 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E ARG* 2.7 22.6 + - + +
108E LYS* 4.1 3.6 - - - +
110E LEU* 1.3 72.2 - - - +
112E ALA* 1.3 67.5 + - - +
114E TRP* 3.1 7.4 + - - +
115E TRP* 3.0 18.8 + - - +
211E ILE* 4.4 15.1 - - + +
342E LEU* 4.2 31.0 - - + -
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Residues in contact with ALA 112 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108E LYS 3.2 15.1 + - - +
109E ASN* 4.5 2.0 - - - +
111E ALA* 1.3 74.4 - - - +
113E GLU* 1.3 58.8 + - - +
115E TRP* 2.3 55.8 + - + +
116E THR* 3.9 3.6 - - + -
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Residues in contact with GLU 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E ASN 3.6 7.5 - - - +
110E LEU 4.0 4.5 - - - +
111E ALA 3.4 0.2 - - - -
112E ALA* 1.3 78.7 - - - +
114E TRP* 1.3 60.4 + - - +
116E THR* 2.3 30.9 + - - +
117E SER* 3.6 7.1 + - - -
262E TRP* 3.6 29.9 + - + +
266E PHE* 4.5 4.8 - - + -
377E CYS* 3.3 24.4 - - - +
378E LEU* 3.3 30.2 - - + -
381E ILE* 5.6 5.5 - - - +
483E LYS* 4.9 8.2 - - - +
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Residues in contact with TRP 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E LEU 3.8 1.5 + - - +
111E ALA* 3.1 15.9 + - - +
112E ALA 3.1 0.6 - - - -
113E GLU* 1.3 78.6 - - - +
115E TRP* 1.3 62.8 + + - +
116E THR 3.1 1.7 + - - -
117E SER* 4.2 2.3 + - - -
118E VAL* 3.0 34.3 - - + +
209E ALA* 4.0 22.2 - - + -
210E GLN 4.5 0.2 - - - -
211E ILE* 3.3 33.9 - - + -
237E ALA* 4.1 9.0 - - + +
238E SER 2.4 44.2 - - - -
239E LEU* 4.1 4.5 - - + -
259E ARG* 2.5 39.9 - - - +
262E TRP* 3.4 38.0 - + + -
263E TRP* 4.3 4.2 - + - -
301E GLU* 4.0 1.7 + - - -
338E VAL* 4.3 8.3 - - + -
340E GLY* 5.5 0.4 - - - -
342E LEU* 4.5 11.7 - - + -
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Residues in contact with TRP 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E ALA 3.0 11.9 + - - +
112E ALA* 2.3 41.0 + - + +
114E TRP* 1.3 71.7 - + + +
116E THR* 1.3 67.3 + - + +
118E VAL* 4.6 0.9 - - - -
119E VAL* 3.3 25.4 - - + +
127E PRO* 3.2 41.3 - - + -
209E ALA* 3.0 26.5 - - + -
210E GLN* 3.3 19.5 - - + -
211E ILE* 3.7 27.8 - - + -
104F VAL* 4.7 9.9 - - + -
105F GLU* 4.5 9.8 + - - -
108F LYS* 3.5 32.7 - - + +
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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