Contacts of the helix formed by residues 96 - 110 (chain D) 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 96 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D PRO* 1.3 75.7 - - - +
97D GLU* 1.3 71.8 + - - +
98D ALA 3.5 1.9 + - - -
99D ALA 3.7 0.2 + - - -
100D VAL* 3.0 29.6 + - - +
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Residues in contact with GLU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D GLY* 1.3 69.4 - - - +
98D ALA* 1.3 52.4 + - - +
100D VAL* 4.7 2.2 - - - -
101D ARG* 2.5 77.1 + - - +
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Residues in contact with ALA 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D PRO* 6.0 2.0 - - + -
96D GLY 3.5 0.8 + - - -
97D GLU* 1.3 74.1 - - - +
99D ALA* 1.3 54.5 + - - +
101D ARG* 2.9 14.1 - - - +
102D ARG* 2.5 52.8 + - + +
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Residues in contact with ALA 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D MET* 5.9 3.1 - - + -
95D PRO* 2.9 41.3 - - + +
96D GLY 3.7 1.2 + - - -
97D GLU 3.5 1.0 - - - -
98D ALA* 1.3 74.1 - - - +
100D VAL* 1.3 74.0 + - - +
101D ARG 2.9 0.7 + - - -
102D ARG* 3.1 23.8 + - - +
103D SER* 3.2 13.2 + - - -
908D ALA* 3.8 21.3 - - + +
909D GLY* 4.9 3.6 - - - +
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Residues in contact with VAL 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ASP* 5.4 11.2 - - - +
94D MET* 5.6 10.7 - - + +
95D PRO 3.5 12.6 - - - +
96D GLY* 3.0 26.1 + - - +
97D GLU* 3.6 2.7 - - - +
99D ALA* 1.3 77.7 - - - +
101D ARG* 1.3 61.7 + - + +
103D SER* 2.2 30.4 + - - +
104D VAL* 2.9 24.0 + - + +
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Residues in contact with ARG 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D GLU* 2.5 79.5 + - - +
98D ALA* 2.9 14.3 - - - +
99D ALA 2.9 0.2 + - - -
100D VAL* 1.3 74.6 - - + +
102D ARG* 1.3 69.6 + - - +
104D VAL* 3.2 9.7 + - + -
105D GLU* 2.6 42.0 + - - +
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Residues in contact with ARG 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ALA* 2.5 35.7 + - - +
99D ALA* 3.1 16.3 + - - +
101D ARG* 1.3 74.1 - - - +
103D SER* 1.3 65.8 + - - +
105D GLU* 2.9 15.6 + - - +
106D HIS* 2.9 32.2 - - + +
907D PHE* 6.0 1.3 - - - -
908D ALA* 4.2 19.0 - - + +
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Residues in contact with SER 103 (chain D).
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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99D ALA 3.2 6.2 + - - -
100D VAL* 2.2 32.0 + - - +
102D ARG* 1.3 79.7 - - - +
104D VAL* 1.3 66.7 + - - +
106D HIS* 3.2 3.9 + - - +
107D LEU* 3.2 29.2 + - - +
908D ALA* 4.3 3.4 - - - +
909D GLY* 4.4 20.0 - - - -
912D GLY* 4.0 22.7 - - - -
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Residues in contact with VAL 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D VAL* 2.9 25.0 + - + +
101D ARG* 3.6 13.0 - - + +
103D SER* 1.3 81.6 + - - +
105D GLU* 1.3 69.7 + - + +
107D LEU* 3.4 8.2 + - - +
108D GLN* 2.9 42.1 + - - +
113D TRP* 4.0 22.4 - - + +
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Residues in contact with GLU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ARG* 2.6 52.4 + - + +
102D ARG* 2.9 10.3 + - - +
104D VAL* 1.3 83.4 - - + +
106D HIS* 1.3 55.6 + - + +
108D GLN* 3.2 16.7 + - - +
109D LYS* 2.6 54.9 + - - +
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Residues in contact with HIS 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ARG* 2.9 38.8 + - + +
103D SER* 3.6 7.2 - - - +
105D GLU* 1.3 78.0 - - + +
107D LEU* 1.3 60.6 + - + +
108D GLN 3.0 1.3 - - - -
109D LYS* 2.8 14.8 + - + +
110D HIS* 2.6 50.7 + - + -
913D CYS* 4.9 8.1 - - + -
997D LEU* 4.3 24.0 - - + +
998D SER 5.8 0.4 + - - -
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Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D SER* 3.2 21.0 + - - +
104D VAL* 3.8 8.5 - - - +
106D HIS* 1.3 78.1 - - + +
108D GLN* 1.3 53.1 + - + +
110D HIS* 3.1 6.9 + - + +
111D GLY 2.7 28.6 + - - -
112D LEU* 3.0 31.0 + - + -
113D TRP* 4.7 9.6 - - + +
911D HIS* 6.1 3.1 - - + -
912D GLY 4.2 2.7 - - - +
913D CYS* 3.1 39.3 - - + +
917D GLY* 4.0 22.9 - - - -
920D THR* 5.9 0.4 - - - +
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Residues in contact with GLN 108 (chain D).
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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104D VAL* 2.9 30.2 + - - +
105D GLU* 3.2 19.2 - - - +
106D HIS 3.0 0.4 - - - -
107D LEU* 1.3 75.6 - - - +
109D LYS* 1.3 65.5 + - - +
111D GLY* 3.0 14.9 + - - +
113D TRP* 3.7 36.1 - - + +
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Residues in contact with LYS 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D GLU* 2.6 47.0 + - - +
106D HIS* 2.8 27.6 + - + +
108D GLN* 1.3 75.3 - - + +
110D HIS* 1.3 68.2 + - + +
111D GLY 3.7 0.5 + - - -
997D LEU* 5.8 2.9 - - + -
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Residues in contact with HIS 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D HIS* 2.6 43.4 + - + +
107D LEU* 3.2 5.6 - - + -
109D LYS* 1.3 83.4 + - + +
111D GLY* 1.3 62.2 + - - +
112D LEU* 3.0 23.9 - - + +
913D CYS* 5.5 4.5 - - + -
914D THR* 5.4 0.4 - - - -
988D ALA 5.7 0.7 - - - -
997D LEU* 3.7 24.6 - - + +
998D SER* 3.5 33.1 + - - -
999D ASP* 4.1 14.1 + - - +
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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