Contacts of the helix formed by residues 104 - 118 (chain D) in PDB entry 4RB3
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 SER 104 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C LEU* 5.2 1.7 - - - +
114C ILE* 3.8 24.5 - - - +
89D ASP* 5.0 4.2 + - - -
102D PHE* 4.7 4.0 - - - -
103D THR* 1.3 80.3 - - - +
105D PRO* 1.3 69.9 - - - +
106D GLU* 3.2 14.2 + - - +
107D ILE* 2.9 36.1 + - - +
108D GLU* 3.1 18.1 + - - +
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Residues in contact with PRO 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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103D THR* 4.2 8.1 - - - +
104D SER* 1.3 84.5 - - - +
106D GLU* 1.3 64.2 + - - +
108D GLU* 3.1 9.8 + - + +
109D ALA* 2.8 33.5 + - - +
112D ARG* 5.1 0.5 + - - -
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Residues in contact with GLU 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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110C LEU* 3.7 29.8 - - + +
104D SER* 3.3 18.4 + - - -
105D PRO* 1.3 82.9 - - + +
107D ILE* 1.3 57.5 + - - +
109D ALA* 3.8 5.1 - - - +
110D LEU* 2.9 36.8 + - + +
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Residues in contact with ILE 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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107C ILE* 4.6 16.2 - - + +
110C LEU* 3.8 25.4 - - + -
111C GLN* 4.1 21.1 - - + -
114C ILE* 3.8 26.0 - - + -
127C LEU* 5.8 0.7 - - + -
89D ASP* 5.7 0.4 - - - +
102D PHE* 5.1 0.4 - - + -
104D SER* 2.9 19.1 + - - +
106D GLU* 1.3 73.8 - - - +
108D GLU* 1.3 64.7 + - - +
110D LEU* 3.1 6.7 + - - +
111D GLN* 2.8 51.6 + - + +
127D LEU* 4.2 21.5 - - + -
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Residues in contact with GLU 108 (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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87D HIS* 2.9 15.4 + - + -
89D ASP* 3.4 3.5 - - - +
104D SER 3.1 21.2 + - - +
105D PRO* 3.6 9.6 - - + +
107D ILE* 1.3 77.8 - - - +
109D ALA* 1.3 63.0 + - - +
111D GLN* 2.8 30.2 + - - +
112D ARG* 3.2 43.1 + - - +
122D LEU* 5.3 1.7 - - - +
125D HIS* 3.1 10.6 + - - -
201D MN 2.0 36.9 + - - -
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Residues in contact with ALA 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 PRO 2.8 20.5 + - - +
106D GLU* 3.8 6.3 - - - +
108D GLU* 1.3 72.2 - - - +
110D LEU* 1.3 62.2 + - + +
112D ARG* 3.3 27.8 + - - +
113D GLU* 3.2 21.6 + - - +
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Residues in contact with LEU 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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104C SER* 4.8 5.8 - - - +
106C GLU* 3.9 31.6 - - + -
107C ILE* 3.9 18.4 - - + -
110C LEU* 3.5 27.1 - - + -
106D GLU* 2.9 23.0 + - + +
107D ILE* 3.1 4.2 + - - +
109D ALA* 1.3 72.8 - - + +
111D GLN* 1.3 60.0 + - - +
113D GLU* 3.4 29.9 + - - +
114D ILE* 2.9 37.9 + - + +
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Residues in contact with GLN 111 (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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107C ILE* 4.5 10.5 - - + -
127C LEU* 3.4 19.3 - - + +
129C LEU* 3.7 30.4 - - + +
107D ILE* 2.8 39.6 + - + +
108D GLU* 2.8 35.1 + - - +
110D LEU* 1.3 71.4 - - - +
112D ARG* 1.3 63.8 + - - +
114D ILE* 3.3 4.8 + - - -
115D ALA* 3.1 22.0 + - - +
122D LEU* 4.0 9.7 - - + +
125D HIS* 3.2 34.7 + - - -
127D LEU* 4.5 2.3 - - - +
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Residues in contact with ARG 112 (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 PRO 5.1 0.8 + - - -
108D GLU* 3.2 30.4 + - - +
109D ALA* 3.4 29.9 + - - +
111D GLN* 1.3 78.9 - - - +
113D GLU* 1.3 56.7 + - - +
115D ALA* 3.2 7.0 + - - +
116D ARG* 2.9 30.1 + - - +
120D PHE 5.0 0.2 - - - +
122D LEU* 4.1 24.7 - - + +
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Residues in contact with GLU 113 (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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106C GLU* 6.2 0.3 - - - -
109D ALA 3.2 9.9 + - - +
110D LEU* 3.5 32.0 - - - +
111D GLN 3.3 0.2 - - - -
112D ARG* 1.3 77.4 - - - +
114D ILE* 1.3 65.4 + - - +
116D ARG* 3.4 6.0 + - - +
117D LYS* 2.8 37.0 + - + +
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Residues in contact with ILE 114 (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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91C LEU* 4.9 2.2 - - + -
102C PHE* 3.9 33.2 - - + -
103C THR 4.9 3.1 - - - +
104C SER* 3.7 33.0 - - - +
107C ILE* 3.8 14.1 - - + -
129C LEU* 4.0 13.9 - - + -
110D LEU* 2.9 33.3 + - + +
111D GLN* 3.3 6.3 + - - +
113D GLU* 1.3 84.8 - - - +
115D ALA* 1.3 62.2 + - - +
117D LYS* 3.2 10.8 + - + +
118D HIS* 2.8 39.9 + - + +
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Residues in contact with ALA 115 (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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91C LEU* 4.3 18.8 - - + -
129C LEU* 4.6 1.1 - - + +
111D GLN 3.1 13.3 + - - +
112D ARG 3.2 8.5 + - - +
114D ILE* 1.3 76.2 - - - +
116D ARG* 1.3 61.7 + - - +
118D HIS* 3.0 12.3 + - - +
119D GLY 3.4 0.2 + - - -
120D PHE* 3.0 35.0 + - + +
122D LEU* 4.2 30.3 - - + +
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Residues in contact with ARG 116 (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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134C LEU* 4.5 10.9 - - + +
112D ARG 2.9 16.9 + - - +
113D GLU* 3.8 7.2 - - - +
115D ALA* 1.3 70.2 - - - +
117D LYS* 1.3 55.1 + - - +
118D HIS 2.8 15.2 + - - -
119D GLY* 2.9 13.3 + - - -
120D PHE 3.3 13.8 + - - +
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Residues in contact with LYS 117 (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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113D GLU* 2.8 28.4 + - + +
114D ILE* 3.3 14.1 - - + +
116D ARG* 1.3 71.6 - - - +
118D HIS* 1.3 69.3 + - + +
119D GLY 3.6 0.2 - - - -
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Residues in contact with HIS 118 (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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91C LEU* 3.9 18.9 - - + +
100C ILE* 3.7 29.2 - - + +
101C GLU 4.6 2.4 + - - -
102C PHE* 4.1 17.9 - - + +
114D ILE* 2.8 38.1 + - + +
115D ALA 3.0 8.3 + - - +
116D ARG 2.9 1.4 - - - -
117D LYS* 1.3 90.6 + - + +
119D GLY* 1.3 58.0 + - - +
120D PHE* 3.3 18.4 - - + -
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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
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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