Contacts of the helix formed by residues 115 - 130 (chain D) in PDB entry 4KZX
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 VAL 115 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D LEU* 4.9 8.5 - - + -
114D ALA* 1.3 78.8 - - - +
116D ARG* 1.3 71.8 + - + +
117D ARG 3.3 0.4 - - - -
118D ALA* 3.4 2.5 + - - +
119D CYS* 3.1 30.9 + - - -
138D VAL* 5.3 9.4 - - + -
142D LEU* 3.9 28.9 - - + -
150D MET* 5.4 5.8 - - + -
152D PHE* 4.2 21.5 - - + -
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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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109C PHE* 4.0 23.0 - - - -
130C LYS 4.8 0.2 + - - -
131C GLU* 3.3 44.2 + - - +
132C VAL* 4.2 13.2 - - - +
133C ALA* 4.9 3.6 - - - +
114D ALA* 4.5 1.4 - - + +
115D VAL* 1.3 80.3 - - + +
117D ARG* 1.3 60.3 + - - +
119D CYS* 4.8 2.9 - - - -
120D TYR* 2.9 66.3 + - + +
150D MET* 5.9 6.9 - - - +
152D PHE* 4.3 21.4 - - + -
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Residues in contact with ARG 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D LYS* 5.2 0.3 - - - -
112D GLY 5.1 0.6 + - - -
113D LEU* 4.3 35.6 - - - +
114D ALA* 4.2 18.6 - - + +
115D VAL 3.3 1.0 - - - +
116D ARG* 1.3 79.4 - - - +
118D ALA* 1.3 64.9 + - - +
120D TYR* 4.1 2.4 - - - +
121D GLY* 2.9 22.2 + - - -
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Residues in contact with ALA 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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105D LEU* 3.7 24.0 - - + -
108D LYS* 3.8 28.6 - - + +
109D LEU* 4.2 2.7 - - + -
113D LEU* 5.0 4.3 - - + -
114D ALA 3.7 18.4 + - - +
115D VAL 3.4 4.0 + - - +
116D ARG 3.3 0.4 - - - -
117D ARG* 1.3 82.3 - - - +
119D CYS* 1.4 63.0 + - - +
121D GLY* 3.3 0.7 + - - -
122D VAL* 3.0 28.7 + - - +
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Residues in contact with CYS 119 (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 LEU* 4.8 11.0 - - - -
109D LEU* 6.3 0.4 - - - -
115D VAL* 3.1 24.7 + - - +
116D ARG 4.2 1.1 - - - +
118D ALA* 1.4 78.3 - - - +
120D TYR* 1.3 63.6 + - - +
122D VAL* 3.0 9.1 + - - +
123D LEU* 2.9 23.4 + - - +
136D VAL* 4.7 12.8 - - + +
138D VAL* 4.0 18.2 - - - -
152D PHE* 3.1 54.5 - - + +
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Residues in contact with TYR 120 (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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131C GLU* 3.5 27.4 + - + +
133C ALA* 5.1 11.4 - - + +
116D ARG* 2.9 58.0 + - + +
117D ARG* 4.1 2.7 - - - +
119D CYS* 1.3 78.6 - - - +
121D GLY* 1.3 58.0 + - - +
123D LEU* 3.5 25.1 - - + +
124D ARG* 2.8 31.2 + - + +
152D PHE* 5.3 11.7 - + - -
153D VAL 6.0 0.2 - - - -
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Residues in contact with GLY 121 (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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108D LYS* 5.4 6.3 - - - -
117D ARG 2.9 18.5 + - - -
118D ALA 3.7 1.3 - - - -
120D TYR* 1.3 75.2 - - - +
122D VAL* 1.3 64.6 + - - +
124D ARG* 3.2 7.5 + - - +
125D PHE* 2.9 24.3 + - - +
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Residues in contact with VAL 122 (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 GLN* 3.6 44.0 - - + +
104D SER* 5.0 3.6 - - - -
105D LEU* 5.2 7.6 - - + +
108D LYS* 4.0 24.4 - - + +
118D ALA 3.0 17.2 + - - +
119D CYS* 3.5 7.4 - - - +
121D GLY* 1.3 74.2 - - - +
123D LEU* 1.3 57.5 + - - +
125D PHE* 3.2 6.6 + - - +
126D ILE* 2.9 37.3 + - + +
136D VAL* 4.8 13.9 - - + -
186D VAL* 6.3 0.4 - - + -
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Residues in contact with LEU 123 (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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119D CYS 2.9 15.5 + - - +
120D TYR* 3.5 27.4 - - + +
122D VAL* 1.3 77.3 - - - +
124D ARG* 1.3 61.4 + - - +
126D ILE* 2.8 28.8 - - - +
127D MET 2.9 11.6 + - - -
134D CYS* 3.6 12.1 - - - -
136D VAL* 5.7 2.9 - - + +
152D PHE* 4.3 11.0 - - + +
153D VAL* 3.4 23.6 - - - +
154D ASP* 2.5 54.7 - - + +
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Residues in contact with ARG 124 (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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120D TYR* 2.8 18.8 + - + +
121D GLY* 3.2 7.2 + - - +
123D LEU* 1.3 82.1 - - - +
125D PHE* 1.3 58.8 + - - +
127D MET* 3.4 5.9 + - - +
128D GLU* 2.5 68.1 + - + +
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Residues in contact with PHE 125 (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 ARG* 3.6 48.0 - - + -
95D GLY* 4.3 8.1 - - - -
101D GLN* 4.2 15.0 - - - +
121D GLY 2.9 16.1 + - - +
122D VAL* 3.5 7.2 - - - +
124D ARG* 1.3 78.6 - - - +
126D ILE* 1.3 68.3 + - + +
128D GLU* 3.2 11.2 + - + +
129D SER* 3.0 23.9 + - - -
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Residues in contact with ILE 126 (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 GLY 3.7 21.9 - - - +
101D GLN* 3.7 28.0 - - + +
122D VAL* 2.9 23.0 + - + +
123D LEU* 2.8 28.9 - - - +
125D PHE* 1.3 78.6 - - + +
127D MET* 1.3 61.9 + - - +
129D SER* 3.0 22.3 + - - -
130D GLY 3.6 2.3 + - - -
131D ALA* 3.7 15.1 + - + +
134D CYS* 2.5 49.4 - - + -
136D VAL* 5.2 6.1 - - + -
186D VAL* 5.9 2.5 - - + -
188D ILE* 5.1 7.0 - - + -
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Residues in contact with MET 127 (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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123D LEU* 2.9 14.1 + - + +
124D ARG* 3.7 8.5 - - - +
126D ILE* 1.3 77.0 - - - +
128D GLU* 1.3 61.2 + - - +
130D GLY* 2.8 21.1 + - - -
131D ALA* 3.9 24.2 - - - +
132D LYS 5.4 1.8 - - - +
133D GLY* 5.6 2.0 - - - -
134D CYS* 5.9 0.9 - - - -
154D ASP* 2.8 33.4 - - - +
155D GLY* 5.3 9.0 - - - -
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Residues in contact with GLU 128 (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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124D ARG* 2.5 66.8 + - + +
125D PHE* 3.4 14.8 - - + +
126D ILE 3.2 0.2 - - - -
127D MET* 1.3 74.1 - - - +
129D SER* 1.3 64.6 + - - +
130D GLY* 2.8 7.1 + - - -
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Residues in contact with SER 129 (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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93D THR* 3.4 22.2 + - - -
95D GLY* 3.9 12.2 - - - -
96D LEU* 4.5 16.9 - - - +
125D PHE* 3.0 18.6 + - - -
126D ILE* 3.0 17.4 + - - -
128D GLU* 1.3 76.6 - - - +
130D GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 130 (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 LEU* 5.0 4.2 - - - +
127D MET* 2.8 15.5 + - - -
128D GLU 2.8 6.9 - - - -
129D SER* 1.3 82.6 - - - +
131D ALA* 1.3 62.5 + - - +
191D PRO* 4.2 5.4 - - - +
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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