Contacts of the helix formed by residues 117 - 137 (chain D) in PDB entry 4RZR
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 ASP 117 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ILE* 4.1 12.3 - - - +
115D VAL* 3.5 5.2 - - - +
116D ARG* 1.3 100.5 + - + +
118D TYR* 1.3 59.8 + - - +
119D ARG* 3.0 13.5 + - - +
120D GLU* 2.9 25.4 + - - +
121D ALA* 3.0 22.3 + - - +
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Residues in contact with TYR 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET 4.3 2.3 + - - -
2D ILE* 3.9 22.7 - - + -
117D ASP* 1.3 73.0 - - - +
119D ARG* 1.3 55.8 + - - +
120D GLU 3.4 0.2 - - - -
121D ALA* 3.4 3.6 - - - +
122D TYR* 2.8 33.1 + - - +
144D ILE* 3.7 16.8 - - + -
145D SER* 3.8 25.3 - - - -
146D LYS* 3.2 27.2 + - - +
165D VAL* 3.8 20.9 - - + +
166D ILE 4.3 3.4 + - - -
167D ASP* 3.7 29.4 - - + -
168D ASP* 3.2 26.9 + - - -
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Residues in contact with ARG 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ASP* 3.0 12.1 + - - +
118D TYR* 1.3 74.8 - - - +
120D GLU* 1.3 66.1 + - + +
122D TYR* 3.5 7.0 + - + +
123D ASN* 3.2 38.4 + - - +
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Residues in contact with GLU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D LYS 4.9 0.5 - - - +
115D VAL* 3.6 22.2 - - + +
116D ARG* 2.9 57.9 + - - +
117D ASP* 2.9 18.2 + - - +
119D ARG* 1.3 72.1 - - + +
121D ALA* 1.3 60.5 + - - +
123D ASN* 3.3 7.7 + - - +
124D LEU* 2.9 28.2 + - - +
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Residues in contact with ALA 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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2D ILE* 4.2 6.3 - - + -
4D LEU* 4.1 1.2 - - - +
111D ILE* 3.9 19.7 - - + -
115D VAL* 4.0 8.8 - - + +
117D ASP 3.0 15.3 + - - +
118D TYR* 3.4 12.1 - - - +
119D ARG 3.3 0.2 - - - -
120D GLU* 1.3 72.8 - - - +
122D TYR* 1.3 66.2 + - - +
124D LEU* 3.0 4.8 + - - +
125D GLY 2.8 20.1 + - - -
144D ILE* 3.6 31.6 - - + +
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Residues in contact with TYR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D TYR 2.8 21.1 + - - +
119D ARG* 3.6 8.3 - - - +
121D ALA* 1.3 71.2 - - - +
123D ASN* 1.3 63.9 + - - +
125D GLY 3.1 2.6 + - - -
126D LEU* 3.0 52.5 + - + +
144D ILE* 3.8 8.7 - - - +
163D ILE* 3.4 46.0 + - + +
164D LYS* 5.1 1.8 - - - -
165D VAL* 3.9 21.5 - - + -
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Residues in contact with ASN 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 ARG* 3.2 27.9 + - - +
120D GLU* 3.3 10.5 + - - +
121D ALA 3.2 0.2 - - - -
122D TYR* 1.3 80.1 - - - +
124D LEU* 1.3 61.0 + - - +
126D LEU* 3.3 21.4 + - - +
127D GLU* 2.9 35.7 + - - +
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Residues in contact with LEU 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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4D LEU* 4.6 0.7 - - + -
95D TYR* 3.9 28.0 - - + +
111D ILE* 4.0 35.7 - - + -
114D LYS* 5.2 3.8 - - + -
115D VAL* 4.2 14.8 - - + -
120D GLU 2.9 13.9 + - - +
121D ALA* 3.5 9.9 - - - +
123D ASN* 1.3 75.0 - - - +
125D GLY* 1.3 56.4 + - - +
127D GLU* 3.1 24.4 + - - +
128D ILE* 2.8 48.5 + - + +
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Residues in contact with GLY 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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4D LEU* 3.9 16.5 - - - +
121D ALA 2.8 13.8 + - - -
122D TYR 3.1 5.3 + - - -
124D LEU* 1.3 76.5 - - - +
126D LEU* 1.3 55.0 + - - +
128D ILE* 3.2 6.2 + - - +
129D LYS* 2.9 32.2 + - - +
142D VAL* 4.1 6.6 - - - +
163D ILE* 3.8 15.7 - - - -
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Residues in contact with LEU 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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122D TYR* 3.0 44.9 + - + +
123D ASN* 3.6 20.6 - - - +
124D LEU 3.3 0.2 - - - -
125D GLY* 1.3 71.7 - - - +
127D GLU* 1.3 66.2 + - + +
129D LYS* 3.3 13.4 + - - +
130D ASN* 3.0 32.1 + - - +
163D ILE* 4.1 19.3 - - + -
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Residues in contact with GLU 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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95D TYR* 4.1 15.0 + - + +
123D ASN* 2.9 22.8 + - - +
124D LEU* 3.1 27.2 + - - +
126D LEU* 1.3 75.6 - - + +
128D ILE* 1.3 64.4 + - - +
130D ASN* 3.4 6.0 + - - +
131D LYS* 2.9 24.4 + - - +
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Residues in contact with ILE 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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4D LEU* 3.9 31.9 - - + -
6D VAL* 4.4 10.3 - - + -
92D LEU* 3.6 24.9 - - + -
95D TYR* 3.8 40.4 - - + -
109D LEU* 4.2 13.9 - - + -
124D LEU* 2.8 28.9 + - + +
125D GLY* 3.5 7.2 - - - +
127D GLU* 1.3 73.2 - - - +
129D LYS* 1.3 61.7 + - - +
131D LYS* 3.3 2.5 + - - +
132D ILE* 3.1 34.1 + - + +
140D VAL* 5.3 0.4 - - + -
142D VAL* 5.1 4.5 - - + -
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Residues in contact with LYS 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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125D GLY 2.9 21.9 + - - +
126D LEU* 3.7 13.9 - - - +
128D ILE* 1.3 76.4 - - - +
130D ASN* 1.3 65.8 + - - +
132D ILE* 3.3 2.4 + - - +
133D LEU* 2.9 24.6 + - - +
138D ILE 4.7 1.4 - - - +
139D THR* 5.8 0.4 - - - +
140D VAL* 3.0 38.8 + - + +
142D VAL* 3.7 25.1 - - + -
161D ASN* 3.1 27.3 + - - -
162D GLY 3.5 18.6 + - - +
163D ILE* 4.2 15.9 - - + -
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Residues in contact with ASN 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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126D LEU* 3.0 23.3 + - - +
127D GLU* 3.6 6.5 - - - +
129D LYS* 1.3 77.8 - - - +
131D LYS* 1.3 57.0 + - - +
133D LEU* 3.2 11.4 + - - +
134D GLU* 2.8 33.0 + - - +
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Residues in contact with LYS 131 (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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91D LEU* 4.1 23.6 - - + -
94D GLU* 5.2 4.7 - - - -
95D TYR* 3.5 33.9 - - + +
127D GLU 2.9 12.9 + - - +
128D ILE* 3.3 4.7 + - - +
130D ASN* 1.3 76.1 - - - +
132D ILE* 1.3 58.1 + - + +
134D GLU* 3.3 23.0 + - - +
135D LYS* 3.0 59.8 + - + +
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Residues in contact with ILE 132 (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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6D VAL* 4.5 4.0 - - + -
88D ILE* 3.8 39.0 - - + -
91D LEU* 4.4 17.7 - - + -
92D LEU* 4.1 10.5 - - + -
128D ILE* 3.1 34.8 + - + +
129D LYS* 3.9 3.4 - - - +
131D LYS* 1.3 75.8 - - + +
133D LEU* 1.3 57.5 + - - +
136D GLU* 2.8 26.7 + - + -
137D LYS 3.3 3.5 + - - -
138D ILE* 3.4 26.0 + - + +
140D VAL* 4.0 27.6 - - + -
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Residues in contact with LEU 133 (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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129D LYS 2.9 17.8 + - - +
130D ASN* 3.7 10.3 - - - +
132D ILE* 1.3 76.2 - - - +
134D GLU* 1.3 60.1 + - - +
137D LYS* 2.8 55.8 + - + +
138D ILE 3.6 7.3 + - - +
139D THR* 4.1 25.4 - - + -
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Residues in contact with GLU 134 (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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130D ASN 2.8 21.5 + - - +
131D LYS* 3.6 29.6 + - - +
133D LEU* 1.3 75.2 - - - +
135D LYS* 1.3 72.4 + - + +
137D LYS* 3.4 19.3 + - - +
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Residues in contact with LYS 135 (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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91D LEU* 3.9 26.2 - - + -
131D LYS* 3.0 45.6 + - + +
134D GLU* 1.3 96.6 - - + +
136D GLU* 1.3 73.1 + - + +
137D LYS* 5.0 3.2 + - - -
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Residues in contact with GLU 136 (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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18D VAL* 4.0 11.6 - - - +
84D VAL* 3.9 11.6 - - + +
87D ARG* 2.6 58.7 + - + +
88D ILE* 3.9 24.0 - - + -
91D LEU* 4.7 6.5 - - + +
132D ILE 2.8 11.3 + - - +
135D LYS* 1.3 90.6 - - + +
137D LYS* 1.3 75.8 + - - +
138D ILE* 3.2 20.6 + - + +
405D GOL 4.6 1.0 + - - -
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Residues in contact with LYS 137 (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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14D GLN* 3.9 6.2 - - - +
18D VAL* 3.5 30.0 - - + +
132D ILE 3.3 0.2 + - - -
133D LEU* 2.8 42.9 + - + +
134D GLU* 3.4 18.9 + - - +
135D LYS 5.0 3.6 + - - -
136D GLU* 1.3 79.2 - - - +
138D ILE* 1.3 59.5 + - - +
139D THR* 5.4 0.2 - - - +
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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
------------------------------------------------------------
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