Contacts of the helix formed by residues 125 - 146 (chain D) in PDB entry 1R5I
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 ASN 125 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D LEU* 3.9 16.7 - - + +
70D LEU* 5.4 4.0 - - - +
71D GLU* 4.7 8.5 + - - +
121D PHE 3.3 13.8 + - - +
122D ILE 3.0 13.4 + - - +
123D SER 3.3 0.2 - - - -
124D GLN* 1.3 79.1 - - - +
126D LYS* 1.3 62.8 + - - +
127D ASN* 3.3 11.1 + - - +
128D PHE* 3.0 38.2 + - + +
129D GLN* 3.3 8.8 + - - +
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Residues in contact with LYS 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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123D SER 4.6 1.2 + - - +
124D GLN 3.7 4.6 + - - -
125D ASN* 1.3 71.6 + - - +
127D ASN* 1.3 86.9 + - - +
129D GLN* 3.1 18.9 + - + +
130D GLU* 3.1 53.8 + - + +
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Residues in contact with ASN 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D ASN* 3.2 8.4 + - - +
126D LYS* 1.3 102.1 + - - +
128D PHE* 1.3 63.4 + - - +
130D GLU* 3.2 9.9 + - - +
131D LEU* 3.0 40.9 + - - +
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Residues in contact with PHE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 4.7 2.9 - - + -
66D TYR* 4.0 28.0 - + - -
68D GLY* 3.5 34.1 - - - -
69D LEU* 3.7 21.5 - - + -
122D ILE* 4.3 21.5 - - + -
125D ASN* 3.0 34.0 + - + +
127D ASN* 1.3 78.5 - - - +
129D GLN* 1.3 60.5 + - - +
131D LEU* 3.2 4.5 + - - +
132D TRP* 2.8 57.6 + + + +
178D TRP* 3.6 27.8 - + - -
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Residues in contact with GLN 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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0D SER* 3.1 23.4 + - - +
1D MET* 3.1 32.8 + - + +
3D LEU* 5.8 2.1 - - - +
122D ILE* 2.8 45.8 + - + +
123D SER* 3.5 21.3 + - - +
125D ASN 3.3 5.2 + - - +
126D LYS* 3.1 16.3 + - + +
128D PHE* 1.3 77.5 - - - +
130D GLU* 1.3 62.7 + - + +
133D ASP* 2.9 28.9 + - - +
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Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D LYS* 3.1 48.6 + - + +
127D ASN* 3.2 12.4 + - - +
129D GLN* 1.3 78.0 - - + +
131D LEU* 1.3 63.3 + - + +
133D ASP* 3.4 7.2 + - - +
134D LYS* 2.9 23.6 + - - +
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Residues in contact with LEU 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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127D ASN* 3.0 34.6 + - - +
128D PHE* 3.8 5.4 - - + +
130D GLU* 1.3 78.1 - - + +
132D TRP* 1.3 62.4 + - - +
134D LYS* 3.1 6.3 + - + +
135D ALA* 2.9 18.2 + - - +
172D ASN* 3.2 35.2 - - - +
176D LEU* 3.4 24.9 - - + -
178D TRP* 3.5 26.5 - - + +
179D PHE* 3.3 19.7 - - + -
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Residues in contact with TRP 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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1D MET* 3.0 51.4 - - + -
2D LYS* 5.5 3.8 - - + -
65D ASP* 3.3 20.1 + - - -
66D TYR* 4.0 19.5 - + - -
128D PHE* 2.8 40.1 + + + +
131D LEU* 1.3 71.3 - - - +
133D ASP* 1.3 67.0 + - - +
135D ALA* 2.9 18.0 + - - +
136D VAL* 3.1 21.9 + - + +
178D TRP* 4.0 5.5 - + - -
182D LEU* 3.9 20.2 - - + +
205D ASP* 3.8 23.3 - - + -
206D PHE* 3.7 34.6 - + + +
209D ALA* 3.9 18.8 - - + -
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Residues in contact with ASP 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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0D SER* 3.7 33.9 + - - +
1D MET* 3.8 17.4 - - - +
129D GLN* 2.9 23.8 + - - +
130D GLU* 3.7 6.9 - - - +
132D TRP* 1.3 80.2 - - - +
134D LYS* 1.3 58.8 + - - +
136D VAL* 3.0 11.1 + - - +
137D LYS* 2.8 27.0 + - - +
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Residues in contact with LYS 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 GLU 2.9 14.7 + - - +
131D LEU* 3.1 12.3 + - + +
133D ASP* 1.3 77.4 - - - +
135D ALA* 1.3 63.4 + - - +
137D LYS* 3.0 13.8 + - + +
138D LEU* 3.0 39.6 + - + +
170D ASP* 2.7 35.0 + - - -
171D LYS* 5.4 8.1 - - - +
172D ASN* 3.1 28.1 + - - +
179D PHE* 3.7 13.7 - - + -
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Residues in contact with ALA 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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131D LEU 2.9 12.4 + - - +
132D TRP* 2.9 10.1 + - - +
134D LYS* 1.3 75.9 - - - +
136D VAL* 1.3 62.6 + - - +
138D LEU* 3.6 0.4 + - - -
139D THR* 3.0 28.9 + - - -
179D PHE* 3.7 19.9 - - + -
182D LEU* 3.6 29.8 - - + -
183D LEU* 3.4 17.5 - - + +
206D PHE* 4.2 4.9 - - + -
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Residues in contact with VAL 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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132D TRP* 3.1 31.5 + - + +
133D ASP* 3.0 9.7 + - - +
135D ALA* 1.3 74.8 - - - +
137D LYS* 1.3 67.3 + - - +
139D THR* 3.1 4.9 + - - -
140D LYS* 3.0 53.1 + - - +
206D PHE* 3.8 25.8 - - + -
209D ALA* 3.8 20.4 - - + +
210D VAL* 4.0 9.0 - - + -
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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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133D ASP 2.8 12.4 + - - +
134D LYS* 3.3 16.2 - - + +
136D VAL* 1.3 79.5 - - - +
138D LEU* 1.3 70.9 + - + +
140D LYS* 3.2 9.1 + - - +
141D GLU* 3.1 46.9 + - + +
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Residues in contact with LEU 138 (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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134D LYS* 3.0 45.0 + - + +
135D ALA 4.1 3.1 - - - +
137D LYS* 1.3 84.0 - - + +
139D THR* 1.3 61.3 + - - +
141D GLU* 3.1 27.8 + - - +
142D MET* 2.9 29.0 + - - +
167D PHE* 3.5 42.3 - - + -
170D ASP* 4.5 8.3 - - - +
179D PHE* 4.5 15.0 - - + -
183D LEU* 4.5 9.4 - - + -
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Residues in contact with THR 139 (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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135D ALA 3.0 19.9 + - - -
136D VAL 3.1 5.7 + - - -
138D LEU* 1.3 76.0 - - - +
140D LYS* 1.3 57.3 + - - +
142D MET* 3.3 13.3 + - + +
143D LYS* 2.9 25.1 + - - +
182D LEU 4.4 0.2 + - - -
183D LEU* 3.6 17.3 - - - +
186D GLY* 4.2 20.4 - - - +
189D LEU* 6.2 0.9 - - + -
190D ILE* 3.6 10.1 - - + +
206D PHE* 3.6 12.8 - - + -
210D VAL* 3.6 35.9 - - + -
211D PHE* 5.9 0.2 - - + -
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Residues in contact with LYS 140 (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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136D VAL* 3.0 31.6 + - + +
137D LYS* 3.4 9.4 - - - +
139D THR* 1.3 75.0 - - - +
141D GLU* 1.3 65.6 + - + +
143D LYS* 2.9 30.4 + - + +
144D ILE* 3.3 11.2 + - - +
209D ALA 3.4 19.5 + - - -
210D VAL* 3.2 31.6 + - + +
212D GLU 3.7 5.1 + - - -
213D ASP* 3.5 28.2 + - - +
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Residues in contact with GLU 141 (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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137D LYS* 3.1 39.0 + - - +
138D LEU* 3.1 28.9 + - - +
140D LYS* 1.3 76.3 - - - +
142D MET* 1.3 57.4 + - - +
144D ILE* 3.1 13.7 + - - +
145D LYS* 2.9 44.2 + - + +
167D PHE* 3.9 17.4 - - + -
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Residues in contact with MET 142 (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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138D LEU 2.9 11.0 + - - +
139D THR* 3.3 24.0 - - + +
141D GLU* 1.3 74.7 - - - +
143D LYS* 1.3 65.6 + - - +
145D LYS* 3.8 9.6 - - - -
146D LEU* 3.1 44.6 + - + +
162D LYS 5.6 0.2 - - - -
163D VAL* 4.6 9.0 - - - -
166D LEU* 3.8 21.1 - - + -
167D PHE* 4.1 15.7 - - + -
183D LEU* 3.1 39.5 - - + +
186D GLY 4.3 3.4 - - - -
187D VAL* 3.5 25.8 - - + +
190D ILE* 4.3 4.8 - - + +
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Residues in contact with LYS 143 (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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139D THR 2.9 11.7 + - - +
140D LYS* 2.9 23.2 - - + +
142D MET* 1.3 76.6 - - - +
144D ILE* 1.3 55.8 + - + +
147D LYS 4.1 0.3 + - - -
190D ILE* 3.4 24.7 - - + -
193D TYR* 4.2 24.3 + - + -
194D TYR* 2.5 29.6 + - + -
210D VAL* 3.9 17.9 + - + +
211D PHE* 3.7 41.0 + - + +
213D ASP* 4.3 10.9 + - - -
47H LEU* 5.4 9.9 - - + +
50H LEU* 3.9 21.7 - - + +
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Residues in contact with ILE 144 (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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140D LYS 3.3 10.7 + - - +
141D GLU* 3.1 10.4 + - - +
143D LYS* 1.3 76.0 - - + +
145D LYS* 1.3 60.5 + - + +
146D LEU 3.1 1.6 - - - -
147D LYS* 2.7 41.2 + - + +
43H GLU* 4.2 8.1 - - - +
46H LYS* 3.6 48.7 - - + +
47H LEU* 4.5 11.7 - - + -
50H LEU* 4.1 20.6 - - + -
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Residues in contact with LYS 145 (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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141D GLU* 2.9 45.5 + - - +
142D MET* 4.0 7.2 - - - +
144D ILE* 1.3 76.2 - - + +
146D LEU* 1.3 60.4 + - + +
147D LYS* 3.3 3.5 + - - +
148D GLY 5.1 0.2 + - - -
149D GLN* 4.1 12.5 - - - +
166D LEU* 3.8 35.1 + - + +
167D PHE* 4.3 12.5 - - - -
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Residues in contact with LEU 146 (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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142D MET* 3.1 36.6 + - + +
144D ILE 3.0 0.2 + - - -
145D LYS* 1.3 77.1 - - + +
147D LYS* 1.3 62.4 + - - +
148D GLY 3.2 3.3 + - - -
149D GLN* 3.3 37.5 + - + +
151D LEU* 4.2 24.2 - - + +
162D LYS* 4.3 17.0 - - + -
166D LEU* 4.0 22.7 - - + -
187D VAL* 4.3 18.6 - - + -
190D ILE* 4.8 5.6 - - + -
194D TYR* 2.9 26.2 + - + +
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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
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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