Contacts of the helix formed by residues 125 - 142 (chain D) in PDB entry 4ILW
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 PRO 125 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ASP 4.8 0.4 - - - +
124D LEU* 1.3 95.5 - - + +
126D ARG* 1.4 65.3 + - - +
127D ASP* 4.3 8.3 - - + +
128D ALA* 2.9 26.9 + - + +
129D VAL* 3.2 9.9 + - - +
204D GLU* 5.5 1.6 - - - +
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Residues in contact with ARG 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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119D ASN* 6.0 0.6 - - - +
120D TYR* 3.5 63.5 - - + +
124D LEU 3.5 2.2 + - - -
125D PRO* 1.4 70.9 - - - +
127D ASP* 1.3 61.7 + - - +
129D VAL 3.3 1.0 + - - -
130D ASP* 2.9 36.2 + - - +
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Residues in contact with ASP 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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125D PRO* 3.2 6.2 - - + +
126D ARG* 1.3 81.5 - - - +
128D ALA* 1.3 57.4 + - - +
130D ASP* 3.5 13.6 + - - +
131D SER* 3.1 27.7 + - - -
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Residues in contact with ALA 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D LEU* 4.4 7.6 - - + +
125D PRO* 2.9 31.4 + - + +
127D ASP* 1.3 76.7 - - - +
129D VAL* 1.3 65.7 + - - +
131D SER* 3.5 4.4 + - - -
132D ALA* 3.2 22.7 + - - +
204D GLU* 3.5 39.5 - - + +
211D LEU* 5.0 0.2 - - - +
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Residues in contact with VAL 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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117D ILE* 4.1 8.3 - - + -
120D TYR* 3.7 26.9 - - + -
121D THR* 3.9 28.5 - - + +
124D LEU* 4.1 10.3 - - + +
125D PRO 3.2 9.7 + - - +
126D ARG 3.6 6.7 - - - +
128D ALA* 1.3 75.8 - - - +
130D ASP* 1.3 67.4 - - - +
131D SER 3.1 1.0 + - - -
132D ALA* 3.1 11.6 + - - +
133D ILE* 3.1 34.0 + - + +
162D PHE* 4.2 10.1 - - + -
211D LEU* 4.0 16.4 - - + -
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Residues in contact with ASP 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ILE* 3.5 12.8 - - - +
120D TYR* 2.4 28.4 + - - -
126D ARG* 2.9 23.2 + - - +
127D ASP* 3.6 14.1 - - - +
128D ALA 3.4 0.2 - - - -
129D VAL* 1.3 74.1 - - - +
131D SER* 1.3 56.6 + - - +
133D ILE* 3.5 2.1 + - - +
134D GLU* 3.0 38.0 + - - +
150D ARG* 3.0 36.1 + - - +
152D TYR* 5.5 0.2 - - - -
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Residues in contact with SER 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 ASP 3.1 17.3 + - - -
128D ALA* 4.0 6.1 - - - -
129D VAL 3.2 0.4 - - - -
130D ASP* 1.3 74.5 - - - +
132D ALA* 1.3 60.7 + - - +
134D GLU* 3.5 10.8 + - - +
135D LYS* 2.9 51.5 + - - -
204D GLU* 5.5 2.9 + - - -
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Residues in contact with ALA 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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124D LEU* 6.3 0.4 - - + -
128D ALA 3.2 14.5 + - - +
129D VAL 3.1 4.6 + - - +
131D SER* 1.3 78.9 + - - +
133D ILE* 1.3 61.5 + - - +
135D LYS* 3.4 7.6 + - - +
136D ALA* 3.0 23.3 + - - +
204D GLU* 6.1 4.9 - - + +
211D LEU* 4.0 20.9 - - + -
212D PHE* 3.8 30.3 - - + +
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Residues in contact with ILE 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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115D TYR* 4.2 11.7 - - + -
117D ILE* 3.6 25.6 - - + -
129D VAL* 3.1 39.2 + - + +
130D ASP 3.9 2.5 - - - +
132D ALA* 1.3 74.3 - - - +
134D GLU* 1.3 59.4 + - - +
136D ALA* 3.0 7.5 + - - +
137D LEU* 2.9 36.0 + - + +
160D ILE* 3.8 39.7 - - + -
162D PHE* 5.3 1.3 - - + -
196D PHE* 4.7 4.5 - - + -
211D LEU* 4.5 9.9 - - + -
215D ALA* 4.4 16.8 - - + -
219D LEU* 5.3 3.1 - - + -
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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
----------------------------------------------------------
115D TYR* 3.5 21.8 + - + +
117D ILE* 5.7 0.2 - - - +
130D ASP* 3.0 21.4 + - - +
131D SER* 3.7 11.5 - - - +
133D ILE* 1.3 76.3 - - - +
135D LYS* 1.3 63.5 + - - +
137D LEU* 3.3 9.1 + - + +
138D LYS* 3.0 22.1 + - - +
141D GLU* 5.1 0.3 - - - +
150D ARG* 3.3 27.7 + - - -
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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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131D SER* 2.9 40.1 + - - +
132D ALA* 3.7 6.5 - - - +
133D ILE 3.3 0.2 - - - -
134D GLU* 1.3 78.1 - - - +
136D ALA* 1.3 60.8 + - - +
138D LYS* 3.3 17.1 + - + +
139D VAL* 3.1 25.3 + - + +
212D PHE* 3.7 21.9 - - + -
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Residues in contact with ALA 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 ALA 3.0 13.6 + - - +
133D ILE 3.0 9.5 + - - +
135D LYS* 1.3 76.7 - - - +
137D LEU* 1.3 61.9 + - - +
139D VAL* 3.3 16.5 - - - +
140D TRP* 3.5 14.0 + - - -
212D PHE* 3.6 15.0 - - + +
215D ALA* 3.8 9.0 - - + -
216D ALA* 3.5 29.3 - - - +
219D LEU* 3.8 10.8 - - + -
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Residues in contact with LEU 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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115D TYR* 3.4 52.9 - - + +
133D ILE* 2.9 22.3 + - + +
134D GLU* 3.6 9.4 - - + +
136D ALA* 1.3 72.7 - - - +
138D LYS* 1.3 56.1 + - - +
139D VAL 3.0 1.3 - - - -
140D TRP* 2.6 31.0 + - - +
141D GLU* 2.9 17.3 + - - +
148D PHE* 3.8 40.1 - - + -
158D ILE* 5.4 0.2 - - + -
160D ILE* 5.8 0.4 - - + -
219D LEU* 3.6 33.7 - - + -
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Residues in contact with LYS 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 GLU 3.0 14.1 + - - +
135D LYS* 3.3 20.2 - - + +
137D LEU* 1.3 74.4 - - - +
139D VAL* 1.3 64.9 + - + +
141D GLU* 3.4 19.6 + - + +
142D GLU* 2.8 49.4 + - + +
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Residues in contact with VAL 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 LYS* 3.1 15.7 + - + +
136D ALA* 3.3 11.2 - - - +
137D LEU 2.9 0.4 + - - -
138D LYS* 1.3 76.4 - - + +
140D TRP* 1.3 68.8 + - + +
142D GLU* 3.6 23.0 + - - +
143D VAL* 3.9 2.6 - - - +
212D PHE* 3.8 26.0 - - + -
216D ALA* 4.8 2.5 - - + -
234D LEU* 4.6 3.4 - - + -
248D PHE* 3.9 17.3 - - + -
250D LEU* 3.6 46.5 - - + +
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Residues in contact with TRP 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 ALA 3.5 21.2 + - - -
137D LEU* 2.6 12.9 + - - +
139D VAL* 1.3 76.8 - - + +
141D GLU* 1.3 61.6 + - - +
142D GLU 3.2 2.0 + - - -
143D VAL* 3.5 7.4 + - + +
144D THR* 2.9 26.6 + - - +
148D PHE* 4.6 7.6 - + + -
216D ALA* 2.8 30.1 + - - +
219D LEU* 3.7 16.4 - - + -
220D GLY* 3.6 19.4 - - - +
223D LEU* 3.8 23.3 - - + -
225D LEU* 3.5 18.8 - - + -
234D LEU* 3.8 14.6 - - + -
235D MET* 4.4 5.4 - - - -
250D LEU* 3.8 31.2 - - + -
254D ASP* 4.1 10.3 - - + -
258D ILE* 3.8 40.2 - - + -
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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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134D GLU 5.1 0.5 - - - +
137D LEU* 2.9 9.7 + - - +
138D LYS* 3.4 29.3 + - + +
140D TRP* 1.3 77.3 - - - +
142D GLU* 1.3 62.1 + - - +
144D THR* 3.1 18.3 - - - +
146D LEU 3.6 20.6 - - - +
147D THR* 4.0 5.5 - - + +
148D PHE* 3.2 54.0 + - + +
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Residues in contact with GLU 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 LYS* 2.8 46.3 + - + +
139D VAL* 3.6 21.0 - - - +
140D TRP 3.2 0.6 - - - -
141D GLU* 1.3 78.8 - - - +
143D VAL* 1.3 67.0 + - + +
144D THR 3.6 0.4 - - - -
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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