Contacts of the helix formed by residues 150 - 166 (chain D) in PDB entry 4U9W
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 GLY 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D TYR* 3.3 12.8 + - - -
148D ARG 3.7 0.2 - - - -
149D LYS* 1.3 77.9 - - - +
151D LEU* 1.3 58.3 + - - +
152D GLY 3.3 2.5 - - - -
153D LYS* 3.4 7.2 + - - +
154D PHE* 2.9 27.9 + - - +
301D COA 2.7 25.4 + - - -
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Residues in contact with LEU 151 (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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48D TYR* 3.8 27.5 + - + -
53D LEU* 3.9 27.6 - - + -
55D VAL* 4.2 18.2 - - + -
57D ILE* 4.3 8.1 - - + -
111D ALA* 4.2 9.2 - - + -
119D VAL* 4.7 4.3 - - + -
120D ALA* 3.7 25.4 - - + -
142D LEU* 4.0 9.6 - - + -
146D VAL* 4.2 13.7 - - + +
149D LYS* 3.4 3.2 + - - +
150D GLY* 1.3 74.8 - - - +
152D GLY* 1.3 57.0 + - - +
154D PHE* 3.1 4.2 + - + +
155D LEU* 2.8 54.9 + - + +
301D COA 3.9 0.8 + - - -
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Residues in contact with GLY 152 (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 VAL* 4.6 3.8 - - - +
142D LEU* 3.8 15.3 - - - +
151D LEU* 1.3 77.7 - - - +
153D LYS* 1.3 61.6 + - - +
155D LEU* 3.2 7.0 + - - +
156D ILE* 3.1 26.2 + - - +
185D PHE* 3.5 8.1 - - - -
301D COA 3.1 31.6 + - - -
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Residues in contact with LYS 153 (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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150D GLY* 3.7 6.3 - - - +
151D LEU 3.3 0.2 - - - -
152D GLY* 1.3 74.2 - - - +
154D PHE* 1.3 59.1 + - - +
156D ILE* 3.3 3.5 + - - +
157D GLN* 2.8 54.2 + - - +
185D PHE* 3.5 12.6 - - + -
189D ALA* 4.8 12.4 + - + +
190D LEU* 3.4 27.6 - - + +
301D COA 3.1 32.8 + - - +
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Residues in contact with PHE 154 (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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219C LYS 4.2 3.8 - - - -
220C PHE* 4.1 22.4 - - + -
44D VAL 4.6 2.0 - - - -
45D PHE* 3.5 40.6 - + - -
47D LYS 4.0 17.5 - - - -
48D TYR* 3.4 30.3 - + + -
57D ILE* 3.8 15.9 - - + -
150D GLY 2.9 17.9 + - - +
151D LEU* 3.1 7.2 + - + +
153D LYS* 1.3 77.8 - - - +
155D LEU* 1.3 57.3 + - - +
157D GLN* 3.2 17.9 + - + +
158D ILE* 2.9 55.4 + - + +
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Residues in contact with LEU 155 (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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57D ILE* 4.2 30.7 - - + -
109D LEU* 3.7 28.7 - - + +
111D ALA* 5.2 3.6 - - + -
120D ALA* 4.0 26.9 - - + -
121D PHE* 4.5 18.2 - - - +
122D SER* 4.9 3.8 - - - +
140D VAL* 4.5 9.4 - - + -
142D LEU* 4.2 13.7 - - + -
151D LEU* 2.8 26.9 + - + +
152D GLY* 3.5 7.4 - - - +
154D PHE* 1.3 74.1 - - - +
156D ILE* 1.3 58.2 + - + +
158D ILE* 3.1 7.8 + - + +
159D LEU* 2.9 30.2 + - - +
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Residues in contact with ILE 156 (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 SER* 5.4 0.2 - - - +
137D CYS* 4.1 13.2 - - + -
140D VAL* 4.1 15.3 - - + -
152D GLY 3.1 14.5 + - - +
153D LYS 3.9 2.5 - - - +
155D LEU* 1.3 73.7 - - + +
157D GLN* 1.3 61.3 + - - +
159D LEU* 3.2 27.1 + - + +
160D GLN 2.9 24.1 + - - -
171D VAL* 5.1 3.6 - - + -
173D LEU* 5.6 1.1 - - + -
185D PHE* 4.2 3.6 - - + -
186D PHE* 3.9 19.7 - - + -
190D LEU* 3.9 20.9 - - + -
192D PHE* 3.6 26.5 - - + -
216D ARG* 3.5 19.6 + - - +
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Residues in contact with GLN 157 (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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219C LYS* 3.5 53.6 + - + +
45D PHE* 5.5 2.2 - - + -
153D LYS* 2.8 45.2 + - + +
154D PHE* 3.2 23.1 + - + +
156D ILE* 1.3 77.4 - - - +
158D ILE* 1.3 56.0 + - + +
160D GLN* 3.3 1.2 + - - +
161D LEU* 2.9 28.8 + - - +
190D LEU* 5.6 1.2 - - + +
216D ARG* 4.2 13.6 - - - +
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Residues in contact with ILE 158 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D LEU* 4.1 19.5 - - + -
45D PHE* 3.4 46.4 - - + +
57D ILE* 4.1 19.3 - - + -
109D LEU* 3.6 19.3 - - + -
154D PHE* 2.9 32.7 + - + +
155D LEU* 3.1 13.0 + - + +
157D GLN* 1.3 73.8 - - - +
159D LEU* 1.3 65.5 + - - +
161D LEU* 3.1 8.8 + - + +
162D MET* 3.0 34.8 + - + +
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Residues in contact with LEU 159 (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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109D LEU* 3.9 12.1 - - + -
122D SER* 3.4 20.9 - - - +
124D PHE* 3.6 32.8 - - + -
135D LEU* 3.3 24.9 - - + +
137D CYS* 3.6 29.6 - - + -
155D LEU 2.9 16.2 + - - +
156D ILE* 3.5 20.6 - - + +
158D ILE* 1.3 75.8 - - - +
160D GLN* 1.3 56.7 + - - +
162D MET* 3.5 16.6 + - + -
163D ALA* 2.9 25.8 + - - +
171D VAL* 4.0 9.4 - - + -
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Residues in contact with GLN 160 (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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219C LYS* 4.2 13.1 + - - -
156D ILE 2.9 7.6 + - - +
157D GLN 3.6 4.7 - - - +
159D LEU* 1.3 74.6 - - - +
161D LEU* 1.3 60.5 + - - +
163D ALA* 3.3 1.7 + - - +
164D ASN* 3.0 56.5 + - - -
171D VAL* 3.7 19.7 - - + +
192D PHE* 5.1 0.2 - - + -
216D ARG* 2.7 81.5 + - - +
217D ARG 3.5 12.4 + - - +
218D THR* 4.5 2.7 - - - +
219D LYS* 4.8 9.0 + - - +
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Residues in contact with LEU 161 (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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161C LEU* 4.0 13.7 - - + -
164C ASN* 4.5 13.7 - - + +
219C LYS* 3.9 19.2 - - + +
39D LEU* 4.5 8.7 - - + -
42D PHE* 3.4 60.1 - - + -
45D PHE* 4.1 25.1 - - + -
157D GLN 2.9 14.0 + - - +
158D ILE* 3.4 10.5 - - - +
160D GLN* 1.3 77.2 - - - +
162D MET* 1.3 58.1 + - + +
164D ASN* 3.3 4.8 + - + +
165D SER* 2.9 24.6 + - - -
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Residues in contact with MET 162 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D PRO* 3.7 39.5 - - + +
39D LEU* 4.2 20.2 - - + -
42D PHE* 5.5 0.4 - - + -
59D CYS* 3.9 13.0 - - - -
109D LEU* 3.9 5.2 - - + -
124D PHE* 3.5 26.7 - - + -
126D PHE* 4.9 5.6 - - + -
135D LEU* 4.3 6.1 - - + -
158D ILE* 3.0 26.4 + - + +
159D LEU* 3.6 26.0 - - + +
161D LEU* 1.3 76.1 - - + +
163D ALA* 1.3 61.4 + - - +
165D SER* 2.9 8.5 + - - +
166D THR* 2.8 34.7 + - + +
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Residues in contact with ALA 163 (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 LEU* 3.9 15.9 - - + +
159D LEU 2.9 19.5 + - - +
160D GLN 3.3 6.7 + - - +
162D MET* 1.3 77.0 - - - +
164D ASN* 1.3 59.2 + - - +
166D THR* 3.9 5.2 - - - -
167D GLN 3.3 1.6 + - - -
168D MET* 2.9 37.9 + - + +
170D LYS 4.5 0.7 - - - +
171D VAL* 3.6 20.6 - - + -
218D THR* 3.8 14.1 - - + -
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Residues in contact with ASN 164 (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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45C PHE* 3.5 19.0 - - - -
157C GLN* 3.9 16.7 - - - +
161C LEU* 4.4 6.5 - - + -
219C LYS* 4.3 9.1 - - - +
160D GLN* 3.0 40.6 + - - -
161D LEU* 3.6 9.4 - - + +
162D MET 3.1 0.2 - - - -
163D ALA* 1.3 75.9 - - - +
165D SER* 1.3 63.3 + - - +
167D GLN* 3.1 11.8 + - - -
218D THR* 3.3 12.2 - - - +
219D LYS* 2.8 38.6 + - - +
220D PHE* 3.7 12.4 + - - -
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Residues in contact with SER 165 (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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42C PHE* 4.7 9.4 - - - +
44C VAL* 3.5 22.5 - - - +
45C PHE* 3.8 9.2 - - - -
161C LEU* 4.3 8.0 - - - +
38D PRO 4.5 4.9 + - - -
42D PHE* 3.8 30.3 - - - -
161D LEU 2.9 13.1 + - - -
162D MET* 2.9 23.9 + - - +
164D ASN* 1.3 76.0 - - - +
166D THR* 1.3 62.9 + - - +
167D GLN 3.4 0.2 - - - -
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Residues in contact with THR 166 (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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44C VAL* 4.8 7.3 - - - +
28D LYS* 4.5 8.3 - - - +
32D ALA* 3.8 21.3 - - + -
35D LEU* 3.8 28.5 - - + -
38D PRO* 5.3 2.0 - - + -
126D PHE* 3.5 14.8 - - + -
162D MET* 2.8 23.5 + - + +
165D SER* 1.3 81.8 - - - +
167D GLN* 1.3 69.2 + - - +
168D MET* 3.3 33.5 - - - +
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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