Contacts of the helix formed by residues 152 - 170 (chain D) in PDB entry 4O9U
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 152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150D PHE 3.5 0.6 + - - -
151D PRO* 1.3 72.6 - - - +
153D GLN* 1.3 62.6 + - - +
154D LYS* 3.3 3.8 - - - -
155D ALA* 3.5 17.9 + - - +
156D VAL* 3.6 17.7 + - - +
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Residues in contact with GLN 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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148D ILE* 4.0 6.4 - - - +
149D LEU* 3.4 30.1 - - - +
150D PHE* 3.1 52.2 + - + +
151D PRO 3.2 0.8 - - - -
152D GLY* 1.3 73.6 - - - +
154D LYS* 1.3 59.3 + - + +
155D ALA 3.0 5.6 - - - -
156D VAL* 3.2 8.6 + - - -
157D ASN* 2.8 43.9 + - - +
196D LEU* 4.5 0.9 - - - +
197D PRO* 3.4 39.2 - - + +
260D LEU 5.4 0.6 + - - -
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Residues in contact with LYS 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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152D GLY* 3.3 1.9 - - - -
153D GLN* 1.3 82.6 - - + +
155D ALA* 1.3 56.6 + - - +
157D ASN* 4.7 4.7 - - - +
158D ALA* 3.3 25.3 + - - +
257D TRP* 5.5 11.5 - - - -
260D LEU 6.1 2.9 - - - +
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Residues in contact with ALA 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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152D GLY* 3.5 14.9 + - - +
153D GLN 3.0 0.4 - - - -
154D LYS* 1.3 79.9 - - - +
156D VAL* 1.3 60.8 + - + +
157D ASN 3.5 0.4 - - - -
158D ALA* 4.0 3.9 + - - +
159D LEU* 3.3 24.6 + - - +
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Residues in contact with VAL 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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150D PHE* 3.5 34.8 - - + -
152D GLY 3.6 9.6 + - - +
153D GLN* 3.4 11.0 - - - +
155D ALA* 1.3 80.9 - - + +
157D ASN* 1.3 65.8 + - - +
158D ALA 3.4 0.2 - - - -
159D LEU* 3.5 16.0 - - + +
160D VAL* 3.1 32.3 + - + +
193D LEU* 4.7 3.3 - - + +
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Residues in contact with ASN 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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150D PHE* 4.3 4.0 - - - -
153D GLN* 2.8 25.9 + - - +
154D LYS* 4.7 4.7 - - - +
156D VAL* 1.3 79.8 - - - +
158D ALA* 1.3 56.8 + - - +
159D LEU 3.1 4.5 - - - -
160D VAL* 3.6 4.1 + - - +
161D LEU* 3.3 21.8 + - - +
190D PHE* 3.5 24.6 - - + -
193D LEU* 2.7 62.6 + - - +
194D MET* 3.7 6.3 + - - -
197D PRO* 4.7 8.1 - - - +
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Residues in contact with ALA 158 (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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154D LYS 3.3 21.0 + - - +
155D ALA* 4.0 5.2 - - - +
156D VAL 3.4 0.4 - - - -
157D ASN* 1.3 76.9 - - - +
159D LEU* 1.3 58.7 + - - +
161D LEU* 4.3 11.9 - - + +
162D ALA* 3.5 21.4 + - - +
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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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155D ALA 3.3 18.2 + - - +
156D VAL* 3.5 18.8 - - + +
157D ASN 3.1 0.6 - - - -
158D ALA* 1.3 76.2 - - - +
160D VAL* 1.3 66.5 + - + +
161D LEU 3.3 0.2 - - - -
162D ALA* 3.3 5.9 + - + +
163D LEU* 3.0 54.3 + - + +
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Residues in contact with VAL 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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156D VAL* 3.1 17.8 + - + +
157D ASN 3.9 4.9 - - - +
159D LEU* 1.3 76.2 - - + +
161D LEU* 1.3 52.5 + - - +
163D LEU* 3.0 14.9 + - + +
164D THR* 2.8 38.0 + - + +
186D LEU* 3.8 17.7 - - + +
189D LEU* 4.0 19.5 - - + -
190D PHE* 3.8 28.0 - - + +
193D LEU* 3.8 21.5 - - + -
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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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123D LEU* 5.5 10.5 - - + -
157D ASN 3.3 14.6 + - - +
158D ALA* 4.3 9.4 - - + +
160D VAL* 1.3 77.5 - - - +
162D ALA* 1.3 57.4 + - - +
164D THR* 2.7 32.6 + - - +
165D VAL* 2.9 31.3 + - + +
190D PHE* 3.5 42.3 - - + -
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Residues in contact with ALA 162 (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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158D ALA 3.5 17.3 + - - +
159D LEU* 3.3 7.7 + - + +
161D LEU* 1.3 78.5 - - - +
163D LEU* 1.3 59.6 + - + +
165D VAL* 3.6 9.5 - - - +
166D VAL* 3.1 33.0 + - + +
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Residues in contact with LEU 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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159D LEU* 3.0 50.7 + - + +
160D VAL* 3.0 14.2 + - + +
162D ALA* 1.3 78.1 - - + +
164D THR* 1.3 58.5 + - - +
166D VAL* 3.5 8.8 + - + +
167D ILE* 3.0 34.0 + - + +
186D LEU* 3.7 14.4 - - + -
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Residues in contact with THR 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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123D LEU* 5.0 7.1 - - - +
160D VAL* 2.8 27.4 + - + +
161D LEU* 2.7 21.3 + - - +
163D LEU* 1.3 75.3 - - - +
165D VAL* 1.3 56.5 + - - +
167D ILE* 3.2 4.0 + - - +
168D GLY* 2.6 31.4 + - - -
183D PHE* 3.4 20.0 - - - -
186D LEU* 3.2 47.6 - - + +
187D ALA* 4.0 8.9 - - - +
190D PHE* 4.7 2.7 - - + -
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Residues in contact with VAL 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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123D LEU* 4.8 14.1 - - + -
161D LEU* 2.9 29.7 + - + +
162D ALA* 3.6 13.5 - - - +
164D THR* 1.3 83.5 + - - +
166D VAL* 1.3 56.1 + - + +
168D GLY* 3.3 2.0 + - - +
169D LEU* 2.8 49.5 + - + +
183D PHE* 5.6 0.9 - - - -
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Residues in contact with VAL 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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162D ALA 3.1 19.1 + - - +
163D LEU* 3.9 11.7 - - + +
164D THR 3.3 0.2 - - - -
165D VAL* 1.3 78.2 - - + +
167D ILE* 1.3 62.9 + - + +
169D LEU* 3.7 8.1 + - + +
170D SER* 3.2 22.7 + - - -
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Residues in contact with ILE 167 (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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163D LEU* 3.0 18.8 + - + +
164D THR* 3.5 5.2 - - - +
166D VAL* 1.3 74.8 - - + +
168D GLY* 1.3 61.9 + - - +
170D SER* 2.5 26.7 + - - +
171D LEU* 3.0 14.0 - - - +
179D SER* 3.4 25.8 - - - +
182D LEU* 3.8 36.1 - - + +
183D PHE* 3.5 16.4 - - + +
186D LEU* 3.4 26.5 - - + -
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Residues in contact with GLY 168 (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 ILE* 4.1 16.3 - - - +
164D THR 2.6 20.8 + - - -
165D VAL* 3.6 2.5 - - - -
167D ILE* 1.3 73.1 - - - +
169D LEU* 1.3 56.6 + - - +
170D SER 3.1 0.2 - - - -
171D LEU* 3.1 31.1 + - - +
172D LEU* 4.4 1.2 + - - +
183D PHE* 3.6 21.2 - - - -
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Residues in contact with LEU 169 (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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165D VAL* 2.8 35.4 + - + +
166D VAL* 4.0 7.6 - - + +
168D GLY* 1.3 70.9 - - - +
170D SER* 1.3 58.6 + - - +
171D LEU 3.2 2.1 + - - -
172D LEU* 3.7 42.8 + - + +
173D TRP* 4.1 7.8 + - - -
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Residues in contact with SER 170 (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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166D VAL* 3.2 17.5 + - - -
167D ILE* 2.5 24.0 + - - +
168D GLY 3.1 1.0 - - - -
169D LEU* 1.3 75.9 - - - +
171D LEU* 1.3 58.4 + - - +
172D LEU 3.3 0.4 - - - -
173D TRP* 4.0 19.6 + - - +
174D ASN* 2.9 33.4 + - - +
179D SER* 4.0 17.5 + - - -
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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