Contacts of the helix formed by residues 149 - 165 (chain D) in PDB entry 5EWL
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 SER 149 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133D ILE* 3.7 6.7 - - - -
148D PRO* 1.4 75.5 - - - +
150D ILE* 1.3 64.3 + - - +
151D GLU* 3.6 16.1 + - - +
152D GLN* 2.9 40.6 + - - +
153D GLN* 3.2 23.0 + - - +
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Residues in contact with ILE 150 (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 ILE* 3.6 24.6 - - + +
134D MET 4.1 14.6 - - - +
149D SER* 1.3 73.3 - - - +
151D GLU* 1.3 69.1 + - - +
153D GLN* 3.3 7.4 + - - +
154D ALA* 2.9 27.8 + - - +
177D PRO 3.8 4.5 - - - +
178D GLY* 3.7 18.6 - - - +
181D ASP* 4.3 8.3 - - + +
182D PHE* 3.7 43.1 - - + +
231D TYR* 3.3 32.3 - - + +
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Residues in contact with GLU 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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149D SER* 3.7 15.2 - - - +
150D ILE* 1.3 89.1 + - - +
152D GLN* 1.4 61.8 + - - +
154D ALA* 3.6 3.7 + - - +
155D SER* 3.2 21.3 + - - -
181D ASP* 3.8 29.4 - - - +
185D LYS* 3.7 43.1 + - + +
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Residues in contact with GLN 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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147D GLY 5.2 0.2 + - - -
148D PRO* 3.8 15.7 - - + +
149D SER* 2.9 44.2 + - - +
151D GLU* 1.4 73.6 - - - +
153D GLN* 1.4 61.5 + - - +
155D SER* 2.8 25.7 + - - +
156D VAL* 3.1 16.2 + - + +
185D LYS* 5.6 0.2 - - - +
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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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133D ILE* 3.8 17.7 - - - +
148D PRO* 3.3 47.1 + - + +
149D SER 3.2 12.7 + - - +
150D ILE* 3.6 4.5 - - - +
152D GLN* 1.4 76.1 - - - +
154D ALA* 1.3 64.2 + - - +
156D VAL* 3.0 13.8 + - + +
157D MET* 2.9 30.0 + - - +
182D PHE* 5.7 1.1 - - + -
259D PRO* 3.2 17.9 - - + +
260D SER* 2.8 39.9 + - - -
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Residues in contact with ALA 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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150D ILE 2.9 17.1 + - - +
151D GLU 3.6 6.5 - - - +
152D GLN 3.4 0.2 - - - -
153D GLN* 1.3 74.4 - - - +
155D SER* 1.3 60.7 + - - +
157D MET* 3.5 4.5 + - - +
158D LEU* 3.3 18.2 + - - +
182D PHE* 3.8 24.3 - - + -
185D LYS* 3.9 18.8 - - + -
186D ILE* 3.5 31.3 - - + +
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Residues in contact with SER 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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151D GLU 3.2 12.8 + - - -
152D GLN* 2.8 19.0 + - - +
153D GLN 3.2 0.8 - - - -
154D ALA* 1.3 72.6 - - - +
156D VAL* 1.4 58.3 + - - +
158D LEU* 3.0 12.3 + - - +
159D ASN* 2.7 47.1 + - - -
185D LYS* 4.7 15.3 - - - +
189D THR* 5.8 3.8 - - - -
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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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152D GLN* 3.2 19.5 - - + +
153D GLN* 3.0 12.7 + - + +
155D SER* 1.4 82.9 + - - +
157D MET* 1.3 61.7 + - + +
159D ASN* 3.2 12.6 + - + +
160D ILE* 3.1 36.9 + - + +
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Residues in contact with MET 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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153D GLN* 2.9 19.1 + - - +
154D ALA 3.5 8.3 - - - +
156D VAL* 1.3 77.2 - - + +
158D LEU* 1.3 55.2 + - - +
160D ILE* 3.4 14.3 - - + +
161D MET* 3.2 36.5 + - + +
182D PHE* 3.7 29.4 - - + -
229D LEU* 3.7 28.5 - - + -
230D LEU 4.6 2.0 - - - +
257D ILE* 3.5 49.7 - - + +
258D VAL* 4.0 15.7 - - - +
259D PRO* 4.6 6.5 - - + -
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Residues in contact with LEU 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 ALA 3.3 16.7 + - - +
155D SER* 3.0 9.7 + - - +
157D MET* 1.3 73.7 - - - +
159D ASN* 1.3 55.7 + - - +
161D MET* 3.2 26.2 + - + +
162D GLU* 2.8 33.8 + - - +
169D PHE* 4.3 3.6 - - + -
185D LYS* 5.4 0.7 - - + -
186D ILE* 3.8 33.7 - - + +
189D THR* 3.7 36.3 - - + +
190D ILE* 4.5 4.3 - - + -
197D TRP* 3.6 36.9 - - + -
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Residues in contact with ASN 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 SER* 2.7 40.0 + - - -
156D VAL* 3.2 13.5 + - + +
158D LEU* 1.3 74.6 - - - +
160D ILE* 1.4 60.4 + - - +
162D GLU* 3.4 7.7 + - - +
163D GLU* 3.2 22.5 + - - +
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Residues in contact with ILE 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 29.4 + - + +
157D MET* 3.4 17.7 - - + +
159D ASN* 1.4 73.3 - - + +
161D MET* 1.3 64.0 + - - +
163D GLU* 3.3 14.4 + - - +
164D TYR* 3.3 32.5 - - + -
166D TRP* 4.1 21.8 - - + -
257D ILE* 4.4 21.5 - - + -
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Residues in contact with MET 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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157D MET 3.2 20.6 + - - +
158D LEU* 3.2 29.0 + - + +
160D ILE* 1.3 77.0 - - - +
162D GLU* 1.4 61.2 + - - +
164D TYR 3.5 1.4 + - - -
165D ASP 3.0 4.7 + - - -
166D TRP* 2.8 61.9 + - + +
169D PHE* 4.2 11.2 - - + -
197D TRP* 3.6 13.7 - - + -
227D ILE* 3.9 18.6 - - + -
229D LEU* 3.5 33.4 - - + -
257D ILE* 3.8 15.0 - - + -
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Residues in contact with GLU 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 LEU 2.8 19.6 + - - +
159D ASN* 3.8 8.3 - - - +
161D MET* 1.4 71.2 - - - +
163D GLU* 1.4 57.4 + - - +
165D ASP* 3.0 25.6 + - - +
167D TYR* 3.4 18.3 + - + +
195D VAL* 5.5 3.6 - - + -
197D TRP* 3.8 12.2 - - + -
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Residues in contact with GLU 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 ASN 3.2 12.9 + - - +
160D ILE* 3.4 13.0 - - - +
161D MET 3.3 0.2 - - - -
162D GLU* 1.4 76.7 - - - +
164D TYR* 1.3 83.3 + - + +
165D ASP* 3.7 4.9 + - - +
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Residues in contact with TYR 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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160D ILE* 3.3 34.9 + - + -
163D GLU* 1.3 95.1 - - + +
165D ASP* 1.4 70.4 + - - +
166D TRP* 3.2 52.8 + + + +
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Residues in contact with ASP 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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161D MET 3.0 6.1 + - - -
162D GLU 3.0 9.3 - - - +
163D GLU 3.3 5.8 - - - +
164D TYR* 1.4 81.1 - - - +
166D TRP* 1.3 61.6 + - - +
167D TYR* 2.7 51.5 + - + -
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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