Contacts of the helix formed by residues 167 - 180 (chain D) in PDB entry 5LS6
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 167 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165D PHE* 3.7 14.4 - - + -
166D ILE* 1.3 77.9 - - - +
168D ASP* 1.3 75.8 + - - +
169D GLU* 3.6 25.4 + - - +
170D ILE* 2.9 24.6 + - + +
171D PHE* 2.6 35.6 + - - +
303E ASP* 5.2 7.0 - - - +
348E SER 4.6 0.5 - - - +
349E ASN* 4.2 2.6 + - - -
350E VAL* 2.5 48.5 + - + +
351E THR* 4.6 2.6 - - - +
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Residues in contact with ASP 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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167D ASN* 1.3 75.5 + - - +
169D GLU* 1.3 61.4 + - - +
171D PHE* 3.0 7.4 + - - +
172D VAL* 3.0 28.9 + - - +
243D LYS* 5.3 9.5 + - - -
247D LEU* 3.8 32.8 - - + +
303E ASP* 4.7 8.1 - - - +
348E SER* 3.0 38.8 - - - +
349E ASN* 3.3 17.8 + - - +
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Residues in contact with GLU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LYS* 3.0 26.9 + - - +
34D ARG* 3.2 23.1 + - - -
167D ASN* 3.6 21.1 + - - +
168D ASP* 1.3 77.9 - - - +
170D ILE* 1.3 68.1 + - + +
172D VAL* 4.5 5.3 - - - +
173D GLU* 3.0 35.8 + - - +
335E LYS* 4.1 19.8 - - + +
349E ASN* 4.2 9.3 + - - +
350E VAL 4.2 0.9 - - - +
351E THR* 3.4 20.9 + - - +
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Residues in contact with ILE 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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23D TYR* 4.6 8.7 - - + +
26D LEU* 5.1 9.5 - - + +
27D ARG* 4.4 27.4 - - + +
30D LYS* 4.7 15.7 - - + +
165D PHE* 3.8 17.3 - - + -
166D ILE* 3.7 20.4 - - + -
167D ASN* 2.9 38.0 + - + +
169D GLU* 1.3 86.3 - - + +
171D PHE* 1.3 58.0 + - - +
173D GLU* 3.9 8.6 - - + +
174D LEU* 3.0 25.7 + - + +
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Residues in contact with PHE 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ILE* 3.9 19.5 - - + +
167D ASN 2.6 20.7 + - - +
168D ASP* 3.0 6.2 + - - +
170D ILE* 1.3 72.1 - - - +
172D VAL* 1.3 62.0 + - + +
174D LEU* 3.3 15.9 + - + +
175D VAL* 2.9 47.2 + - + +
224D PHE* 4.6 0.7 - + - -
227D ILE* 3.5 31.9 - - + -
240D LEU* 4.3 35.7 - - + -
243D LYS* 4.8 13.2 - - + -
244D TYR* 4.7 13.7 - + + -
247D LEU* 4.7 13.9 - - + -
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Residues in contact with VAL 172 (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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168D ASP 3.0 17.3 + - - +
169D GLU* 3.9 4.9 + - - +
171D PHE* 1.3 76.2 - - + +
173D GLU* 1.3 56.8 + - + +
175D VAL* 3.3 5.5 + - - +
176D ASN* 2.8 35.9 + - + +
244D TYR* 4.5 11.2 - - + -
247D LEU* 3.2 36.3 - - + +
248D THR* 4.2 24.2 - - + -
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Residues in contact with GLU 173 (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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26D LEU* 3.3 22.5 - - + +
29D LEU* 5.9 1.9 - - - +
30D LYS* 2.8 49.3 + - - +
169D GLU* 3.0 22.4 + - - +
170D ILE* 3.9 7.9 - - - +
171D PHE 3.4 0.2 - - - -
172D VAL* 1.3 78.7 - - + +
174D LEU* 1.3 55.5 + - - +
176D ASN* 3.7 8.9 - - - +
177D ALA* 2.9 31.5 + - - +
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Residues in contact with LEU 174 (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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19D VAL* 4.0 37.0 - - + +
22D GLU* 4.8 4.9 - - + -
23D TYR* 4.4 22.9 - - + +
26D LEU* 3.7 10.3 - - + +
166D ILE* 4.3 15.7 - - + -
170D ILE* 3.0 19.8 + - + +
171D PHE* 3.4 22.0 - - + +
172D VAL 3.2 0.2 - - - -
173D GLU* 1.3 74.4 - - - +
175D VAL* 1.3 61.0 + - + +
177D ALA 3.7 0.5 - - - -
178D LEU* 3.0 32.0 + - + +
227D ILE* 4.3 20.0 - - + -
231D PHE* 4.9 9.2 - - + -
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Residues in contact with VAL 175 (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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171D PHE* 2.9 49.7 + - + +
172D VAL* 3.6 5.4 - - - +
174D LEU* 1.3 73.9 - - + +
176D ASN* 1.3 58.7 - - - +
178D LEU* 3.2 9.3 + - - +
179D GLY* 2.9 26.3 + - - -
223D ILE* 5.1 8.8 - - + +
224D PHE* 4.5 16.6 - - + -
227D ILE* 5.1 3.4 - - + -
244D TYR* 3.4 43.7 - - + +
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Residues in contact with ASN 176 (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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172D VAL* 2.8 22.0 + - + +
173D GLU* 3.7 10.3 - - - +
175D VAL* 1.3 73.3 - - - +
177D ALA* 1.3 55.4 + - - +
179D GLY* 2.9 4.4 + - - -
180D GLN* 2.8 42.4 + - - +
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Residues in contact with ALA 177 (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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22D GLU* 3.6 23.1 - - + +
25D ARG* 4.4 5.5 + - - +
26D LEU* 3.5 31.9 - - + -
173D GLU 2.9 22.2 + - - +
174D LEU 3.7 1.8 - - - +
175D VAL 3.4 0.2 - - - -
176D ASN* 1.3 73.2 - - - +
178D LEU* 1.3 55.2 + - - +
180D GLN* 4.5 6.9 - - - +
181D TYR* 3.3 20.6 + - - +
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Residues in contact with LEU 178 (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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15D TRP* 3.6 29.8 - - + +
18D ARG* 5.7 1.6 - - + -
19D VAL* 3.3 38.6 - - + +
22D GLU* 5.6 2.9 - - + +
174D LEU* 3.0 18.8 + - + +
175D VAL* 3.6 5.6 - - - +
177D ALA* 1.3 77.2 - - - +
179D GLY* 1.3 57.8 + - - +
181D TYR* 3.9 11.0 - - + -
182D ASN* 3.2 21.8 + - - -
223D ILE* 3.6 42.7 - - + +
227D ILE* 4.0 12.8 - - + -
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Residues in contact with GLY 179 (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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175D VAL 2.9 14.3 + - - -
176D ASN* 2.9 3.3 + - - -
178D LEU* 1.3 73.4 - - - +
180D GLN* 1.3 64.7 + - - +
181D TYR 3.2 1.6 + - - -
182D ASN* 3.6 19.6 + - - +
214D PRO* 5.7 6.7 - - - +
215D PRO 5.9 2.7 - - - -
220D SER* 5.7 7.6 - - - -
223D ILE* 6.1 2.0 - - - +
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Residues in contact with GLN 180 (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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176D ASN* 2.8 29.5 + - - +
177D ALA* 4.5 5.8 - - - -
179D GLY* 1.3 71.1 - - - +
181D TYR* 1.3 63.2 + - - +
182D ASN* 4.7 0.9 - - - +
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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