Contacts of the helix formed by residues 237 - 249 (chain D) in PDB entry 6DV9
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 ASP 237 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235D ILE* 3.3 12.5 - - - +
236D VAL* 1.3 83.0 - - + +
238D GLU* 1.3 61.3 + - - +
239D ASN* 2.9 36.5 + - - +
240D LEU* 3.2 27.8 + - + +
241D TYR* 3.2 17.0 + - - +
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Residues in contact with GLU 238 (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 TYR* 4.2 25.2 + - + -
236D VAL 3.3 6.2 + - - +
237D ASP* 1.3 72.5 + - - +
239D ASN* 1.3 66.2 + - - +
241D TYR* 3.4 2.8 + - - +
242D ARG* 3.0 58.4 + - - +
256D MET* 4.1 18.6 - - + +
365D ILE* 4.9 8.6 - - - +
16F ARG* 3.6 18.1 - - - -
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Residues in contact with ASN 239 (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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218D ARG* 6.2 4.5 - - - +
237D ASP* 2.9 13.4 + - - +
238D GLU* 1.3 79.8 - - - +
240D LEU* 1.3 65.3 + - - +
242D ARG* 3.2 19.8 + - - +
243D GLU* 3.0 28.6 + - + +
16F ARG* 5.3 5.5 + - - -
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Residues in contact with LEU 240 (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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218D ARG* 6.6 0.2 - - - +
221D ASP* 4.4 9.0 - - + +
222D ILE* 3.7 30.5 - - + +
225D THR* 3.9 21.8 - - + +
235D ILE* 3.8 19.5 - - + -
237D ASP* 3.2 29.5 + - + +
239D ASN* 1.3 76.8 - - - +
241D TYR* 1.3 62.1 + - - +
243D GLU* 3.1 6.7 + - - +
244D LEU* 3.0 46.9 + - + +
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Residues in contact with TYR 241 (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 TYR* 3.4 57.7 - + + -
136D ILE* 4.2 9.6 - - + -
235D ILE* 3.6 28.5 - - + -
237D ASP 3.2 14.4 + - - +
238D GLU 3.8 4.3 - - - +
239D ASN 3.3 0.2 - - - -
240D LEU* 1.3 79.0 - - - +
242D ARG* 1.3 63.9 + - - +
244D LEU* 3.2 5.2 + - - +
245D VAL* 3.1 45.6 + - + +
252D PHE* 3.7 21.3 - + - -
254D GLY* 3.2 34.3 + - - -
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Residues in contact with ARG 242 (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 TYR* 4.8 5.9 + - - -
238D GLU* 3.0 58.0 + - - +
239D ASN* 3.5 20.4 + - - +
240D LEU 3.2 0.2 - - - -
241D TYR* 1.3 81.1 - - - +
243D GLU* 1.3 57.8 + - + +
245D VAL* 3.6 4.5 + - - +
246D ASP* 3.0 30.0 + - + +
364D GLU* 5.5 4.6 + - - -
16F ARG* 3.5 38.9 - - - +
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Residues in contact with GLU 243 (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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218D ARG* 3.3 28.4 + - - +
222D ILE* 3.5 25.7 - - + +
239D ASN* 3.0 18.2 + - + +
240D LEU* 3.5 9.0 - - - +
242D ARG* 1.3 74.8 - - + +
244D LEU* 1.3 65.3 + - - +
246D ASP* 3.2 16.1 + - - +
247D ARG* 3.0 63.7 + - - +
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Residues in contact with LEU 244 (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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222D ILE* 4.1 25.6 - - + +
225D THR* 3.6 26.2 - - + -
226D PHE* 4.9 4.7 - - + +
229D LEU* 4.4 12.1 - - + -
235D ILE* 3.7 22.2 - - + -
240D LEU* 3.0 42.7 + - + +
241D TYR* 3.2 8.7 + - - +
243D GLU* 1.3 78.3 - - - +
245D VAL* 1.3 57.1 + - - +
248D TYR* 2.8 42.5 + - + +
249D GLY 3.4 3.3 + - - -
252D PHE* 3.4 21.5 - - + -
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Residues in contact with VAL 245 (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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241D TYR* 3.1 44.2 + - + +
242D ARG* 4.1 4.7 - - - +
244D LEU* 1.3 73.1 - - - +
246D ASP* 1.3 65.3 + - - +
247D ARG 3.2 0.7 + - - -
249D GLY* 3.3 26.9 + - - -
252D PHE* 3.7 15.5 - - + -
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Residues in contact with ASP 246 (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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242D ARG* 3.0 20.9 + - + +
243D GLU* 3.2 19.9 + - - +
245D VAL* 1.3 76.2 - - - +
247D ARG* 1.3 63.0 + - + +
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Residues in contact with ARG 247 (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 LEU* 5.9 0.5 - - - +
155D MET* 4.0 8.2 - - - +
158D GLU* 2.8 40.2 + - - -
215D GLU* 5.5 1.4 + - - -
218D ARG* 5.4 0.8 - - - +
219D LEU* 3.5 18.1 - - - +
222D ILE* 3.7 25.3 - - - +
243D GLU* 3.0 49.5 + - - +
245D VAL 4.2 0.2 - - - -
246D ASP* 1.3 86.0 - - + +
248D TYR* 1.3 85.4 + - + +
249D GLY 3.4 4.5 + - - -
250D GLU* 5.1 5.9 + - - +
251D TYR* 4.9 3.1 - - - -
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Residues in contact with TYR 248 (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 LEU* 3.8 36.1 + - + -
155D MET* 3.2 30.1 - - - +
222D ILE* 4.2 11.4 - - + +
223D TRP* 3.4 18.4 - + - -
226D PHE* 3.4 57.4 - + + -
244D LEU* 2.8 24.6 + - + +
247D ARG* 1.3 100.3 + - + +
249D GLY* 1.3 62.1 + - - +
250D GLU 3.1 2.5 - - - -
251D TYR* 3.0 23.1 + + + +
252D PHE* 3.1 13.3 - - + -
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Residues in contact with GLY 249 (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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244D LEU 3.4 0.4 + - - -
245D VAL* 3.3 35.6 + - - -
247D ARG 3.4 3.0 + - - -
248D TYR* 1.3 77.3 - - - +
250D GLU* 1.3 60.1 + - - +
251D TYR 3.0 1.5 + - - -
252D PHE* 3.2 22.2 - - - +
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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