Contacts of the strand formed by residues 234 - 241 (chain D) in PDB entry 6DBV
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 ILE 234 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199D GLU 5.7 0.2 - - - +
200D LEU* 6.1 1.3 - - + -
204D GLN* 6.0 2.9 - - - +
216D VAL 3.5 1.7 - - - +
217D TYR* 3.0 8.2 - - - -
218D PHE* 2.9 57.8 + - + +
232D ARG* 3.2 53.2 - - + +
233D LEU* 1.3 79.5 - - - +
235D ARG* 1.3 64.6 + - - +
236D LEU* 5.6 3.1 - - + +
249D CYS* 4.2 14.8 - - - -
250D THR 3.3 14.8 - - - +
251D ILE* 3.7 19.5 - - + -
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Residues in contact with ARG 235 (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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215D CYS* 3.6 19.7 - - - +
216D VAL 3.5 3.6 - - - -
217D TYR* 3.3 29.4 + - + -
233D LEU 4.2 1.2 + - - -
234D ILE* 1.3 77.0 - - - +
236D LEU* 1.3 66.4 + - - +
237D HIS* 3.7 36.2 - - - +
248D THR* 5.1 4.9 + - - +
249D CYS* 3.6 0.5 - - - -
250D THR* 2.9 53.3 + - + +
252D LEU* 3.6 27.7 - - + +
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Residues in contact with LEU 236 (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 VAL* 4.9 7.2 - - + -
182D VAL* 4.3 10.8 - - + -
200D LEU* 6.0 1.3 - - + -
215D CYS* 3.3 7.4 - - - -
216D VAL* 2.9 58.6 + - + +
218D PHE* 3.6 34.1 - - + -
234D ILE* 5.6 4.3 - - + +
235D ARG* 1.3 78.5 - - - +
237D HIS* 1.3 59.3 + - - +
238D VAL* 3.5 27.4 - - + -
247D LEU* 3.8 18.6 - - + -
248D THR 3.3 13.0 - - - +
249D CYS* 4.2 8.7 - - + -
250D THR* 5.1 0.2 - - - -
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Residues in contact with HIS 237 (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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214D ASP* 3.6 26.9 + - - -
215D CYS* 4.4 5.8 - - + +
235D ARG* 3.7 28.7 - - - +
236D LEU* 1.3 73.6 - - - +
238D VAL* 1.3 65.3 + - - +
239D GLU* 3.0 30.1 + - + +
247D LEU* 3.5 0.3 - - - -
248D THR* 2.9 47.2 + - + +
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Residues in contact with VAL 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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145D ILE* 4.3 23.1 - - + -
147D SER* 2.6 21.6 + - - +
154D VAL* 5.5 4.3 - - + -
184D LEU* 4.9 11.7 - - + -
214D ASP* 3.3 37.1 + - + +
216D VAL* 4.9 2.0 - - + -
236D LEU* 3.5 28.3 - - + -
237D HIS* 1.3 72.7 + - - +
239D GLU* 1.3 64.4 + - - +
240D LEU* 6.0 3.4 - - + -
246D VAL 3.9 2.9 - - - +
247D LEU* 3.5 24.0 - - + -
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Residues in contact with GLU 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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147D SER* 3.3 9.4 + - - +
148D ARG* 4.6 17.7 - - - +
237D HIS* 3.0 54.2 + - + +
238D VAL* 1.3 74.1 - - - +
240D LEU* 1.3 65.6 + - - +
241D LEU* 3.3 7.7 + - + +
246D VAL* 2.7 65.6 + - + +
247D LEU* 3.7 4.2 - - - -
248D THR* 4.1 4.5 + - - +
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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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145D ILE* 5.9 3.4 - - + -
147D SER* 3.8 25.6 + - - +
148D ARG* 3.7 9.4 + - - +
150D LYS* 3.2 45.8 - - + +
152D ALA* 5.1 16.6 - - + -
184D LEU* 5.4 5.2 - - + -
186D ASP* 5.2 4.0 - - - +
238D VAL* 5.8 3.1 - - + -
239D GLU* 1.3 72.8 - - - +
241D LEU* 1.3 60.3 + - - +
242D LEU* 2.8 25.0 + - + +
243D GLY 6.3 0.4 - - - -
244D SER 3.6 4.9 - - - -
245D PRO* 3.7 29.2 - - + -
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Residues in contact with LEU 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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148D ARG* 3.7 21.5 - - - +
239D GLU* 3.3 6.3 + - + -
240D LEU* 1.3 67.9 - - - +
242D LEU* 1.3 68.3 + - - +
244D SER* 2.9 35.7 + - - +
246D VAL* 4.5 13.5 - - + -
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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