Contacts of the strand formed by residues 238 - 245 (chain C) in PDB entry 3DLX
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 ALA 238 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU* 4.1 3.4 - - + -
205C GLY 3.1 10.1 - - - +
207C PHE* 3.3 12.1 - - - +
208C ALA* 3.3 42.2 - - + +
234C MET 3.9 1.8 + - - -
235C CYS 5.0 0.2 - - - +
236C LYS 3.7 2.3 - - - +
237C ALA* 1.3 78.6 + - - +
239C GLU* 1.3 66.6 + - - +
240C THR 3.3 3.9 + - - +
241C THR* 3.8 12.2 - - + +
267C HIS* 4.0 4.3 - - - -
393D HIS* 5.8 2.4 - - - -
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Residues in contact with GLU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C GLY 2.9 12.1 + - - +
206C ASP* 3.5 13.9 - - - +
238C ALA* 1.3 71.4 - - - +
240C THR* 1.3 64.4 + - - +
267C HIS* 3.3 16.6 + - - -
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Residues in contact with THR 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C ASP 3.0 8.6 + - - -
207C PHE* 3.1 29.9 - - + +
208C ALA 3.0 22.7 + - - +
238C ALA* 4.3 0.4 - - - -
239C GLU* 1.3 80.1 + - - +
241C THR* 1.3 64.6 + - - +
242C VAL* 4.1 2.7 - - + -
267C HIS* 3.4 8.2 - - + -
268C ARG* 3.5 48.3 + - + +
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Residues in contact with THR 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C ALA* 3.7 17.3 - - + +
210C VAL* 5.1 0.9 - - - -
235C CYS* 2.8 37.3 - - - +
238C ALA* 3.8 17.3 - - + +
240C THR* 1.3 76.5 - - - +
242C VAL* 1.3 60.0 + - - +
243C VAL* 4.1 9.5 - - - +
265C TYR 2.7 21.3 + - - +
266C VAL* 3.6 2.9 - - - -
267C HIS* 2.9 19.2 + - + +
268C ARG* 2.9 25.8 + - - +
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Residues in contact with VAL 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ALA* 3.8 42.4 - - + +
50C VAL* 4.3 3.4 - - + -
73C LEU* 3.5 22.2 - - + +
207C PHE* 4.1 23.3 - - + -
208C ALA 2.8 14.5 + - - +
209C LEU* 4.2 10.8 - - + -
210C VAL* 2.9 26.7 + - - +
240C THR* 4.1 8.3 - - + -
241C THR* 1.3 78.3 - - - +
243C VAL* 1.3 61.4 + - - +
268C ARG* 3.4 12.8 - - + +
269C LEU 6.1 0.2 - - - -
270C ILE* 5.2 1.6 - - + -
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Residues in contact with VAL 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LEU* 4.5 0.7 - - - -
210C VAL* 3.3 29.4 - - + +
212C ALA* 4.0 14.1 - - + -
221C VAL* 4.3 7.0 - - + -
235C CYS* 4.3 10.1 - - - -
241C THR* 4.3 11.2 - - - +
242C VAL* 1.3 76.3 - - - +
244C GLU* 1.3 64.2 + - - +
245C VAL* 4.0 21.5 - - + -
266C VAL* 4.1 20.2 - - + -
268C ARG 2.9 12.5 + - - +
269C LEU* 3.4 12.2 - - + +
270C ILE* 2.9 30.2 + - - +
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Residues in contact with GLU 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C PRO* 2.8 29.6 - - + +
71C GLU 3.7 0.3 + - - -
72C ASN* 2.9 24.8 + - + -
73C LEU* 2.8 34.7 + - + +
210C VAL 2.9 16.5 + - - +
211C LYS* 3.5 5.4 - - + +
212C ALA 3.0 25.1 + - - +
243C VAL* 1.3 75.0 - - - +
245C VAL* 1.3 59.4 + - - +
270C ILE* 3.1 20.0 - - + +
272C GLY* 4.6 2.5 - - - +
275C TYR* 2.8 29.6 + - - +
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Residues in contact with VAL 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C ALA* 3.5 14.8 - - + -
213C TRP 3.9 4.0 - - - +
214C LYS 3.9 8.5 - - - +
215C ALA* 3.7 23.1 - - + +
221C VAL* 4.6 0.9 - - + -
243C VAL* 4.0 9.9 - - + -
244C GLU* 1.3 77.9 - - - +
246C GLU* 1.3 61.3 + - - +
247C GLU 3.4 23.1 - - - +
248C ILE* 3.7 22.0 - - + -
269C LEU* 3.8 12.3 - - + -
270C ILE 2.9 15.6 + - - +
271C LYS* 3.3 8.3 - - - -
272C GLY 2.9 23.0 + - - -
275C TYR* 3.3 4.6 + - - -
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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