Contacts of the strand formed by residues 238 - 245 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393C HIS* 5.5 4.2 - - - -
60D LEU* 4.0 4.3 - - + -
205D GLY 3.2 9.0 - - - +
207D PHE* 3.4 35.0 - - - +
208D ALA* 3.5 18.4 - - + +
234D MET 3.9 1.6 + - - -
235D CYS 4.7 0.9 + - - +
236D LYS 3.6 4.2 - - - +
237D ALA* 1.3 80.7 - - - +
239D GLU* 1.3 65.9 + - - +
240D THR 3.4 3.4 - - - +
241D THR* 4.3 8.4 + - - +
267D HIS* 4.4 6.6 - - - -
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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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434C LYS* 5.5 11.7 - - - +
205D GLY 2.9 13.8 + - - +
206D ASP* 3.4 13.0 + - - +
238D ALA* 1.3 72.8 - - - +
240D THR* 1.3 64.1 + - - +
267D HIS* 3.6 14.0 + - - -
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Residues in contact with THR 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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206D ASP 2.9 8.8 + - - -
207D PHE* 3.1 31.6 - - + +
208D ALA 3.0 23.3 + - - +
238D ALA* 4.5 1.1 - - - -
239D GLU* 1.3 80.1 + - - +
241D THR* 1.3 62.7 + - - +
242D VAL* 4.1 3.4 - - + -
267D HIS* 3.6 8.9 + - + +
268D ARG* 3.6 46.2 + - + +
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Residues in contact with THR 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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208D ALA* 3.8 12.7 - - + +
210D VAL* 4.7 4.3 - - + -
234D MET 4.1 0.3 + - - -
235D CYS* 2.8 39.6 + - - -
238D ALA* 4.3 7.1 + - - +
240D THR* 1.3 71.7 - - - +
242D VAL* 1.3 63.4 + - - +
243D VAL* 3.6 24.5 - - + -
265D TYR 3.1 22.4 + - - +
266D VAL* 4.3 1.8 - - - -
267D HIS* 3.0 16.4 + - - +
268D ARG 3.1 23.9 + - - +
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Residues in contact with VAL 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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49D ALA* 3.9 24.9 - - + +
50D VAL* 4.5 2.5 - - + -
73D LEU* 3.3 33.7 - - + +
207D PHE* 4.5 7.4 - - + -
208D ALA 2.9 15.9 + - - +
209D LEU* 4.1 12.3 - - + -
210D VAL* 3.0 24.1 + - - +
240D THR* 4.1 11.0 - - + +
241D THR* 1.3 75.1 - - - +
243D VAL* 1.3 63.4 + - - +
268D ARG* 3.3 33.7 - - + +
270D ILE* 5.0 1.8 - - + -
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Residues in contact with VAL 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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73D LEU* 4.3 2.5 - - - -
210D VAL* 3.3 20.4 - - + +
212D ALA* 3.8 28.9 - - + -
221D VAL* 4.0 9.2 - - + -
235D CYS* 4.5 3.6 - - - -
241D THR* 3.6 26.2 - - + -
242D VAL* 1.3 73.2 - - - +
244D GLU* 1.3 65.8 + - - +
245D VAL* 4.0 0.7 - - + -
266D VAL* 3.9 20.9 - - + -
268D ARG 2.8 10.2 + - - +
269D LEU* 3.3 23.8 - - + +
270D ILE* 3.0 26.3 + - - +
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Residues in contact with GLU 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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70D PRO* 2.9 29.3 - - + +
72D ASN* 3.1 14.2 + - - -
73D LEU* 2.7 35.0 + - + +
210D VAL 2.8 19.6 + - - +
211D LYS* 3.5 8.6 - - + +
212D ALA 2.9 25.8 + - - +
243D VAL* 1.3 73.7 - - - +
245D VAL* 1.3 61.1 + - - +
270D ILE* 3.3 23.1 - - + -
272D GLY 4.7 0.2 - - - +
275D TYR* 2.6 39.3 + - - +
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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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212D ALA* 3.4 22.2 - - + +
213D TRP 4.0 2.5 - - - +
214D LYS 3.7 21.3 - - - +
215D ALA* 3.8 11.7 - - + +
243D VAL* 4.0 1.3 - - + -
244D GLU* 1.3 79.0 - - - +
246D GLU* 1.3 60.1 + - - +
247D GLU 3.5 23.1 - - - +
248D ILE* 3.9 19.7 - - + -
269D LEU* 3.8 13.5 - - + -
270D ILE 3.0 18.0 + - - +
271D LYS* 3.4 4.9 - - - -
272D GLY* 2.7 26.0 + - - -
275D TYR* 3.4 6.9 + - - -
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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