Contacts of the strand formed by residues 270 - 273 (chain D) in PDB entry 6DBU
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 GLU 270 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265D PRO* 3.5 4.2 - - - +
266D ILE* 2.9 40.1 + - + -
267D GLY* 3.5 27.9 + - - +
268D TYR 3.8 2.3 - - - +
269D HIS* 1.3 80.3 - - - +
271D TYR* 1.3 62.9 + - - +
289D TYR* 2.1 42.0 + - + -
290D VAL 3.7 3.6 - - - -
291D GLY* 4.7 1.8 - - - -
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Residues in contact with TYR 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D LEU* 3.6 45.0 - - + +
211D ALA 5.3 3.3 + - - -
263D ALA* 4.9 8.5 - - + -
264D SER 3.4 3.8 - - - +
265D PRO* 3.4 38.8 - - + +
267D GLY 5.6 0.2 - - - -
268D TYR 4.4 4.6 + - - -
269D HIS* 3.8 38.7 - + - -
270D GLU* 1.3 75.5 - - - +
272D ILE* 1.3 62.2 + - - +
273D ILE* 3.8 11.7 + - + +
289D TYR* 3.7 3.8 - - - -
290D VAL* 2.9 41.5 + - + +
292D LEU* 3.8 13.9 - - + -
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Residues in contact with ILE 272 (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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1D MET* 3.4 39.5 - - + -
262D ILE 3.7 1.7 - - - +
263D ALA* 3.7 0.5 - - - -
264D SER* 2.9 54.3 + - - +
266D ILE* 4.2 25.2 - - + +
270D GLU 4.2 0.8 - - - -
271D TYR* 1.3 71.0 - - - +
273D ILE* 1.3 66.8 + - - +
274D PHE* 3.9 20.4 + - + -
287D CYS* 5.4 1.8 - - + -
288D THR 3.5 13.2 - - - +
289D TYR* 4.4 6.1 - - + +
302D ARG* 5.9 3.4 - - + -
325D GLY* 4.9 2.0 - - - +
350D PHE* 3.8 17.9 - - + -
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Residues in contact with ILE 273 (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 VAL* 5.4 4.9 - - + -
210D LEU* 5.3 7.0 - - + -
219D LEU* 5.4 11.0 - - + -
256D LEU* 6.0 0.2 - - + -
258D ILE* 3.7 31.0 - - + -
261D ALA* 3.8 17.3 - - + -
262D ILE 3.8 1.8 - - - +
263D ALA* 3.6 29.2 - - + -
271D TYR* 4.0 19.1 - - + +
272D ILE* 1.3 75.8 - - - +
274D PHE* 1.3 65.2 + - - +
275D GLY* 3.9 2.0 - - - +
284D ARG* 5.4 0.4 + - - +
287D CYS* 3.6 2.3 - - - +
288D THR* 2.9 50.5 + - - +
290D VAL* 4.7 15.5 - - + -
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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