Contacts of the strand formed by residues 276 - 282 (chain D) in PDB entry 2RHB
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 LYS 276 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89D LYS* 6.1 1.5 - - - +
267D ASP* 2.8 41.9 + - - +
269D ILE* 3.3 4.5 + - + +
270D PRO 3.9 0.2 - - - -
271D MET 2.8 42.3 + - - +
272D ASP* 4.8 4.3 - - - +
273D SER* 3.9 17.6 + - - +
274D THR 3.9 0.4 + - - -
275D VAL* 1.3 74.1 - - - +
277D ASN* 1.3 62.2 + - - +
278D TYR* 3.5 31.6 - - + +
292D CYS 3.6 0.2 - - - +
293D SER* 3.6 3.1 - - - -
294D VAL* 2.7 46.0 + - - +
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Residues in contact with ASN 277 (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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266D GLU 4.4 0.7 - - - +
267D ASP* 4.2 10.6 - - - +
268D PHE* 3.7 32.8 + - + -
269D ILE* 4.9 11.6 - - + +
275D VAL* 4.2 11.9 + - - +
276D LYS* 1.3 78.3 - - - +
278D TYR* 1.3 69.8 + - - +
291D VAL* 3.5 19.2 - - + +
292D CYS 3.5 0.9 - - - -
293D SER* 3.2 30.3 + - - -
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Residues in contact with TYR 278 (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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251D MET* 6.1 3.0 - - - -
265D LEU* 3.6 41.1 - - + -
266D GLU 3.8 1.8 - - - -
267D ASP* 3.8 35.1 + - + -
268D PHE* 3.8 6.1 - - - -
276D LYS* 3.5 43.3 - - + +
277D ASN* 1.3 77.1 - - - +
279D PHE* 1.3 60.3 + - - +
280D ILE* 3.3 25.1 + - + +
291D VAL 3.2 3.3 + - - -
292D CYS* 2.7 36.3 + - - +
294D VAL* 4.0 28.0 - - + -
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Residues in contact with PHE 279 (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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264D LYS 3.5 2.9 - - - +
266D GLU* 3.2 56.3 + - + +
268D PHE* 3.9 9.3 - - + -
278D TYR* 1.3 69.4 - - - +
280D ILE* 1.3 63.4 + - - +
281D THR* 3.7 2.8 + - - -
288D SER* 4.8 2.5 - - - -
289D LYS 3.4 14.8 - - - -
290D CYS* 3.5 40.8 - - + -
291D VAL 4.2 1.3 - - - +
13E GLY 3.8 22.7 - - - -
14E HIS* 4.3 4.9 - - + -
61E ARG* 4.4 7.0 - - - -
63E ILE* 3.6 32.3 - - + -
163E ASN* 3.3 27.8 - - - -
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Residues in contact with ILE 280 (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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245D LEU* 3.8 23.8 - - + -
248D LEU* 4.7 5.4 - - + -
254D LEU* 3.9 23.3 - - + -
263D LEU* 4.2 19.5 - - + -
264D LYS 3.1 10.3 - - - +
265D LEU* 4.0 15.7 - - + +
278D TYR* 3.3 18.1 - - + -
279D PHE* 1.3 74.1 - - - +
281D THR* 1.3 65.2 + - - +
288D SER* 3.4 2.4 - - - -
289D LYS 2.9 32.7 + - - +
292D CYS* 3.7 30.7 - - + -
294D VAL* 3.9 12.8 - - + -
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Residues in contact with THR 281 (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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263D LEU* 3.5 1.9 - - - -
264D LYS* 2.7 52.6 + - - +
266D GLU* 5.0 0.3 + - - -
279D PHE* 4.0 6.6 + - - -
280D ILE* 1.3 78.9 + - - +
282D ASP* 1.3 69.1 + - - +
283D ALA* 3.5 1.2 + - - -
286D GLY 4.7 0.7 - - - +
287D SER 3.8 4.3 - - - +
288D SER* 3.8 7.0 - - - -
162E VAL* 3.7 41.5 - - + +
163E ASN* 3.0 24.3 + - - +
165E VAL* 4.3 8.6 - - + +
167E LEU* 5.0 0.7 - - + -
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Residues in contact with ASP 282 (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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240D PHE* 3.4 20.2 - - + -
245D LEU* 4.8 2.6 - - + +
257D ARG* 3.2 24.3 + - - -
262D PRO 4.3 1.0 - - - +
263D LEU* 3.2 27.8 - - + +
280D ILE* 4.3 1.0 - - - +
281D THR* 1.3 70.4 - - - +
283D ALA* 1.3 64.4 + - - +
284D GLN* 3.3 5.7 + - - +
285D THR* 2.6 46.6 + - - +
286D GLY* 3.3 17.8 + - - -
287D SER 2.8 18.6 + - - +
288D SER* 4.7 0.2 - - - +
167E LEU* 3.6 7.6 - - - +
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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