Contacts of the strand formed by residues 278 - 283 (chain D) in PDB entry 1RHQ
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 278 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230D PHE* 3.6 9.6 - - + +
265D PHE* 3.3 32.9 + - + -
267D GLY* 4.1 10.9 - - - +
273D LEU* 3.0 42.8 + - + -
274D THR* 4.4 5.7 - - - +
275D GLY 4.7 0.2 - - - +
276D LYS 3.5 15.1 + - - +
277D PRO* 1.3 72.3 - - - +
279D LEU* 1.3 61.8 + - - +
280D PHE* 3.8 21.5 + - + -
323E VAL 4.6 0.2 + - - -
325E ALA 3.7 16.4 + - - -
326E ASP* 2.9 21.1 + - - +
327E PHE* 3.5 24.8 - - + -
328E LEU 3.1 24.9 + - - +
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Residues in contact with LEU 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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193D PHE* 5.9 0.4 - - + -
198D TYR* 5.2 1.1 - - - +
229D SER* 5.5 1.8 - - - -
230D PHE 2.9 13.3 + - - +
231D VAL* 3.4 27.0 - - + +
232D CYS 2.8 26.7 + - - -
277D PRO* 3.6 26.5 - - + +
278D LYS* 1.3 77.7 - - - +
280D PHE* 1.3 61.0 + - - +
281D ILE* 3.8 7.7 + - + -
328E LEU* 3.4 30.7 - - + -
366E PHE* 4.0 22.2 - - + -
394E LEU* 4.4 4.7 - - + -
398E LEU* 4.4 11.0 - - + -
400E PHE* 4.3 16.6 - - + -
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Residues in contact with PHE 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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215D MET* 5.7 0.2 - - - -
230D PHE* 4.2 10.8 - + - -
232D CYS* 4.1 26.5 - - + +
234D LEU* 5.5 7.2 - - + -
258D LEU* 6.0 1.1 - - + -
261D ILE* 4.8 8.5 - - + -
262D THR* 3.4 35.0 - - + -
265D PHE* 3.5 34.1 - + - -
278D LYS* 3.8 28.5 - - + -
279D LEU* 1.3 76.4 - - - +
281D ILE* 1.3 64.7 + - - +
282D ILE* 3.5 17.6 + - + +
327E PHE* 4.0 15.3 - + - -
328E LEU* 2.8 15.6 + - - +
329E TYR* 3.6 13.2 - + + -
330E ALA 3.5 16.8 + - - -
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Residues in contact with ILE 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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193D PHE* 3.7 30.5 - - + -
231D VAL* 3.9 9.6 - - + -
232D CYS 3.3 7.2 + - - +
233D VAL* 3.3 23.8 - - + -
234D LEU* 3.0 25.1 + - - +
279D LEU* 3.8 8.0 + - + +
280D PHE* 1.3 75.0 - - - +
282D ILE* 1.3 63.0 + - - +
328E LEU* 6.5 0.4 - - + -
330E ALA* 3.7 23.6 - - + +
349E PHE* 3.8 23.1 - - + -
350E ILE* 4.8 8.5 - - + -
353E LEU* 4.2 18.6 - - + -
366E PHE* 5.9 8.7 - - + -
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Residues in contact with ILE 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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234D LEU* 4.2 25.6 - - + -
243D ILE* 5.1 5.4 - - + -
258D LEU* 3.4 39.3 - - + -
280D PHE* 3.6 17.9 - - + +
281D ILE* 1.3 83.6 - - - +
283D GLN* 1.3 62.6 + - - +
284D ALA* 3.9 14.1 + - + +
286D ARG* 6.5 0.4 - - + -
329E TYR* 4.6 6.5 - - + -
330E ALA 3.5 4.9 + - - +
331E TYR* 3.5 32.8 - - + +
332E SER* 3.2 26.5 + - - -
349E PHE* 4.2 1.3 - - - -
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Residues in contact with GLN 283 (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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179D ARG* 3.9 3.3 + - - +
234D LEU 3.2 7.8 + - - +
235D LEU* 3.2 27.7 - - + -
236D SER 3.3 20.6 + - - +
282D ILE* 1.3 72.6 - - - +
284D ALA* 1.3 67.0 + - - +
551D 0ZZ 3.9 13.3 + - - -
332E SER* 2.7 30.0 + - - -
339E SER* 3.9 14.6 - - - -
340E TRP 4.4 6.1 + - - +
341E ARG* 4.8 0.4 - - - +
347E SER* 3.2 36.8 + - - +
349E PHE* 3.6 10.0 + - - +
350E ILE* 3.4 15.5 - - + -
385E GLN* 5.0 0.7 + - - -
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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