Contacts of the strand formed by residues 327 - 331 (chain E) 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 PHE 327 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D THR* 3.8 36.6 - - - -
265D PHE* 4.0 7.6 - - + -
266D ARG* 3.9 15.5 - - + -
278D LYS* 3.5 31.9 - - + -
280D PHE* 4.0 19.1 - + - -
323E VAL 3.9 15.3 - - - -
324E GLU* 3.6 29.2 - - - +
325E ALA 3.1 5.9 - - - -
326E ASP* 1.3 79.8 - - - +
328E LEU* 1.3 62.1 + - - +
329E TYR* 3.1 37.9 - + + +
393E MET* 2.9 24.2 + - + +
394E LEU* 3.0 12.5 - - - +
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Residues in contact with LEU 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D LYS 3.1 9.1 + - - +
279D LEU* 3.4 25.4 - - + -
280D PHE* 2.8 30.0 + - - +
281D ILE* 6.5 0.9 - - + -
327E PHE* 1.3 80.5 - - - +
329E TYR* 1.3 79.0 + - - +
330E ALA* 4.1 4.5 - - + +
366E PHE* 3.0 35.2 - - + -
367E MET* 3.7 19.1 - - + -
370E LEU* 4.2 9.2 - - + -
389E ILE* 4.4 1.6 - - + -
390E VAL 3.1 29.4 - - - +
392E SER* 4.3 0.7 - - - +
394E LEU* 3.7 15.7 - - + -
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Residues in contact with TYR 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D LEU* 4.8 4.3 - - + -
262D THR* 4.2 25.4 + - + -
280D PHE* 3.6 13.0 - + + +
282D ILE* 4.6 10.5 - - + -
324E GLU* 5.4 2.8 + - - -
327E PHE* 3.1 46.5 - + + -
328E LEU* 1.3 82.0 - - - +
330E ALA* 1.3 56.9 + - - +
331E TYR* 3.3 40.6 + + + -
388E CYS 3.4 3.3 - - - +
390E VAL* 2.5 57.3 + - + +
393E MET* 4.1 23.8 - - + +
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Residues in contact with ALA 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D PHE 3.5 7.9 + - - -
281D ILE* 3.7 13.5 - - + +
282D ILE* 3.5 18.7 + - - -
328E LEU* 4.1 6.3 + - + +
329E TYR* 1.3 72.7 - - - +
331E TYR* 1.3 62.8 + - - +
349E PHE* 3.6 16.4 - - + -
366E PHE* 5.9 1.3 - - + -
370E LEU* 3.8 38.1 - - + -
388E CYS 3.3 5.6 - - - +
389E ILE* 4.3 4.0 - - + +
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Residues in contact with TYR 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D GLU* 5.3 1.1 - - - -
241D GLY 6.4 0.2 - - - -
258D LEU* 3.8 14.7 - - + +
282D ILE* 3.5 34.3 - - + -
286D ARG* 3.2 48.0 + - + +
329E TYR* 3.3 45.6 - + + -
330E ALA* 1.3 74.6 - - - +
332E SER* 1.3 61.1 + - - +
333E THR 3.2 18.8 - - - +
349E PHE* 3.8 3.4 - - - -
387E PRO* 3.2 7.6 - - - +
388E CYS* 2.6 42.4 + - - +
390E VAL* 3.8 13.2 - - + +
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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