Contacts of the strand formed by residues 325 - 332 (chain E) 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 ALA 325 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74E ASN* 3.4 38.4 - - + +
321E THR* 3.2 6.4 - - - -
322E ILE 2.9 30.3 + - - +
323E ASP 2.9 2.4 + - - -
324E TYR* 1.3 81.1 - - - +
326E GLU* 1.3 61.7 + - - +
327E ILE* 3.5 14.4 + - + +
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Residues in contact with GLU 326 (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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319E LYS* 3.4 54.1 - - + +
320E VAL 3.8 3.1 - - - +
321E THR* 4.5 13.7 - - + +
325E ALA* 1.3 70.8 - - - +
327E ILE* 1.3 65.5 + - - +
328E SER* 3.9 3.0 + - - -
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Residues in contact with ILE 327 (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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74E ASN* 5.5 0.2 - - - +
274E THR* 4.4 12.1 - - + -
275E VAL* 4.0 26.9 - - + -
318E VAL 3.3 2.4 - - - +
319E LYS* 3.5 1.6 - - - -
320E VAL 2.8 43.1 + - - +
322E ILE* 4.2 20.4 - - + +
325E ALA* 4.1 22.2 - - + +
326E GLU* 1.3 76.9 - - - +
328E SER* 1.3 71.6 + - - +
329E PHE* 3.8 23.7 - - + -
343E PRO* 4.4 5.8 - - + -
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Residues in contact with SER 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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317E VAL* 4.3 13.1 - - - +
318E VAL 3.3 4.9 - - - -
319E LYS* 3.4 25.7 - - - +
326E GLU 3.9 3.4 + - - -
327E ILE* 1.3 74.5 - - - +
329E PHE* 1.3 60.5 + - - +
343E PRO* 3.3 10.4 - - - +
344E LYS 3.2 35.5 + - - -
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Residues in contact with PHE 329 (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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295E ILE* 4.6 15.7 - - + -
297E LEU* 5.7 2.7 - - + -
302E PHE* 6.0 1.3 - + - -
305E ILE* 6.0 0.2 - - + -
317E VAL* 3.1 11.6 - - - +
318E VAL* 2.6 38.6 + - + +
320E VAL* 3.7 34.8 - - + -
322E ILE* 4.2 13.9 - - + -
327E ILE* 3.8 28.3 - - + -
328E SER* 1.3 74.6 - - - +
330E MET* 1.3 61.0 + - - +
341E PHE* 3.5 42.0 - + + -
342E TYR* 3.3 26.2 - - - -
343E PRO* 3.5 22.7 - - + -
344E LYS 4.8 3.4 - - - -
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Residues in contact with MET 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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315E SER* 5.0 15.5 - - - +
316E LYS 3.1 16.6 - - - +
317E VAL* 3.8 22.7 - - + -
329E PHE* 1.3 73.2 - - - +
331E LEU* 1.3 61.2 + - - +
332E TRP* 4.1 0.4 + - + -
340E THR* 3.7 3.0 - - + +
341E PHE* 3.3 6.6 + - - -
342E TYR* 2.5 63.0 + - + +
343E PRO* 4.4 2.9 - - - +
344E LYS* 5.4 8.1 - - + +
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Residues in contact with LEU 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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306E ILE* 6.2 0.2 - - + -
309E GLN* 5.3 7.0 - - + -
311E LEU* 5.8 3.6 - - + -
313E VAL 4.8 0.7 - - - +
314E ILE 3.5 1.0 - - - +
315E SER* 3.0 6.2 - - - -
316E LYS* 2.6 49.7 + - + +
318E VAL* 4.1 15.3 - - + -
329E PHE 4.1 0.8 - - - -
330E MET* 1.3 72.0 - - - +
332E TRP* 1.3 59.3 + - - +
333E CYS* 5.1 7.6 - - - -
340E THR 3.6 3.6 - - - -
341E PHE* 3.7 21.8 - - + -
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Residues in contact with TRP 332 (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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314E ILE* 3.0 8.3 - - + +
315E SER* 4.2 7.4 - - - +
330E MET* 4.1 0.8 + - + -
331E LEU* 1.3 72.6 - - - +
333E CYS* 1.3 63.9 + - - +
338E VAL* 3.6 2.1 - - - +
339E GLU* 2.6 33.9 + - + -
340E THR* 2.6 42.9 + - + +
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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