Contacts of the strand formed by residues 325 - 333 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B ASN* 3.6 28.0 - - + +
274B THR* 5.5 0.2 - - - -
321B THR* 3.2 7.2 - - - -
322B ILE 2.8 34.9 + - - +
323B ASP 3.2 0.4 - - - -
324B TYR* 1.3 79.9 - - - +
326B GLU* 1.3 61.5 + - - +
327B ILE* 3.5 17.3 + - + +
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B LYS* 3.0 55.7 + - + +
320B VAL 3.9 3.4 - - - +
321B THR* 4.4 11.8 - - + +
325B ALA* 1.3 70.5 - - - +
327B ILE* 1.3 62.8 + - - +
328B SER* 3.9 5.5 + - - -
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Residues in contact with ILE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B THR* 4.2 13.7 - - + -
275B VAL* 3.9 30.1 - - + -
318B VAL 3.6 0.5 - - - +
319B LYS* 3.4 5.2 - - - -
320B VAL 2.9 40.4 + - - +
322B ILE* 3.9 19.5 - - + +
325B ALA* 3.9 27.1 - - + +
326B GLU* 1.3 73.1 - - - +
328B SER* 1.3 67.7 + - - +
329B PHE* 3.8 28.2 - - + -
343B PRO* 5.3 4.5 - - + -
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Residues in contact with SER 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B VAL* 4.8 6.1 - - - -
318B VAL 3.6 4.0 - - - -
319B LYS* 3.3 27.7 - - - +
326B GLU* 3.9 7.3 + - - -
327B ILE* 1.3 75.5 - - - +
329B PHE* 1.3 62.8 + - - +
343B PRO* 3.3 6.9 - - - +
344B LYS* 3.3 43.3 + - - -
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Residues in contact with PHE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B VAL* 6.0 0.9 - - + -
295B ILE* 5.3 12.1 - - + -
297B LEU* 5.8 3.1 - - + -
302B PHE* 6.0 2.2 - + - -
305B ILE* 5.8 0.2 - - + -
317B VAL* 3.6 6.8 - - - +
318B VAL 2.7 45.5 + - - +
320B VAL* 3.9 27.6 - - + -
322B ILE* 4.3 11.7 - - + -
327B ILE* 3.8 29.8 - - + -
328B SER* 1.3 72.1 - - - +
330B MET* 1.3 61.7 + - - +
341B PHE* 3.4 48.5 - + + -
342B TYR 3.2 7.9 - - - +
343B PRO* 3.6 37.0 - - + -
344B LYS* 4.9 2.2 - - - -
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Residues in contact with MET 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B SER* 4.3 10.8 - - - +
316B LYS 3.9 9.9 - - - +
317B VAL* 3.9 18.4 - - + -
329B PHE* 1.3 72.8 - - - +
331B LEU* 1.3 60.0 + - - +
332B TRP* 3.8 31.6 - - + +
340B THR 3.8 0.7 - - - +
341B PHE* 3.4 8.0 - - - -
342B TYR* 2.6 67.8 + - + +
344B LYS* 3.8 37.6 - - + +
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Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B ILE* 4.5 6.1 - - + -
309B GLN* 4.2 20.2 - - + -
310B ASP 4.3 12.1 - - - +
311B LEU* 5.5 0.7 - - + -
313B VAL* 5.4 2.7 - - + +
314B ILE 3.6 0.3 - - - +
315B SER* 3.1 6.6 - - - -
316B LYS* 3.0 46.9 + - + +
318B VAL* 3.8 15.5 - - + -
330B MET* 1.3 74.2 - - - +
332B TRP* 1.3 65.5 + - - +
333B CYS* 3.2 33.9 - - + -
338B VAL* 3.9 16.4 - - + -
340B THR 3.6 10.3 - - - +
341B PHE* 3.7 21.8 - - + -
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Residues in contact with TRP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B ILE* 3.2 25.6 - - + -
315B SER* 3.5 28.5 - - - -
330B MET* 3.8 24.9 - - + +
331B LEU* 1.3 75.7 - - - +
333B CYS* 1.3 57.1 + - - +
338B VAL* 3.7 1.6 - - - +
339B GLU* 2.7 35.4 + - + -
340B THR* 3.0 44.6 + - + +
342B TYR* 3.2 29.9 + + - -
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Residues in contact with CYS 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ASP 4.4 0.2 - - - -
311B LEU* 3.7 46.2 - - - +
313B VAL 3.3 22.7 + - - +
314B ILE* 3.0 21.8 + - - +
331B LEU* 3.2 33.7 - - - -
332B TRP* 1.3 75.7 - - - +
334B LYS* 1.3 63.8 + - - +
337B HIS 3.4 7.9 - - - +
338B VAL* 4.2 5.6 - - - -
339B GLU* 4.0 3.8 - - - +
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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