Contacts of the strand formed by residues 325 - 334 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ASN* 3.5 30.5 - - + +
274A THR* 4.8 1.8 - - - +
321A THR* 3.3 6.7 - - - +
322A ILE 2.7 41.0 + - - +
323A ASP 3.0 0.4 - - - -
324A TYR* 1.3 74.5 - - - +
326A GLU* 1.3 61.2 + - - +
327A ILE* 3.7 17.8 + - + +
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Residues in contact with GLU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A LYS* 3.3 48.2 + - + +
320A VAL 4.0 4.0 - - - +
321A THR* 4.4 12.8 - - + +
325A ALA* 1.3 72.1 - - - +
327A ILE* 1.3 65.6 + - - +
328A SER* 4.0 2.6 + - - -
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Residues in contact with ILE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A THR* 4.5 7.4 - - + -
275A VAL* 4.1 30.7 - - + -
318A VAL 3.4 1.7 - - - +
319A LYS* 3.4 4.5 - - - -
320A VAL 2.9 40.9 + - - +
322A ILE* 4.4 16.6 - - + -
325A ALA* 4.2 21.3 - - + +
326A GLU* 1.3 78.6 - - - +
328A SER* 1.3 68.3 + - - +
329A PHE* 3.6 29.3 - - + -
343A PRO* 4.5 6.5 - - + -
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Residues in contact with SER 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A VAL* 4.1 10.1 - - - +
318A VAL 3.6 4.0 - - - -
319A LYS* 3.3 28.9 - - - +
326A GLU* 4.0 3.9 + - - -
327A ILE* 1.3 73.8 - - - +
329A PHE* 1.3 62.9 + - - +
343A PRO* 3.2 7.1 - - - +
344A LYS* 2.8 40.2 + - - -
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Residues in contact with PHE 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ILE* 4.9 15.0 - - + -
297A LEU* 5.7 3.6 - - + -
302A PHE* 5.4 6.1 - + - -
305A ILE* 6.2 0.4 - - + -
316A LYS 3.6 0.2 - - - +
317A VAL* 3.3 8.5 - - - +
318A VAL* 2.7 40.7 + - + +
320A VAL* 4.1 23.8 - - + -
322A ILE* 4.1 14.1 - - + -
327A ILE* 3.6 36.3 - - + -
328A SER* 1.3 77.4 - - - +
330A MET* 1.3 62.7 + - - +
331A LEU 4.0 0.2 - - - -
341A PHE* 3.5 43.5 - + + -
342A TYR* 3.3 8.5 - - - +
343A PRO* 3.5 33.4 - - + -
344A LYS* 5.3 0.4 - - - -
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Residues in contact with MET 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A SER* 4.5 12.3 - - - +
316A LYS 3.6 6.1 - - - +
317A VAL* 4.0 26.9 - - + -
329A PHE* 1.3 73.6 - - - +
331A LEU* 1.3 59.7 + - - +
332A TRP* 3.9 22.3 + - + +
340A THR 3.6 2.4 - - - +
341A PHE* 3.3 26.6 - - - -
342A TYR* 2.8 51.5 + - + +
344A LYS* 4.4 16.8 - - + -
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ILE* 5.3 1.6 - - + -
309A GLN* 3.9 34.3 - - + +
310A ASP 4.1 15.9 - - - +
311A LEU* 5.4 1.1 - - + -
313A VAL 5.2 0.2 - - - +
314A ILE 4.2 0.2 - - - -
315A SER* 2.8 25.5 - - - -
316A LYS* 3.0 20.1 + - + +
318A VAL* 3.9 11.2 - - + -
329A PHE 4.0 0.4 - - - -
330A MET* 1.3 70.8 - - - +
332A TRP* 1.3 69.1 + - - +
333A CYS* 4.0 13.7 - - - -
338A VAL* 3.8 31.9 - - + -
340A THR 3.7 0.9 - - - +
341A PHE* 3.5 30.1 - - + -
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Residues in contact with TRP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A ILE* 3.3 24.9 - - + -
315A SER* 3.4 28.7 - - - -
330A MET* 4.1 21.4 - - + +
331A LEU* 1.3 76.5 - - - +
333A CYS* 1.3 61.7 + - - +
338A VAL* 3.6 1.6 - - - -
339A GLU* 2.7 36.6 + - + -
340A THR* 2.9 44.2 + - + +
342A TYR* 3.5 24.6 + + - -
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Residues in contact with CYS 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ASP 4.8 0.4 - - - -
311A LEU* 3.7 38.8 - - - +
313A VAL 3.3 19.5 - - - +
314A ILE* 2.6 35.4 + - - +
331A LEU* 4.0 23.3 - - - -
332A TRP* 1.3 82.9 - - - +
334A LYS* 1.3 62.2 + - - +
336A GLY 5.2 0.2 - - - +
337A HIS 3.3 14.8 - - - +
338A VAL* 4.1 4.0 - - - -
339A GLU* 3.7 5.6 - - - +
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Residues in contact with LYS 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A ILE* 4.9 6.5 - - + -
333A CYS* 1.3 76.4 - - - +
335A ASP* 1.3 72.6 + - - +
336A GLY 3.2 1.3 - - - -
337A HIS* 2.9 38.1 + - + -
339A GLU* 3.4 25.7 - - - +
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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