Contacts of the strand formed by residues 337 - 343 (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 HIS 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A GLY* 3.3 24.7 - - - +
311A LEU* 4.0 5.6 + - - -
333A CYS* 3.3 5.5 - - - -
334A LYS* 2.9 49.8 + - + -
335A ASP* 4.2 14.7 + - + +
336A GLY* 1.3 78.9 - - - +
338A VAL* 1.3 77.6 + - - +
339A GLU* 3.3 21.0 + - - -
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Residues in contact with VAL 338 (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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229A GLY 2.8 14.4 + - - +
230A TYR* 3.8 24.7 - - + +
231A ALA* 3.2 26.9 + - + +
235A ILE* 3.9 17.5 - - + -
306A ILE* 4.1 12.3 - - + +
309A GLN* 6.1 0.4 - - + -
311A LEU* 3.6 21.2 - - + +
331A LEU* 3.8 30.3 - - + -
332A TRP 3.6 4.7 - - - -
333A CYS* 4.1 1.8 - - - -
337A HIS* 1.3 84.1 - - - +
339A GLU* 1.3 62.0 + - - +
340A THR 4.0 7.0 - - - +
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Residues in contact with GLU 339 (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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231A ALA* 3.4 17.5 - - - +
234A ALA* 4.1 12.6 - - - +
332A TRP* 2.7 21.5 + - + +
333A CYS 3.7 7.0 - - - +
334A LYS* 3.4 41.6 - - + +
337A HIS* 3.3 20.1 + - - -
338A VAL* 1.3 74.5 - - - +
340A THR* 1.3 62.3 - - + +
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Residues in contact with THR 340 (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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234A ALA* 5.1 5.3 + - - +
235A ILE* 4.5 6.1 - - - +
249A HIS* 4.8 8.3 - - - -
330A MET 3.6 0.7 - - - +
331A LEU* 3.7 2.8 - - - +
332A TRP* 2.9 57.4 + - + +
338A VAL* 4.3 3.8 - - - -
339A GLU* 1.3 82.5 - - + +
341A PHE* 1.3 68.4 + - - +
342A TYR* 3.7 20.4 - - + -
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Residues in contact with PHE 341 (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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235A ILE* 3.5 39.0 - - + +
249A HIS* 3.6 8.0 + - - +
302A PHE* 3.8 32.5 - + - -
305A ILE* 4.3 20.9 - - + -
306A ILE* 4.1 12.3 - - + -
309A GLN* 5.2 5.8 - - + -
318A VAL* 4.2 14.6 - - + -
320A VAL* 5.1 0.2 - - + -
329A PHE* 3.5 44.9 - + + -
330A MET 3.3 9.4 - - - -
331A LEU* 3.5 35.2 - - + -
338A VAL* 4.6 1.6 - - + -
340A THR* 1.3 78.1 + - - +
342A TYR* 1.3 61.8 + - - +
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Residues in contact with TYR 342 (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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249A HIS* 4.0 18.4 - + + +
293A SER* 5.2 1.1 - - - +
329A PHE* 3.3 6.0 - - - -
330A MET* 2.8 59.7 + - + +
332A TRP* 3.5 18.1 + + - -
340A THR* 3.7 35.9 - - + -
341A PHE* 1.3 76.4 - - - +
343A PRO* 1.3 92.5 - - + +
344A LYS* 5.3 2.0 - - - -
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Residues in contact with PRO 343 (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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249A HIS* 5.1 7.0 - - + -
275A VAL* 4.5 13.9 - - + -
293A SER* 3.2 34.0 + - - +
295A ILE* 5.2 7.0 - - + -
327A ILE* 4.5 11.2 - - + -
328A SER 3.2 11.7 - - - +
329A PHE* 3.5 22.6 - - + -
341A PHE 4.9 0.2 - - - +
342A TYR* 1.3 105.0 - - + +
344A LYS* 1.3 61.8 + - - +
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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