Contacts of the strand formed by residues 340 - 343 (chain A) in PDB entry 2RIB
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 TRP 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A PRO* 3.6 24.0 - - + -
277A ASN* 2.8 24.0 + - - -
293A LEU* 3.5 20.4 - - + +
295A MET* 3.4 25.8 - - + -
312A LEU* 4.1 8.5 - - + -
314A TYR* 3.4 33.2 - + - -
315A SER* 3.5 17.7 - - - -
316A ASN* 2.8 31.7 + - - +
317A TRP* 3.6 27.8 - + + -
318A ALA* 2.8 32.9 + - - +
321A GLU* 3.8 1.4 - - - +
332A VAL* 4.0 9.9 - - + -
333A GLU 3.4 5.4 - - - +
334A ILE* 4.2 10.1 - - + +
335A PHE* 4.7 0.2 - - - -
338A GLY 3.5 7.2 - - - -
339A LYS* 1.3 81.6 - - - +
341A ASN* 1.3 60.1 + - - +
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Residues in contact with ASN 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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317A TRP* 4.0 5.2 - - - -
321A GLU* 2.8 24.8 - - + +
332A VAL* 3.5 0.5 - - - -
333A GLU* 2.8 56.2 + - + +
335A PHE* 3.4 29.0 - - + -
340A TRP* 1.3 77.2 - - - +
342A ASP* 1.3 68.9 + - - +
343A ARG* 3.4 7.1 + - - +
356A GMH 3.0 24.4 + - - -
401A CA 2.6 22.5 - - - -
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Residues in contact with ASP 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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304A PHE* 3.8 17.1 - - + -
317A TRP* 3.7 7.7 - - + -
321A GLU* 3.0 10.6 - - - +
322A PRO* 3.1 17.2 - - + +
323A ASN 3.1 4.6 + - - -
324A ASP* 2.6 32.7 + - - +
329A GLU* 3.1 22.2 - - - +
331A CYS 3.1 12.1 - - - +
341A ASN* 1.3 78.7 + - - +
343A ARG* 1.3 58.3 + - - +
401A CA 2.5 47.2 - - - -
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Residues in contact with ARG 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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292A PHE* 4.3 13.0 - - + -
329A GLU* 3.8 12.8 + - - -
330A ASP 3.7 0.7 + - - -
331A CYS* 2.7 35.7 + - - +
333A GLU* 3.0 38.9 + - + +
335A PHE* 5.1 3.6 - - - -
341A ASN* 3.4 12.8 + - - +
342A ASP* 1.3 75.3 - - - +
344A ALA* 1.3 81.4 + - - +
347A GLU* 3.6 27.1 + - + +
349A ARG* 3.2 22.0 - - - +
356A GMH 3.6 24.5 + - - -
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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