Contacts of the strand formed by residues 347 - 354 (chain A) in PDB entry 2ODP
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 ILE 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A HIS* 3.3 22.9 - - + +
234A ASN* 3.4 26.2 - - - +
333A GLN* 3.6 32.8 - - - +
337A LEU* 4.3 3.8 - - + -
343A ALA 3.4 22.2 - - - +
344A TRP* 3.6 17.9 - - + +
345A GLN 3.3 2.2 - - - +
346A GLU* 1.3 78.6 - - - +
348A ARG* 1.3 67.1 + - - +
349A HIS* 3.4 36.1 + - + +
382A ARG* 4.7 1.9 + - - -
385A TYR* 3.2 17.1 - - - +
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Residues in contact with ARG 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLN* 3.0 55.8 + - - +
228A GLN* 3.5 29.0 + - - +
230A SER 3.4 20.6 + - - -
231A GLY* 4.3 0.6 - - - -
232A HIS* 2.7 32.9 + - - +
233A LEU* 3.4 23.8 - - + +
234A ASN 2.8 26.9 + - - +
269A ILE* 6.1 1.4 - - - +
270A ASN 5.5 0.4 + - - -
346A GLU 4.5 3.6 + - - +
347A ILE* 1.3 75.7 - - - +
349A HIS* 1.3 61.7 + - - +
384A ASP* 3.7 20.4 - - - +
385A TYR* 3.7 28.0 - - + -
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Residues in contact with HIS 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 4.8 0.7 - - - -
234A ASN* 3.5 12.3 + - + -
236A TYR* 2.7 32.7 + + + -
330A MET* 3.6 15.9 - - + -
344A TRP* 3.9 19.5 - + - -
347A ILE* 3.4 41.1 + - + +
348A ARG* 1.3 73.0 - - - +
350A ALA* 1.3 62.1 + - - +
351A ILE 4.2 0.2 - - - -
376A LEU* 3.4 41.3 - - + +
382A ARG* 5.8 2.0 - - - -
384A ASP 5.5 0.2 - - - +
385A TYR* 2.9 14.4 + - - +
386A LEU* 3.2 8.5 + - + +
387A ASP* 3.0 24.6 + - - +
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Residues in contact with ALA 350 (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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225A ILE* 4.0 26.0 - - + -
233A LEU* 4.1 12.8 - - + -
234A ASN 2.9 9.1 + - - +
235A LEU* 3.3 20.9 - - + +
236A TYR* 2.8 28.1 + - - -
349A HIS* 1.3 74.5 - - - +
351A ILE* 1.3 62.7 + - - +
352A ILE* 5.4 0.7 - - + -
387A ASP* 3.3 11.2 - - + +
389A TYR* 5.5 1.1 - - + -
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Residues in contact with ILE 351 (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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236A TYR* 3.5 24.5 - - + +
238A LEU* 4.2 15.5 - - + -
323A LEU* 4.0 22.9 - - + -
326A VAL* 3.8 22.2 - - + -
330A MET* 4.4 2.0 - - + -
350A ALA* 1.3 77.9 - - - +
352A ILE* 1.3 61.8 + - - +
353A LEU* 4.0 12.8 - - + -
372A ILE* 3.9 18.2 - - + -
386A LEU* 4.2 12.6 - - + -
387A ASP 2.8 14.1 + - - +
388A ILE* 3.4 24.2 - - + -
389A TYR* 2.7 33.3 + - - +
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Residues in contact with ILE 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ILE* 3.9 18.6 - - + -
235A LEU* 3.7 27.8 - - + -
236A TYR 2.9 10.6 + - - +
237A LEU* 3.6 11.8 - - + +
238A LEU 2.9 26.4 + - - +
260A MET* 3.8 34.8 - - + -
350A ALA 5.0 0.2 - - - -
351A ILE* 1.3 79.2 - - - +
353A LEU* 1.3 69.9 + - - +
354A LEU* 3.9 5.8 + - + +
389A TYR* 3.4 15.0 - - + -
391A ILE* 3.9 26.2 - - + -
429A PHE* 4.2 2.0 - - + -
432A MET* 4.0 7.0 - - + -
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Residues in contact with LEU 353 (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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238A LEU* 3.3 34.8 - - + +
278A PHE* 4.4 10.8 - - + -
319A THR* 4.0 28.3 - - + -
322A ALA* 5.1 0.7 - - + -
323A LEU* 4.2 13.0 - - + -
351A ILE* 4.0 9.6 - - + -
352A ILE* 1.3 73.2 - - - +
354A LEU* 1.3 61.8 + - - +
355A THR* 3.8 14.6 + - + +
388A ILE* 3.9 22.4 - - + -
389A TYR 2.8 19.3 + - - +
390A ALA* 3.5 7.8 - - + -
391A ILE* 2.9 29.5 + - - +
406A LEU* 4.6 9.2 - - + -
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Residues in contact with LEU 354 (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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237A LEU* 5.8 1.3 - - + -
238A LEU 2.8 11.1 + - - +
239A LEU* 3.6 21.1 - - + -
240A ASP* 3.0 28.2 + - - +
253A PHE* 3.5 49.8 - - + +
256A SER* 4.5 3.6 - - - -
257A ALA* 4.1 13.9 - - + +
260A MET* 4.2 13.2 - - + -
352A ILE* 4.4 12.8 - - + +
353A LEU* 1.3 71.0 - - - +
355A THR* 1.3 60.9 + - - +
391A ILE* 3.3 27.8 - - + +
393A VAL* 4.0 17.7 - - + -
425A LEU* 5.7 0.9 - - + -
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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