Contacts of the strand formed by residues 417 - 424 (chain A) in PDB entry 2B9E
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 PHE 417 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ASP* 5.1 0.4 - - - -
214A ALA* 3.3 47.1 - - + -
215A SER* 4.1 10.3 - - - -
217A LEU* 4.6 7.6 - - + -
218A PRO* 3.8 21.8 - - + -
240A LYS* 3.9 16.8 - - - -
305A ASP* 4.7 2.9 - - - -
357A SER* 3.8 24.5 - - - -
358A THR 3.2 22.2 - - - -
359A CYS* 3.9 10.8 - - + +
360A SER 4.2 8.5 + - - +
361A LEU* 4.7 1.3 - - - +
406A ARG* 3.3 8.2 - - - +
407A ALA* 3.0 33.5 + - + +
415A SER* 3.8 5.2 - - - +
416A GLY* 1.3 77.3 - - - -
418A PHE* 1.3 75.0 + - - +
419A VAL* 4.5 4.5 - - + -
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Residues in contact with PHE 418 (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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356A TYR* 3.9 24.0 - + - -
357A SER* 3.1 8.3 - - - -
358A THR* 2.9 31.6 + - - +
366A ASN* 3.4 64.8 - - + +
367A GLU* 3.5 31.4 - - + -
370A VAL* 3.9 6.3 - - + -
394A GLY* 4.5 0.4 - - - -
404A CYS* 3.6 38.6 - - + -
405A LEU 3.3 16.6 - - - -
406A ARG* 3.9 8.1 - - + -
417A PHE* 1.3 78.7 - - - +
419A VAL* 1.3 60.7 + - - +
420A ALA* 4.2 6.7 - - + -
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Residues in contact with VAL 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 4.4 12.1 - - + -
218A PRO* 4.5 6.1 - - + -
221A LEU* 4.1 17.5 - - + -
355A VAL* 3.2 32.3 - - + -
356A TYR 3.2 5.4 - - - +
357A SER* 4.3 6.5 - - - -
386A ALA* 5.6 0.9 - - + +
404A CYS* 3.3 6.3 - - - +
405A LEU* 2.8 72.2 + - + +
417A PHE* 4.5 5.8 - - + -
418A PHE* 1.3 78.3 - - - +
420A ALA* 1.3 65.4 + - - +
421A VAL* 4.5 1.0 + - - +
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Residues in contact with ALA 420 (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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354A LEU 3.8 0.7 - - - +
355A VAL* 3.4 5.5 - - - +
356A TYR* 2.8 38.8 + - + +
370A VAL* 3.8 24.9 - - + -
383A LEU* 3.9 9.2 - - + -
404A CYS* 3.6 25.6 - - - +
418A PHE* 4.2 2.4 - - + -
419A VAL* 1.3 74.3 - - - +
421A VAL* 1.3 63.7 + - - +
422A ILE* 3.9 4.4 + - + +
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Residues in contact with VAL 421 (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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221A LEU* 3.9 41.5 - - + +
353A ARG* 3.9 29.4 - - + -
354A LEU 3.7 3.1 - - - -
355A VAL* 4.3 7.0 - - + -
383A LEU* 3.4 8.9 - - - +
384A ALA* 2.9 52.0 + - + +
386A ALA* 3.9 17.5 - - + +
403A HIS 5.5 1.8 + - - -
419A VAL* 4.9 1.3 - - + -
420A ALA* 1.3 73.0 - - - +
422A ILE* 1.3 63.1 + - - +
423A GLU* 4.3 2.7 - - + +
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Residues in contact with ILE 422 (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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342A LEU* 4.2 34.5 - - + -
346A LEU* 4.0 13.9 - - + -
353A ARG* 3.3 3.3 - - - +
354A LEU* 2.8 52.6 + - + +
356A TYR* 4.8 1.6 - - + -
370A VAL* 4.4 13.7 - - + -
374A LEU* 4.3 12.1 - - + -
381A PHE* 3.7 33.7 - - + -
382A ARG 3.4 6.3 - - - +
383A LEU* 3.9 16.4 - - + -
420A ALA* 4.6 9.6 - - + +
421A VAL* 1.3 74.8 - - - +
423A GLU* 1.3 64.2 + - - +
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Residues in contact with GLU 423 (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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352A GLN 3.4 7.9 - - - +
353A ARG* 2.8 47.6 + - + +
381A PHE* 3.3 7.3 - - - -
382A ARG* 2.8 80.5 + - - +
384A ALA* 3.5 21.8 - - + +
421A VAL* 4.2 2.2 + - + +
422A ILE* 1.3 80.1 - - - +
424A ARG* 1.3 65.1 + - - +
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Residues in contact with ARG 424 (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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349A PRO 4.9 3.6 + - - -
350A SER* 4.1 16.8 + - - +
351A LEU 3.5 26.2 + - - +
352A GLN* 2.9 43.2 + - + +
380A ALA 4.0 4.9 - - - +
381A PHE* 3.6 18.6 - - + -
382A ARG* 4.4 7.0 + - - -
423A GLU* 1.3 77.6 - - - +
425A VAL* 1.3 74.7 + - - +
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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