Contacts of the strand formed by residues 343 - 351 (chain A) in PDB entry 6BM0
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 GLU 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A ILE* 4.6 7.6 - - - +
337A ILE 3.5 1.0 - - - +
338A SER* 3.6 1.4 - - - -
339A LEU* 2.9 39.5 + - + +
340A LYS 4.3 5.5 + - - +
341A GLY* 3.2 14.0 - - - +
342A GLY* 1.3 78.3 - - - +
344A ILE* 1.3 59.5 + - - +
345A TYR* 3.8 17.7 + - + -
364A LYS* 3.2 30.7 + - - +
365A ALA 5.8 1.1 - - - +
367A ALA* 4.1 17.0 - - + +
508A LYS* 5.9 2.1 + - - -
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Residues in contact with ILE 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A VAL* 3.6 28.0 - - + -
337A ILE 3.3 6.5 - - - +
338A SER* 4.8 8.3 - - - +
342A GLY 3.8 1.1 - - - +
343A GLU* 1.3 78.8 - - - +
345A TYR* 1.3 68.7 + - - +
365A ALA* 3.1 29.0 + - - +
366A ALA 3.3 22.0 + - - +
368A SER* 3.3 31.9 - - - +
374A MET* 5.1 1.1 - - + -
384A LEU* 4.5 5.6 - - + -
394A LEU* 3.8 17.7 - - + -
463A PHE* 3.5 29.4 - - + -
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Residues in contact with TYR 345 (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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318A VAL* 4.6 7.6 - - + -
319A ARG 4.5 1.7 + - - -
320A ILE* 3.3 48.8 - - + +
335A MET 3.7 0.2 - - - +
336A VAL* 3.3 4.3 - - - -
337A ILE* 2.8 38.1 + - + +
339A LEU* 4.0 18.2 - - + -
343A GLU* 3.8 16.9 + - + -
344A ILE* 1.3 87.4 - - - +
346A VAL* 1.3 65.1 + - - +
347A LEU 4.0 0.7 - - - -
362A PHE* 4.4 24.5 - + + -
363A ASP 3.0 18.4 - - - +
364A LYS* 3.6 40.6 + - + +
365A ALA 4.8 0.2 - - - +
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Residues in contact with VAL 346 (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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334A LYS* 3.7 34.3 + - + +
335A MET 3.3 8.7 - - - +
336A VAL* 4.0 18.4 - - + -
345A TYR* 1.3 77.2 - - - +
347A LEU* 1.3 62.6 + - - +
348A THR* 3.6 3.3 + - - -
361A HIS* 3.5 10.2 + - - +
362A PHE* 4.6 2.5 - - - -
363A ASP* 2.9 38.4 + - - +
365A ALA* 4.8 4.3 - - + -
459A ALA 4.8 1.1 - - - +
461A TYR* 4.1 29.8 - - + -
463A PHE* 4.6 12.8 - - + -
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Residues in contact with LEU 347 (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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279A VAL* 5.6 1.1 - - + -
286A LEU* 3.7 25.1 - - + -
334A LYS* 3.4 3.5 - - - -
335A MET* 2.6 69.6 + - + +
337A ILE* 4.0 6.5 - - + +
345A TYR 4.0 1.2 - - - -
346A VAL* 1.3 72.9 - - - +
348A THR* 1.3 66.4 + - - +
349A LEU* 4.0 17.9 + - + +
360A PHE* 3.7 28.9 - - + -
361A HIS 3.1 19.5 - - - +
362A PHE* 3.2 25.7 - - + -
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Residues in contact with THR 348 (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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333A ASP* 3.5 17.0 - - - +
334A LYS* 2.4 37.6 + - + +
346A VAL 4.2 4.2 + - - -
347A LEU* 1.3 73.9 - - - +
349A LEU* 1.3 70.0 + - - +
350A ILE* 3.2 13.7 + - + +
360A PHE* 3.9 2.8 - - - -
361A HIS* 3.2 46.1 + - - +
459A ALA* 6.5 0.2 - - + -
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Residues in contact with LEU 349 (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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271A VAL* 4.2 29.8 - - + -
275A ILE* 4.5 11.4 - - + -
279A VAL* 4.5 10.5 - - + -
288A TYR* 5.0 6.1 - - + -
329A PHE* 4.5 16.6 - - + -
333A ASP* 3.3 31.0 + - + +
335A MET* 5.9 3.4 - - + -
347A LEU* 4.0 17.0 + - + +
348A THR* 1.3 73.9 - - - +
350A ILE* 1.3 64.0 + - - +
351A THR* 3.1 15.2 + - - +
357A VAL* 4.6 12.6 - - + -
359A ALA 4.4 2.0 - - - -
360A PHE* 3.6 30.3 - - + -
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Residues in contact with ILE 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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348A THR* 4.1 14.1 - - + +
349A LEU* 1.3 68.1 - - - +
351A THR* 1.3 63.7 + - - +
352A ASP* 4.8 1.1 - - - +
357A VAL* 3.5 6.1 - - - +
358A ARG* 2.9 73.6 + - + +
359A ALA* 3.2 32.1 + - + +
360A PHE 4.3 12.1 - - - +
361A HIS* 4.4 11.4 - - + -
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Residues in contact with THR 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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275A ILE* 3.5 24.0 - - + +
332A TYR* 6.1 2.5 - - + -
333A ASP* 4.5 5.3 - - - +
349A LEU* 3.1 15.8 + - - +
350A ILE* 1.3 76.8 - - - +
352A ASP* 1.3 77.4 + - - +
355A ARG* 3.8 32.8 - - - +
356A SER 3.3 15.5 + - - +
357A VAL* 5.3 0.7 - - - +
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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