Contacts of the helix formed by residues 339 - 352 (chain A) in PDB entry 3BMW
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 THR 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A TYR* 3.7 30.5 - - + +
337A GLY 4.4 1.1 - - - +
338A SER* 1.3 72.2 + - - +
340A ARG* 1.3 66.0 + - - +
341A PRO* 3.4 1.6 - - - -
342A VAL* 3.2 6.4 - - - +
343A GLU* 2.7 44.1 + - - -
365A TYR* 3.5 33.2 + - + -
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Residues in contact with ARG 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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338A SER* 3.0 13.9 + - - +
339A THR* 1.3 80.7 + - - +
341A PRO* 1.4 61.0 - - + +
343A GLU* 3.0 26.0 + - - +
344A GLN* 2.8 46.0 + - + +
386A THR* 5.3 2.0 - - - +
438A LEU* 3.8 21.5 - - + -
463A LEU 4.0 7.7 + - - -
464A LEU* 3.5 32.1 + - - +
465A ASN* 2.8 29.7 + - - -
484A ALA 4.8 0.8 + - - -
485A GLY* 2.9 35.1 + - - +
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Residues in contact with PRO 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A PHE* 3.4 30.4 - - + +
295A ARG* 5.4 0.7 - - - -
333A PHE* 4.0 6.4 - - + -
338A SER* 3.4 25.4 - - - +
339A THR 3.5 0.4 - - - -
340A ARG* 1.4 92.1 - - + +
342A VAL* 1.3 57.5 + - - +
344A GLN* 3.2 12.7 + - + +
345A ALA* 2.9 28.1 + - - +
436A ARG 6.0 0.9 - - - +
438A LEU* 4.1 17.2 - - + -
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Residues in contact with VAL 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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325A ILE* 3.8 15.7 - - + -
333A PHE* 3.6 33.6 - - + -
334A TYR* 4.5 18.6 - - + +
338A SER 5.4 0.2 + - - -
339A THR* 3.2 17.6 + - - +
341A PRO* 1.3 78.8 - - - +
343A GLU* 1.3 60.9 + - + +
345A ALA* 3.8 0.3 - - - +
346A LEU* 2.9 32.3 + - + +
362A THR* 3.8 20.9 - - + +
365A TYR* 3.8 28.9 - - + -
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Residues in contact with GLU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A THR* 2.7 30.4 + - - +
340A ARG* 3.0 34.3 + - - +
342A VAL* 1.3 75.5 - - - +
344A GLN* 1.3 57.7 + - - +
346A LEU* 3.5 9.1 + - - +
347A ALA* 3.0 27.4 + - - +
365A TYR* 2.6 29.6 + - + +
386A THR* 3.5 22.9 - - + +
387A ALA* 4.4 13.0 - - + +
390A VAL* 4.1 6.1 - - + +
464A LEU* 3.7 21.9 - - + +
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Residues in contact with GLN 344 (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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294A PHE* 3.5 23.2 - - + -
340A ARG* 2.8 27.9 + - - +
341A PRO* 3.6 10.5 - - - +
343A GLU* 1.3 74.3 - - - +
345A ALA* 1.3 60.2 + - - +
347A ALA* 3.2 2.4 + - - +
348A PHE* 2.8 30.7 + - - +
434A ILE* 3.9 10.7 - - + +
435A ASN 2.8 27.3 + - - -
436A ARG* 3.3 21.9 - - - +
438A LEU* 5.2 0.8 - - - +
485A GLY* 3.0 24.5 + - - -
486A GLU 3.7 6.1 + - - -
487A VAL* 3.6 21.0 - - + +
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Residues in contact with ALA 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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290A VAL* 3.8 17.9 - - + +
294A PHE* 4.4 6.9 - - + -
325A ILE* 4.0 11.2 - - + -
333A PHE* 3.5 32.8 - - + -
341A PRO 2.9 12.3 + - - +
342A VAL 3.8 4.3 - - - +
344A GLN* 1.3 74.8 - - - +
346A LEU* 1.3 57.4 + - - +
348A PHE* 3.5 6.7 + - - +
349A THR* 2.9 35.1 + - - -
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Residues in contact with LEU 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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325A ILE* 4.3 11.2 - - + +
342A VAL* 2.9 23.5 + - + +
343A GLU* 3.6 7.0 - - - +
345A ALA* 1.3 76.8 - - - +
347A ALA* 1.3 56.4 + - - +
349A THR* 3.3 5.3 + - - -
350A LEU* 2.9 38.8 + - + +
358A ILE* 4.1 35.0 - - + -
362A THR* 4.1 29.4 - - + +
387A ALA* 3.9 29.8 - - + +
390A VAL* 4.5 8.3 - - + -
391A ILE* 4.3 13.5 - - + -
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Residues in contact with ALA 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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343A GLU 3.0 17.2 + - - +
344A GLN* 3.6 5.8 - - - +
346A LEU* 1.3 76.3 - - - +
348A PHE* 1.3 56.2 + - - +
350A LEU 4.0 0.3 - - - -
351A THR* 2.8 38.4 + - + +
390A VAL* 4.2 5.8 - - + +
394A LEU* 3.7 26.2 - - + -
421A TYR* 4.7 0.2 - - - -
432A VAL* 5.8 1.3 - - + -
434A ILE* 5.1 1.3 - - + -
464A LEU* 4.4 4.0 - - + -
487A VAL* 3.9 26.5 - - + -
489A VAL* 5.9 0.4 - - + -
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Residues in contact with PHE 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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286A PHE* 3.4 30.5 - + - -
290A VAL* 3.8 22.4 - - + -
294A PHE* 4.5 6.7 - + + -
304A LEU* 3.7 35.2 - - + -
307A MET* 4.6 0.2 - - + -
308A ILE* 4.2 16.8 - - + -
344A GLN 2.8 16.6 + - - +
345A ALA* 3.7 6.5 - - - +
347A ALA* 1.3 78.4 - - - +
349A THR* 1.3 61.0 + - - +
351A THR* 3.4 1.2 + - - -
352A SER* 2.7 44.4 + - - -
419A TYR* 3.9 9.2 - + - -
421A TYR* 3.3 37.2 - + - -
434A ILE* 3.9 14.7 - - + +
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Residues in contact with THR 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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286A PHE* 3.6 19.0 - - + -
290A VAL* 4.9 0.5 - - - +
323A THR* 3.4 37.5 + - - +
324A PHE* 4.3 4.9 - - - +
325A ILE* 3.3 18.5 - - + +
345A ALA 2.9 19.6 + - - -
346A LEU* 3.8 5.8 - - - -
348A PHE* 1.3 76.1 - - - +
350A LEU* 1.3 63.6 + - + +
351A THR 3.2 1.0 + - - -
352A SER* 3.3 14.4 + - - +
356A PRO* 3.7 23.6 - - + +
357A ALA 4.9 3.1 - - - +
358A ILE* 6.1 2.7 - - + -
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Residues in contact with LEU 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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16A VAL* 3.7 41.5 - - + -
346A LEU* 2.9 26.2 + - + +
347A ALA 4.0 3.6 - - - +
348A PHE 3.3 0.2 - - - -
349A THR* 1.3 77.2 - - - +
351A THR* 1.3 59.2 + - - +
356A PRO* 4.2 10.1 - - + -
358A ILE* 4.0 11.9 - - + -
390A VAL* 4.2 2.7 - - + +
391A ILE* 3.8 36.3 - - + +
394A LEU* 4.0 28.6 - - + +
395A ALA* 4.5 7.6 - - + +
398A ARG* 2.9 24.6 + - - +
404A ILE* 3.8 6.6 - - - +
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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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347A ALA 2.8 19.2 + - - +
348A PHE 3.4 0.2 + - - -
350A LEU* 1.3 79.7 - - - +
352A SER* 1.3 60.3 + - - +
394A LEU* 4.3 22.9 - - + +
397A LEU* 5.1 0.9 - - + -
398A ARG* 4.2 0.9 - - - -
404A ILE* 4.1 19.1 - - + +
421A TYR* 2.7 29.4 + - - -
423A ARG* 2.9 30.3 + - - +
432A VAL* 3.8 22.4 - - + +
489A VAL* 4.3 14.4 - - + -
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Residues in contact with SER 352 (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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286A PHE* 4.0 22.9 - - - -
308A ILE* 5.0 2.8 - - - +
348A PHE* 2.7 44.9 + - - -
349A THR 3.3 7.9 + - - +
351A THR* 1.3 76.0 - - - +
353A ARG* 1.3 70.1 + - - +
356A PRO* 5.0 0.3 - - - +
398A ARG* 2.8 24.1 + - - -
409A THR* 6.1 1.9 - - - +
421A TYR* 3.8 7.7 + - - -
423A ARG* 3.2 10.7 + - - +
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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