Contacts of the helix formed by residues 326 - 340 (chain A) in PDB entry 6BHG
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 ASP 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A ASP 4.3 6.7 + - - +
299A ASP* 5.3 3.4 - - - +
324A ILE* 3.4 3.1 - - - +
325A GLU* 1.3 77.9 - - - +
327A ILE* 1.3 59.7 + - - +
328A SER* 2.6 31.6 + - - -
329A CYS* 3.1 25.7 + - + +
330A ARG* 2.9 26.7 + - - +
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Residues in contact with ILE 327 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A GLU 3.3 7.0 + - - +
326A ASP* 1.3 72.7 + - - +
328A SER* 1.3 61.5 + - - +
330A ARG* 4.0 30.5 - - - +
331A ASP* 2.9 44.9 + - - +
536A UNX 3.7 20.0 - - - -
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Residues in contact with SER 328 (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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326A ASP* 2.6 22.8 + - - -
327A ILE* 1.3 82.9 - - - +
329A CYS* 1.3 60.0 + - - +
331A ASP* 4.0 5.0 - - - +
332A PHE* 3.0 29.5 + - - +
15B ALA* 6.0 4.0 - - - +
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Residues in contact with CYS 329 (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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298A ASP 3.5 21.8 - - - +
299A ASP 3.8 5.8 - - - -
300A GLY* 3.7 21.3 - - - -
324A ILE* 3.7 4.7 - - + -
326A ASP* 3.1 25.9 + - - +
328A SER* 1.3 81.9 + - - +
330A ARG* 1.3 64.1 + - - +
332A PHE* 3.2 5.8 + - - +
333A ILE* 3.0 28.6 + - - +
505A UNX 3.2 17.9 - - - -
516A UNX 4.0 8.5 - - - -
13B GLY* 5.8 0.4 - - - -
14B ALY 6.1 1.1 - - - -
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Residues in contact with ARG 330 (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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321A TRP* 3.4 28.1 - - + +
322A GLU* 3.8 37.7 + - - +
324A ILE* 3.5 32.9 + - + +
326A ASP 2.9 16.1 + - - +
327A ILE* 3.6 26.2 - - + +
329A CYS* 1.3 75.7 - - - +
331A ASP* 1.3 60.3 + - - +
333A ILE* 3.4 3.1 + - - +
334A GLU* 3.0 29.3 + - - +
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Residues in contact with ASP 331 (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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327A ILE* 2.9 33.8 + - - +
328A SER* 4.0 5.5 - - - +
330A ARG* 1.3 80.5 + - - +
332A PHE* 1.3 62.9 - - - +
334A GLU* 3.4 15.1 + - - +
335A GLU* 3.0 23.4 + - - +
536A UNX 2.5 28.1 - - - -
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Residues in contact with PHE 332 (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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296A PHE* 3.8 22.0 - + - -
328A SER 3.0 19.6 + - - +
329A CYS* 3.2 6.0 + - - +
331A ASP* 1.3 77.2 - - - +
333A ILE* 1.3 68.6 + - + +
335A GLU* 3.2 14.6 + - - +
336A TYR* 2.8 37.5 + + + +
389A TYR* 4.5 7.2 - + - -
512A UNX 3.3 27.8 - - - -
513A UNX 3.7 12.3 - - - -
14B ALY 3.6 54.3 - - + -
15B ALA* 4.8 11.0 - - + -
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Residues in contact with ILE 333 (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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280A ILE* 3.9 28.0 - - + -
296A PHE* 3.8 39.9 - - + -
321A TRP* 3.7 21.3 - - + -
324A ILE* 3.8 9.0 - - + -
329A CYS 3.0 20.9 + - - +
330A ARG 3.9 3.6 - - - +
332A PHE* 1.3 83.5 - - + +
334A GLU* 1.4 65.6 + - - +
336A TYR* 4.3 4.0 - - + -
337A VAL* 2.8 40.4 + - + +
505A UNX 3.6 16.4 - - - -
14B ALY 5.9 0.4 - - + -
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Residues in contact with GLU 334 (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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321A TRP* 3.5 41.4 + - + +
330A ARG* 3.0 16.6 + - - +
331A ASP* 3.8 14.3 - - - +
332A PHE 3.3 0.2 - - - -
333A ILE* 1.4 77.4 - - - +
335A GLU* 1.3 61.9 + - - +
337A VAL* 4.3 0.2 - - - +
338A THR* 2.7 32.6 + - - +
507A UNX 3.0 19.8 - - - -
508A UNX 2.7 28.5 - - - -
526A UNX 4.3 11.7 - - - -
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Residues in contact with GLU 335 (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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331A ASP 3.0 13.6 + - - +
332A PHE* 3.6 16.6 - - - +
334A GLU* 1.3 76.4 - - - +
336A TYR* 1.3 63.9 + - - +
338A THR* 3.9 3.2 - - - -
339A ALA* 3.0 28.3 + - + +
511A UNX 3.9 11.5 - - - -
512A UNX 3.9 14.9 - - - -
526A UNX 3.8 17.0 - - - -
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Residues in contact with TYR 336 (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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260A VAL* 4.1 11.4 - - + -
280A ILE* 6.0 1.1 - - + -
282A ALA* 2.6 45.6 + - + +
294A LEU* 4.9 0.2 - - - +
296A PHE* 3.8 25.2 - + - -
332A PHE* 2.8 27.0 + + + +
333A ILE* 3.7 5.4 - - + +
335A GLU* 1.3 80.1 - - - +
337A VAL* 1.3 73.7 + - + +
339A ALA 3.4 0.5 + - - -
340A TYR* 3.0 10.8 + + - +
343A ARG* 2.9 25.9 + - - -
389A TYR* 3.4 26.5 - + - -
510A UNX 4.2 0.9 - - - -
511A UNX 4.4 1.8 - - - -
512A UNX 3.8 21.1 - - - -
527A UNX 2.6 36.1 - - - -
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Residues in contact with VAL 337 (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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260A VAL* 4.4 10.5 - - + +
261A GLY* 3.9 32.3 - - - +
280A ILE* 4.4 3.8 - - + -
321A TRP* 3.9 24.0 - - + -
333A ILE* 2.8 38.7 + - + +
336A TYR* 1.3 84.3 - - + +
338A THR* 1.3 54.7 + - - +
340A TYR* 3.4 9.5 + - - +
535A UNX 2.7 28.6 - - - -
539A UNX 4.2 7.0 - - - -
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Residues in contact with THR 338 (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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321A TRP* 4.1 1.7 - - - -
334A GLU* 2.7 25.1 + - - +
335A GLU* 3.9 4.0 - - - -
337A VAL* 1.3 78.0 - - - +
339A ALA* 1.3 60.9 + - - +
340A TYR 4.0 1.0 - - - +
507A UNX 2.9 26.1 - - - -
535A UNX 3.7 7.6 - - - -
539A UNX 3.3 19.2 - - - -
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Residues in contact with ALA 339 (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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335A GLU* 3.0 18.4 + - + +
336A TYR 3.9 0.2 - - - +
338A THR* 1.3 77.4 - - - +
340A TYR* 1.3 66.8 + - - +
341A PRO* 3.3 0.9 - - - +
342A ASN* 2.9 27.2 + - + +
510A UNX 3.8 18.2 - - - -
511A UNX 3.9 7.4 - - - -
527A UNX 4.0 0.4 - - - -
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Residues in contact with TYR 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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260A VAL* 3.6 47.5 - - + +
282A ALA 4.4 2.9 - - - -
283A GLU* 5.5 3.6 - - - +
284A THR* 5.4 3.8 + - - -
336A TYR* 3.0 13.9 + - + +
337A VAL 3.5 14.8 - - - +
338A THR 3.4 2.4 - - - +
339A ALA* 1.3 78.8 - - - +
341A PRO* 1.3 84.4 - - + +
342A ASN 3.7 0.2 - - - +
343A ARG* 3.9 34.9 + - - -
503A UNX 4.5 7.2 - - - -
527A UNX 3.5 6.7 - - - -
535A UNX 2.8 24.2 - - - -
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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