Contacts of the helix formed by residues 383 - 402 (chain A) in PDB entry 2B7O
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 HIS 383 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A ASN 4.0 6.5 + - - -
373A HIS* 4.1 15.5 + - + -
382A ARG* 1.3 72.1 - - - +
384A PHE* 1.3 69.2 + - + +
385A ASP* 3.5 39.7 + - + -
386A ARG* 3.0 33.9 + - + +
387A ILE* 3.1 15.6 + - - +
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Residues in contact with PHE 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ARG 3.5 4.8 + - - -
383A HIS* 1.3 74.5 - - + +
385A ASP* 1.3 67.3 + - - +
387A ILE* 3.0 13.5 + - + +
388A VAL* 2.9 46.8 + - + +
444A LEU* 3.7 22.9 - - + +
448A GLN* 3.2 51.0 - - + +
451A GLU* 3.6 38.6 - - + -
452A LEU* 3.9 12.8 - - + -
455A LEU* 3.9 10.8 - - + -
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Residues in contact with ASP 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A HIS* 3.2 22.9 + - + -
384A PHE* 1.3 87.0 - - - +
386A ARG* 1.3 58.9 + - + +
388A VAL* 3.6 7.3 + - - +
389A ASP* 3.0 28.2 + - - +
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Residues in contact with ARG 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASN* 2.8 57.8 + - - +
341A HIS* 3.5 25.7 + - - +
370A GLY 3.5 15.2 + - - -
371A ASN* 3.3 38.7 + - + +
372A THR 5.4 2.4 + - - -
373A HIS* 6.0 2.0 + - - -
383A HIS* 3.0 25.0 + - + +
385A ASP* 1.3 76.7 - - + +
387A ILE* 1.3 65.2 + - - +
389A ASP* 4.5 0.2 - - - -
390A GLU* 3.1 21.0 + - - +
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Residues in contact with ILE 387 (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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367A PRO* 3.3 47.6 - - + +
368A MSE 4.0 18.6 - - + -
371A ASN* 4.5 7.2 - - + -
382A ARG* 4.0 22.4 - - + -
383A HIS 3.1 17.8 + - - +
384A PHE* 3.0 9.8 + - + +
386A ARG* 1.3 72.7 - - - +
388A VAL* 1.3 66.2 + - - +
390A GLU 3.2 9.0 + - - -
391A VAL* 3.3 11.3 + - - +
444A LEU* 3.8 28.5 - - + -
452A LEU* 4.3 22.2 - - + -
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Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A PHE* 2.9 44.1 + - + +
385A ASP* 3.8 9.2 - - - +
387A ILE* 1.3 74.9 - - - +
389A ASP* 1.3 58.7 + - - +
391A VAL* 3.1 5.9 + - - +
392A GLN* 2.8 32.0 + - + +
452A LEU* 4.0 19.1 - - + -
455A LEU* 3.8 28.3 - - + -
459A MSE 5.6 5.2 - - - -
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Residues in contact with ASP 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASN* 2.9 39.5 + - - +
344A ARG* 2.6 32.0 + - - -
385A ASP 3.0 19.4 + - - +
386A ARG 3.9 0.4 - - - +
387A ILE 3.3 0.4 - - - -
388A VAL* 1.3 77.1 - - - +
390A GLU* 1.3 58.4 + - - +
392A GLN* 3.3 9.9 + - - +
393A GLY* 2.7 25.3 + - - -
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Residues in contact with GLU 390 (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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336A SER* 4.1 3.3 + - - +
337A ARG* 3.8 5.0 - - - -
338A MSE 2.9 32.4 + - - +
339A GLY* 3.1 24.4 + - - +
340A ASN* 3.4 15.1 - - - +
343A VAL* 3.8 14.8 - - + +
365A CYS* 4.2 11.6 - - - -
366A ASP 3.9 2.4 - - - +
367A PRO* 3.8 13.2 - - + +
370A GLY* 4.7 1.0 - - - -
371A ASN* 2.8 23.3 + - - +
386A ARG 3.1 10.8 + - - +
387A ILE 3.2 7.4 + - - +
389A ASP* 1.3 73.6 - - - +
391A VAL* 1.3 59.9 + - - +
393A GLY* 3.2 1.7 + - - -
394A PHE* 2.8 28.1 + - - +
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Residues in contact with VAL 391 (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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365A CYS* 4.0 13.5 - - - -
367A PRO* 3.7 22.9 - - + -
387A ILE 3.3 13.4 + - - +
388A VAL* 3.1 8.1 + - + +
390A GLU* 1.3 74.6 - - - +
392A GLN* 1.3 64.5 + - - +
394A PHE* 3.1 5.1 + - + +
395A PHE* 3.0 34.2 + - + -
408A ILE* 4.1 16.6 - - + -
452A LEU* 4.5 15.0 - - + -
456A VAL* 3.9 17.3 - - + -
459A MSE 3.2 23.8 - - - +
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Residues in contact with GLN 392 (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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344A ARG* 4.2 6.5 - - - +
388A VAL* 2.8 22.9 + - + +
389A ASP* 3.3 15.9 - - - +
391A VAL* 1.3 73.8 - - - +
393A GLY* 1.3 61.6 + - - +
395A PHE* 3.3 3.9 + - - +
396A GLU* 3.1 52.7 + - - +
459A MSE 3.1 36.6 - - + +
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Residues in contact with GLY 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A VAL* 3.8 10.5 - - - -
344A ARG* 3.5 33.1 - - - +
389A ASP 2.7 16.0 + - - -
390A GLU 3.6 3.6 - - - -
392A GLN* 1.3 73.1 - - - +
394A PHE* 1.3 61.8 + - - +
396A GLU* 3.3 3.8 + - - +
397A VAL* 3.1 28.6 + - - +
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Residues in contact with PHE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A SER* 4.4 7.6 - - - -
343A VAL* 3.9 11.5 - - + +
347A LEU* 3.7 19.3 - - + -
363A TRP* 3.3 28.3 - + + -
364A GLN 3.7 6.7 - - - -
365A CYS* 3.3 44.6 - - + -
390A GLU 2.8 16.6 + - - +
391A VAL* 3.1 8.3 + - + +
393A GLY* 1.3 71.5 - - - +
395A PHE* 1.3 77.6 + + - +
397A VAL* 3.5 4.7 + - - +
398A HIS* 3.0 49.9 + + - -
405A PRO* 3.6 26.7 - - + -
407A GLY 3.9 9.0 - - - -
408A ILE* 5.9 0.2 - - + -
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Residues in contact with PHE 395 (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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80A PHE* 4.3 9.4 - + - -
391A VAL* 3.0 29.0 + - + -
392A GLN* 3.5 3.4 - - - +
394A PHE* 1.3 85.7 - + - +
396A GLU* 1.3 50.9 + - - +
398A HIS* 3.1 3.1 + - - +
399A ARG* 2.8 67.0 + - + +
405A PRO* 3.5 33.0 - - + -
408A ILE* 5.4 0.9 - - + -
456A VAL* 4.0 11.0 - - + -
459A MSE 2.9 44.9 - - + -
460A LEU* 3.5 41.5 - - + -
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Residues in contact with GLU 396 (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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344A ARG* 2.6 35.2 + - + +
392A GLN* 3.1 46.3 + - - +
393A GLY 3.6 6.1 - - - +
395A PHE* 1.3 72.6 - - - +
397A VAL* 1.3 58.8 + - + +
399A ARG* 3.3 7.9 + - - +
400A ALA* 3.0 33.2 + - - +
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Residues in contact with VAL 397 (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 VAL 3.8 22.0 - - - +
344A ARG* 3.9 12.8 - - + +
347A LEU* 4.0 20.4 - - + -
348A PRO* 3.7 40.2 - - + -
351A VAL* 4.5 4.3 - - + -
393A GLY 3.1 16.4 + - - +
394A PHE 3.6 7.9 - - - +
396A GLU* 1.3 76.2 - - + +
398A HIS* 1.3 62.6 + - + +
400A ALA* 3.7 4.4 + - - +
401A LEU* 3.1 30.2 + - + +
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Residues in contact with HIS 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 4.1 6.7 - - + +
351A VAL* 3.9 18.1 - - + +
363A TRP* 3.4 34.3 - + + +
394A PHE* 3.0 63.8 + + - -
395A PHE 3.1 6.7 + - - +
397A VAL* 1.3 74.9 - - + +
399A ARG* 1.3 68.2 + - - +
401A LEU 3.0 0.9 + - - -
402A GLY* 2.9 20.1 + - - -
403A THR* 2.7 46.8 + - - +
404A HIS 3.8 2.6 + - - -
405A PRO* 3.8 17.5 - - + -
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Residues in contact with ARG 399 (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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395A PHE* 2.8 48.2 + - + +
396A GLU* 3.8 6.5 - - - +
398A HIS* 1.3 71.4 - - - +
400A ALA* 1.3 63.0 + - - +
402A GLY* 3.0 15.2 + - - -
403A THR 5.1 1.1 - - - -
405A PRO* 4.1 20.1 - - - +
459A MSE 2.5 31.3 + - - -
460A LEU* 3.6 13.1 + - - +
462A ASP* 2.6 30.8 + - - +
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Residues in contact with ALA 400 (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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396A GLU 3.0 17.2 + - - +
397A VAL* 4.0 5.4 - - - +
399A ARG* 1.3 76.5 - - - +
401A LEU* 1.3 63.0 + - + +
402A GLY 3.8 0.2 + - - -
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Residues in contact with LEU 401 (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 PRO* 3.9 25.4 - - + +
351A VAL* 3.7 32.5 - - + -
352A GLU* 3.5 31.4 - - + +
397A VAL* 3.1 21.2 + - + +
398A HIS 3.0 3.0 + - - -
400A ALA* 1.3 81.3 - - + +
402A GLY* 1.3 62.5 + - - +
403A THR* 3.7 19.3 - - + +
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Residues in contact with GLY 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A HIS 2.9 6.4 + - - -
399A ARG* 3.0 10.3 + - - -
400A ALA 3.4 0.2 - - - -
401A LEU* 1.3 77.7 - - - +
403A THR* 1.3 62.1 + - - +
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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
------------------------------------------------------------
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