Contacts of the helix formed by residues 383 - 402 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B ASN* 5.8 0.8 - - - +
373B HIS* 4.3 8.6 + + + -
382B ARG* 1.3 72.8 - - - +
384B PHE* 1.3 71.3 + - + +
385B ASP* 3.1 47.5 + - + +
386B ARG* 3.1 37.7 + - + +
387B ILE* 3.2 16.2 + - - +
420B CYS 4.3 4.5 - - - -
421B LEU* 2.8 33.9 + - - +
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Residues in contact with PHE 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ARG 3.5 4.4 + - - -
383B HIS* 1.3 76.3 + - + +
385B ASP* 1.3 71.1 + - - +
387B ILE* 3.1 14.1 + - + +
388B VAL* 2.9 49.5 + - + +
420B CYS* 3.6 15.7 + - - +
444B LEU* 4.3 12.8 - - + -
448B GLN* 3.3 49.6 - - + +
451B GLU* 3.6 39.9 - - + -
452B LEU* 4.1 11.2 - - + -
455B LEU* 3.9 9.9 - - + -
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Residues in contact with ASP 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B HIS* 3.1 27.8 + - + +
384B PHE* 1.3 87.5 - - - +
386B ARG* 1.3 57.4 + - - +
388B VAL* 3.7 8.1 + - - +
389B ASP* 3.0 28.1 + - - +
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Residues in contact with ARG 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ASN* 2.9 57.9 + - - +
341B HIS* 3.8 19.6 + - - +
370B GLY 4.1 4.2 + - - -
371B ASN* 3.3 29.1 + - + +
372B THR 3.4 37.4 + - - +
373B HIS* 5.5 5.6 + - - +
383B HIS* 3.1 28.3 + - + +
385B ASP* 1.3 74.0 - - - +
387B ILE* 1.3 60.9 + - - +
389B ASP* 3.3 0.8 + - - -
390B GLU* 2.9 27.0 + - - +
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Residues in contact with ILE 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B PRO* 3.5 47.1 - - + +
368B MSE 4.2 15.3 - - + -
371B ASN* 4.7 4.5 - - + +
382B ARG* 4.1 22.7 - - + +
383B HIS 3.2 13.8 + - - +
384B PHE* 3.1 13.2 + - + +
386B ARG* 1.3 73.8 - - - +
388B VAL* 1.3 65.4 + - + +
390B GLU 3.2 10.0 + - - -
391B VAL* 3.2 11.3 + - - +
443B ARG 5.8 0.2 - - - +
444B LEU* 3.6 29.4 - - + -
452B LEU* 4.2 23.6 - - + -
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Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B PHE* 2.9 52.0 + - + +
385B ASP* 3.9 7.9 - - - +
387B ILE* 1.3 76.0 - - + +
389B ASP* 1.3 59.9 + - - +
391B VAL* 3.2 4.4 + - - +
392B GLN* 2.9 27.9 + - + +
452B LEU* 3.9 17.7 - - + -
455B LEU* 3.9 18.4 - - + -
459B MSE 3.8 17.1 - - + +
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Residues in contact with ASP 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ASN* 2.8 32.9 + - - +
344B ARG* 2.5 38.0 + - - -
385B ASP 3.0 20.3 + - - +
386B ARG 3.6 0.7 - - - +
387B ILE 3.2 0.2 - - - -
388B VAL* 1.3 76.1 - - - +
390B GLU* 1.3 60.8 + - - +
392B GLN* 4.0 10.3 - - - +
393B GLY 2.9 23.6 + - - -
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Residues in contact with GLU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B SER* 4.3 3.5 + - - +
337B ARG* 3.7 5.0 + - - -
338B MSE 2.7 29.7 + - - +
339B GLY* 2.9 25.7 + - - +
340B ASN* 3.4 12.0 - - - +
343B VAL* 3.8 17.2 - - + +
365B CYS* 4.2 11.3 - - - -
366B ASP 3.9 1.3 - - - +
367B PRO* 3.8 14.8 - - + +
370B GLY* 4.7 1.7 - - - -
371B ASN* 2.9 20.9 + - - +
386B ARG 2.9 17.2 + - - +
387B ILE 3.2 4.4 + - - +
389B ASP* 1.3 76.6 - - - +
391B VAL* 1.3 62.6 + - - +
393B GLY* 3.2 1.9 + - - -
394B PHE* 2.9 22.2 + - - +
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Residues in contact with VAL 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B CYS* 3.9 13.9 - - - -
367B PRO* 3.6 24.7 - - + -
387B ILE 3.2 13.8 + - - +
388B VAL* 3.8 5.6 - - - +
390B GLU* 1.3 73.9 - - - +
392B GLN* 1.3 57.8 + - - +
394B PHE* 3.3 3.8 - - + +
395B PHE* 2.9 53.1 + - + -
408B ILE* 4.0 16.4 - - + -
452B LEU* 4.4 14.4 - - + -
456B VAL* 3.8 12.6 - - + -
459B MSE 3.8 13.2 - - + -
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Residues in contact with GLN 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ARG* 4.1 6.5 - - - +
388B VAL* 2.9 19.4 + - + +
389B ASP* 3.5 13.7 - - - +
391B VAL* 1.3 76.0 - - - +
393B GLY* 1.3 57.2 + - - +
395B PHE* 3.2 8.5 + - - +
396B GLU* 2.8 60.6 + - - +
459B MSE 3.7 34.0 - - + +
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Residues in contact with GLY 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B VAL* 4.1 10.1 - - - -
344B ARG* 3.4 35.7 - - - +
389B ASP 2.9 15.1 + - - -
390B GLU 3.2 2.4 + - - -
392B GLN* 1.3 69.7 - - - +
394B PHE* 1.3 60.5 + - - +
396B GLU* 3.2 4.4 + - - +
397B VAL* 2.8 33.4 + - - +
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Residues in contact with PHE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B SER* 4.5 7.4 - - - -
343B VAL* 4.0 13.2 - - + +
347B LEU* 3.6 19.5 - - + -
363B TRP* 3.4 26.0 - + + -
364B GLN 3.9 8.5 - - - -
365B CYS* 3.5 43.5 - - + -
390B GLU 2.9 12.2 + - - +
391B VAL 3.3 7.9 - - - +
393B GLY* 1.3 76.1 - - - +
395B PHE* 1.3 78.4 + + - +
397B VAL* 3.2 5.9 + - - +
398B HIS* 3.1 50.2 + + - -
405B PRO* 3.7 22.2 - - + -
407B GLY 3.9 8.7 - - - -
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Residues in contact with PHE 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE* 4.1 15.7 - + - -
391B VAL* 2.9 46.4 + - + +
392B GLN* 3.2 10.7 + - - +
394B PHE* 1.3 83.5 - + - +
396B GLU* 1.3 57.0 + - - +
398B HIS* 3.3 1.6 + - - +
399B ARG* 2.9 56.6 + - + +
405B PRO* 3.6 28.5 - - + -
408B ILE* 5.3 0.9 - - + -
456B VAL* 4.0 14.6 - - + -
459B MSE 3.8 27.1 - - + +
460B LEU* 3.3 36.8 - - + -
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B ARG* 3.1 39.3 + - + -
392B GLN* 2.8 43.9 + - - +
393B GLY 3.2 6.3 + - - +
395B PHE* 1.3 76.3 - - - +
397B VAL* 1.3 62.9 + - - +
399B ARG* 3.9 7.0 - - + +
400B ALA* 3.1 25.3 + - - +
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Residues in contact with VAL 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B VAL 3.6 24.9 - - - +
344B ARG* 3.9 8.5 - - + +
347B LEU* 4.0 21.3 - - + -
348B PRO* 3.8 41.2 - - + +
351B VAL* 4.5 5.2 - - + -
393B GLY 2.8 22.7 + - - +
394B PHE 3.2 7.4 + - - +
396B GLU* 1.3 75.9 - - - +
398B HIS* 1.3 63.4 + - + +
400B ALA* 3.5 3.9 + - - +
401B LEU* 3.2 29.7 + - + +
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Residues in contact with HIS 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 4.1 6.5 - - + +
351B VAL* 3.9 18.3 - - + +
363B TRP* 3.4 33.4 - + + -
394B PHE* 3.1 60.6 + + - -
395B PHE 4.0 2.0 - - - +
397B VAL* 1.3 74.5 - - + +
399B ARG* 1.3 61.5 + - - +
401B LEU 3.2 0.5 + - - -
402B GLY* 2.8 26.0 + - - -
403B THR* 2.8 48.4 + - - +
404B HIS 3.8 3.0 + - - -
405B PRO* 3.8 22.7 - - + -
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Residues in contact with ARG 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 2.9 46.2 + - + +
396B GLU* 3.9 6.3 - - + +
398B HIS* 1.3 72.7 - - - +
400B ALA* 1.3 62.3 + - - +
402B GLY* 3.1 13.4 + - - -
403B THR 5.3 0.9 + - - -
404B HIS* 6.1 0.2 - - - -
405B PRO* 3.8 23.3 - - - +
459B MSE 2.8 27.9 + - - -
460B LEU* 3.4 14.6 + - - +
462B ASP* 3.1 29.8 + - - +
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Residues in contact with ALA 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B GLU 3.1 15.5 + - - +
397B VAL* 3.8 4.5 - - - +
399B ARG* 1.3 78.2 - - - +
401B LEU* 1.3 65.8 + - + +
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Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B PRO* 3.9 23.6 - - + +
351B VAL* 3.6 34.1 - - + -
352B GLU* 3.5 35.0 - - + +
397B VAL* 3.2 17.4 + - + +
398B HIS 3.2 2.8 + - - -
400B ALA* 1.3 82.9 - - + +
402B GLY* 1.3 62.2 + - - +
403B THR* 3.4 20.1 + - + +
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Residues in contact with GLY 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B HIS 2.8 6.9 + - - -
399B ARG* 3.1 10.8 + - - -
400B ALA 3.3 0.4 + - - -
401B LEU* 1.3 79.7 - - - +
403B THR* 1.3 61.7 + - - +
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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
------------------------------------------------------------
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