Contacts of the helix formed by residues 342 - 357 (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 LYS 342 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309B PRO* 3.9 27.9 - - + +
338B MSE 3.3 25.7 + - + +
339B GLY 3.2 1.6 + - - -
341B HIS* 1.3 109.9 + - + +
343B VAL* 1.3 59.3 + - - +
344B ARG 3.4 2.7 - - - -
345B ASP* 3.2 8.2 + - - +
346B LEU* 3.0 47.5 + - + +
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Residues in contact with VAL 343 (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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336B SER* 4.2 10.5 - - - +
338B MSE 4.3 9.2 - - + -
339B GLY 3.2 15.9 + - - +
340B ASN 4.0 11.2 - - - +
341B HIS 3.9 0.2 - - - -
342B LYS* 1.3 76.6 - - - +
344B ARG* 1.3 65.9 + - + +
346B LEU 4.6 0.2 - - - +
347B LEU* 3.1 57.8 + - + +
365B CYS* 6.1 0.2 - - - -
390B GLU* 3.8 34.3 - - + +
393B GLY* 4.1 7.4 - - - -
394B PHE* 4.0 21.8 - - + +
397B VAL* 3.6 2.2 - - + +
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Residues in contact with ARG 344 (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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340B ASN 3.4 17.4 + - - -
341B HIS 6.2 0.7 - - - +
342B LYS 3.4 0.4 - - - -
343B VAL* 1.3 77.6 - - - +
345B ASP* 1.3 66.5 + - - +
348B PRO* 3.1 23.7 - - - +
389B ASP* 2.5 49.1 + - - -
392B GLN* 4.1 3.0 - - - +
393B GLY* 3.4 34.2 - - - +
396B GLU* 3.1 35.6 + - + +
397B VAL* 3.9 7.5 - - + +
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Residues in contact with ASP 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B HIS 4.5 11.3 - - - +
342B LYS* 3.2 6.5 + - - +
343B VAL 3.2 0.6 - - - -
344B ARG* 1.3 84.9 - - - +
346B LEU* 1.3 69.5 + - + +
347B LEU 3.5 0.2 - - - -
348B PRO* 3.6 7.5 - - - +
349B PRO* 3.6 11.4 - - - +
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B PRO* 3.6 39.7 - - + +
311B MSE 6.1 1.1 - - - +
338B MSE 4.0 14.1 - - + -
342B LYS* 3.0 41.8 + - + +
345B ASP* 1.3 83.3 - - + +
347B LEU* 1.3 65.2 + - - +
349B PRO* 3.4 11.1 - - - +
350B ILE* 3.5 18.8 - - + +
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LEU* 6.2 1.3 - - + -
336B SER* 3.6 21.3 - - - +
338B MSE 4.4 12.9 - - + -
343B VAL* 3.1 32.8 + - + +
346B LEU* 1.3 78.2 - - - +
348B PRO* 1.4 69.9 - - + +
350B ILE* 3.0 27.3 + - + +
351B VAL* 3.0 26.7 + - + +
363B TRP* 4.7 7.4 - - + -
394B PHE* 3.6 31.0 - - + -
397B VAL* 4.0 18.8 - - + -
398B HIS* 4.1 8.7 - - - +
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Residues in contact with PRO 348 (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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343B VAL 3.8 0.9 - - - +
344B ARG 3.1 26.0 - - - +
345B ASP 3.6 3.8 - - - +
347B LEU* 1.4 90.4 - - + +
349B PRO* 1.4 66.6 - - + +
351B VAL* 3.2 2.1 + - - +
352B GLU* 2.8 42.0 + - - +
397B VAL* 3.8 25.4 - - + -
401B LEU* 3.9 12.1 - - + +
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Residues in contact with PRO 349 (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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313B PRO* 3.7 20.2 - - + +
345B ASP 3.6 11.0 - - - +
346B LEU* 3.4 16.6 - - - +
348B PRO* 1.4 97.5 - - + +
350B ILE* 1.3 59.2 + - - +
352B GLU* 3.9 7.4 - - + +
353B LYS* 3.2 26.0 + - - +
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Residues in contact with ILE 350 (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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307B LEU* 4.5 7.9 - - + -
311B MSE 3.8 24.5 - - + +
312B THR 4.1 2.0 - - - -
313B PRO* 3.9 30.5 - - + +
316B ALA* 3.9 19.7 - - + -
338B MSE 3.8 27.1 - - + -
346B LEU* 3.5 20.6 - - + +
347B LEU* 3.0 13.5 + - + +
349B PRO* 1.3 77.5 - - - +
351B VAL* 1.3 64.2 + - - +
353B LYS* 3.3 1.9 + - - +
354B VAL* 3.1 23.7 + - - +
363B TRP* 4.0 20.9 - - + -
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Residues in contact with VAL 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 3.0 36.4 + - + +
348B PRO 3.7 6.1 - - - +
350B ILE* 1.3 76.6 - - - +
352B GLU* 1.3 56.4 + - - +
354B VAL* 3.8 0.9 - - - +
355B GLN* 2.8 38.6 + - + +
363B TRP* 3.7 31.6 - - + +
397B VAL* 4.5 3.1 - - + -
398B HIS* 3.9 14.8 - - + -
401B LEU* 3.6 22.0 - - + -
403B THR* 3.7 28.3 - - + +
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Residues in contact with GLU 352 (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* 2.8 35.1 + - - +
349B PRO* 3.9 7.6 - - + +
351B VAL* 1.3 72.2 - - - +
353B LYS* 1.3 62.5 + - + +
355B GLN* 3.5 6.1 + - - +
356B ALA* 3.1 23.6 + - - +
401B LEU* 3.5 31.6 - - + +
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Residues in contact with LYS 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B PRO* 3.4 28.5 - - + +
314B GLU* 4.3 21.7 + - - +
317B VAL* 3.8 19.8 - - + +
349B PRO 3.2 12.3 + - - +
350B ILE 3.7 3.6 - - - +
351B VAL 3.3 0.2 - - - -
352B GLU* 1.3 75.5 - - - +
354B VAL* 1.3 67.3 + - - +
356B ALA* 3.3 17.7 + - + +
357B THR* 3.5 13.3 - - - +
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Residues in contact with VAL 354 (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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316B ALA* 4.1 17.9 - - + -
317B VAL* 4.2 13.9 - - + -
320B VAL* 3.8 26.5 - - + -
334B LEU* 4.1 10.3 - - + -
350B ILE 3.1 13.8 + - - +
353B LYS* 1.3 73.2 - - - +
355B GLN* 1.3 66.5 + - - +
357B THR* 2.5 31.5 + - - +
358B GLY 4.1 0.3 + - - -
359B HIS 4.2 7.3 - - - +
361B VAL* 4.1 14.4 - - + -
363B TRP* 3.7 31.6 - - + -
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Residues in contact with GLN 355 (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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351B VAL* 2.8 27.8 + - + +
352B GLU* 3.7 6.5 - - - +
354B VAL* 1.3 76.4 - - - +
356B ALA* 1.3 61.5 + - - +
357B THR 3.2 1.4 + - - -
358B GLY* 3.2 14.0 + - - -
359B HIS 4.7 10.7 + - - +
360B GLN* 5.8 3.7 - - - +
361B VAL* 4.9 5.2 + - - +
363B TRP* 2.8 28.9 + - - -
403B THR* 3.5 32.3 - - + +
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Residues in contact with ALA 356 (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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352B GLU 3.1 14.7 + - - +
353B LYS* 3.5 14.1 - - + +
354B VAL 3.1 0.6 - - - -
355B GLN* 1.3 76.7 - - - +
357B THR* 1.3 60.4 + - + +
358B GLY* 3.2 1.6 + - - -
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Residues in contact with THR 357 (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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317B VAL* 3.8 31.6 - - + -
320B VAL* 4.6 3.5 - - + +
321B GLU* 4.6 9.2 - - + +
327B ASN* 5.1 0.9 - - - +
353B LYS 3.5 15.0 - - - +
354B VAL* 2.5 20.8 + - + +
356B ALA* 1.3 76.5 - - - +
358B GLY* 1.3 57.9 + - - +
359B HIS* 3.2 34.9 + - - +
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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