Contacts of the helix formed by residues 342 - 356 (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 LYS 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A PRO* 4.4 16.4 - - + +
338A MSE 3.6 24.7 - - - +
339A GLY 3.2 2.2 + - - -
341A HIS* 1.3 113.0 + - + +
343A VAL* 1.3 60.2 + - - +
344A ARG 3.4 2.2 - - - -
345A ASP* 3.3 9.0 + - - +
346A LEU* 2.9 47.6 + - + +
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Residues in contact with VAL 343 (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* 3.9 4.9 - - - +
338A MSE 3.8 25.8 - - + -
339A GLY 3.1 16.0 + - - +
340A ASN 4.2 4.5 + - - +
341A HIS 3.9 0.2 - - - -
342A LYS* 1.3 77.7 - - - +
344A ARG* 1.3 72.5 + - - +
346A LEU 4.5 0.2 - - - +
347A LEU* 3.1 46.7 + - + +
348A PRO* 3.7 0.7 - - - +
390A GLU* 3.8 29.8 - - + +
393A GLY* 3.8 17.0 - - - +
394A PHE* 4.4 12.3 - - + -
397A VAL* 3.8 2.1 - - - +
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Residues in contact with ARG 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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340A ASN 3.3 24.5 + - - -
341A HIS 5.4 3.1 - - - -
342A LYS 3.4 0.4 - - - -
343A VAL* 1.3 78.0 - - - +
345A ASP* 1.3 64.9 + - - +
348A PRO* 3.1 24.9 - - - +
389A ASP* 2.6 42.4 + - - -
392A GLN* 4.2 3.4 - - - +
393A GLY* 3.5 23.3 - - - +
396A GLU* 2.6 41.7 + - + +
397A VAL* 3.9 10.5 - - + +
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Residues in contact with ASP 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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341A HIS 3.9 17.2 - - - +
342A LYS* 3.3 6.0 + - - +
343A VAL 3.2 0.4 - - - -
344A ARG* 1.3 84.8 - - - +
346A LEU* 1.3 70.4 + - + +
347A LEU 3.6 0.2 - - - -
348A PRO* 3.5 7.4 - - - +
349A PRO* 3.6 11.1 - - - +
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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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309A PRO* 3.3 42.8 - - + +
311A MSE 6.0 2.2 - - - +
338A MSE 3.9 13.9 - - + -
342A LYS* 2.9 43.9 + - + +
345A ASP* 1.3 80.8 - - + +
347A LEU* 1.3 65.0 + - - +
348A PRO* 3.6 0.2 - - - -
349A PRO* 3.4 12.4 - - - +
350A ILE* 3.3 18.9 - - + +
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Residues in contact with LEU 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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307A LEU* 5.9 1.6 - - + -
336A SER* 3.9 17.7 - - - +
338A MSE 3.5 24.1 - - + +
343A VAL* 3.1 24.3 + - + +
346A LEU* 1.3 76.7 - - - +
348A PRO* 1.4 68.3 - - + +
350A ILE* 2.9 22.7 + - + +
351A VAL* 3.0 30.4 + - + +
363A TRP* 4.5 11.4 - - + -
394A PHE* 3.7 31.6 - - + -
397A VAL* 4.0 13.0 - - + -
398A HIS* 4.1 11.2 - - - +
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Residues in contact with PRO 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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343A VAL 3.7 1.3 - - - +
344A ARG 3.1 28.3 - - - +
345A ASP 3.5 10.1 - - - +
347A LEU* 1.4 93.1 - - + +
349A PRO* 1.4 65.3 - - + +
351A VAL* 3.4 0.9 + - - +
352A GLU* 3.0 35.2 + - - +
397A VAL* 3.7 25.8 - - + -
401A LEU* 4.1 11.0 - - + -
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Residues in contact with PRO 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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313A PRO* 3.7 19.8 - - + +
345A ASP 3.6 11.4 - - - +
346A LEU* 3.4 16.2 - - - +
348A PRO* 1.4 97.9 - - + +
350A ILE* 1.3 61.9 + - + +
352A GLU* 3.7 14.4 - - - +
353A LYS* 3.1 25.1 + - - +
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Residues in contact with ILE 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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307A LEU* 4.3 9.9 - - + -
311A MSE 3.9 29.6 - - + +
312A THR 4.1 3.1 - - - -
313A PRO* 4.0 27.1 - - + -
316A ALA* 3.8 21.8 - - + -
338A MSE 3.6 21.5 - - + -
346A LEU* 3.3 22.2 - - + +
347A LEU* 2.9 10.3 + - + +
349A PRO* 1.3 76.8 - - + +
351A VAL* 1.3 67.8 + - - +
353A LYS* 3.8 1.4 - - - +
354A VAL* 3.0 22.7 + - - +
363A TRP* 4.1 20.2 - - + -
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Residues in contact with VAL 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 LEU* 3.0 42.7 + - + +
348A PRO 3.8 0.7 - - - +
350A ILE* 1.3 74.0 - - - +
352A GLU* 1.3 54.0 + - - +
354A VAL* 3.1 2.8 + - - +
355A GLN* 2.7 44.2 + - + +
363A TRP* 3.7 23.6 - - + +
397A VAL* 4.5 4.0 - - + -
398A HIS* 3.9 16.2 - - + -
401A LEU* 3.7 22.9 - - + -
403A THR* 3.8 28.7 - - + +
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Residues in contact with GLU 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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348A PRO* 3.0 28.4 + - - +
349A PRO* 3.7 14.1 - - - +
351A VAL* 1.3 74.3 - - - +
353A LYS* 1.3 64.1 + - - +
355A GLN* 3.3 7.5 + - - +
356A ALA* 3.0 23.4 + - - +
401A LEU* 3.5 31.7 - - + +
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Residues in contact with LYS 353 (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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313A PRO* 3.7 29.6 - - + +
314A GLU* 3.6 25.4 + - + +
317A VAL* 3.7 20.2 - - + +
349A PRO 3.1 15.0 + - - +
350A ILE 3.8 1.8 - - - +
352A GLU* 1.3 79.0 - - - +
354A VAL* 1.3 62.2 + - - +
356A ALA* 3.3 20.2 + - + +
357A THR* 3.7 5.0 + - - +
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Residues in contact with VAL 354 (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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313A PRO 5.0 0.4 - - - +
316A ALA* 3.9 33.9 - - + +
317A VAL* 4.3 4.7 - - + +
320A VAL* 3.8 21.1 - - + -
334A LEU* 4.1 5.6 - - + -
350A ILE 3.0 16.9 + - - +
353A LYS* 1.3 73.2 - - - +
355A GLN* 1.3 67.4 + - - +
357A THR* 2.5 34.5 + - - +
359A HIS 4.3 4.5 - - - +
361A VAL* 4.0 15.7 - - + -
363A TRP* 3.6 33.2 - - + -
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Residues in contact with GLN 355 (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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351A VAL* 2.7 28.9 + - + +
352A GLU* 3.7 6.7 - - - +
354A VAL* 1.3 74.3 - - - +
356A ALA* 1.3 56.6 + - - +
357A THR 3.1 5.4 + - - -
358A GLY* 3.3 11.3 + - - -
359A HIS 4.7 13.2 + - - +
360A GLN* 5.6 2.5 - - - +
361A VAL* 4.9 5.0 + - - +
363A TRP* 3.0 26.6 + - - -
403A THR* 3.7 31.7 - - + +
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Residues in contact with ALA 356 (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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352A GLU 3.0 13.5 + - - +
353A LYS* 3.5 17.9 - - + +
354A VAL 3.1 0.6 - - - -
355A GLN* 1.3 74.8 - - - +
357A THR* 1.3 62.0 + - - +
358A GLY 3.3 1.2 + - - -
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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