Contacts of the helix formed by residues 351 - 366 (chain A) in PDB entry 4B18
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 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A TYR* 4.0 41.5 - - + +
314A SER* 5.4 2.2 - - - +
349A SER* 3.0 8.7 + - - +
350A PRO* 1.3 76.0 - - + +
352A GLU* 1.3 66.7 + - - +
353A SER* 3.3 21.7 + - - +
354A ILE* 3.1 37.6 + - + +
355A LYS 3.2 4.7 + - - -
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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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350A PRO 3.4 6.9 + - - +
351A LYS* 1.3 72.5 - - - +
353A SER* 1.3 57.7 + - - +
355A LYS* 3.3 24.8 + - - +
356A LYS* 2.8 30.1 + - - +
392A ALA* 3.5 9.4 - - - +
393A GLU* 3.0 58.7 + - - +
395A ARG* 6.2 0.7 - - + -
396A THR* 2.9 26.3 + - - +
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Residues in contact with SER 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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351A LYS* 3.7 22.7 + - - +
352A GLU* 1.3 77.5 - - - +
354A ILE* 1.3 60.1 + - - +
356A LYS* 3.3 20.5 + - - +
357A GLU* 2.8 38.0 + - - +
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Residues in contact with ILE 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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310A TYR* 4.1 11.9 - - + -
313A VAL* 4.0 18.6 - - + -
314A SER* 3.6 30.5 - - - +
317A LEU* 3.5 15.3 - - + +
346A LEU* 4.1 28.0 - - + -
349A SER* 3.7 18.8 - - - +
351A LYS* 3.2 33.7 - - + +
353A SER* 1.3 73.7 + - - +
355A LYS* 1.3 60.2 + - - +
357A GLU* 3.3 0.6 + - - -
358A ALA* 2.9 27.7 + - - +
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Residues in contact with LYS 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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346A LEU 4.1 5.8 - - - -
347A LEU* 3.5 31.0 - - - +
348A SER* 4.5 3.1 - - - +
349A SER 3.0 32.3 - - - +
350A PRO 5.0 3.1 + - - -
351A LYS 3.2 7.2 + - - +
352A GLU* 3.3 32.1 + - - +
354A ILE* 1.3 77.2 - - - +
356A LYS* 1.3 59.1 - - - +
358A ALA* 3.3 4.1 + - - +
359A CYS* 2.9 33.8 + - - -
388A ILE* 4.2 13.7 - - + -
391A THR* 5.7 2.4 + - - -
392A ALA* 4.8 8.6 - - + +
396A THR* 4.0 14.4 - - + -
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Residues in contact with LYS 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLU 2.8 18.0 + - - +
353A SER* 3.5 17.3 - - - +
355A LYS* 1.3 78.5 - - - +
357A GLU* 1.3 68.5 + - - +
359A CYS* 3.2 4.7 + - - +
360A TRP* 3.0 27.0 + - - +
395A ARG* 3.9 28.0 - - + +
396A THR* 3.8 28.0 - - - +
399A GLU* 3.7 16.1 - - + +
224B ARG* 3.5 35.8 - - - +
229B SER* 3.2 29.1 + - - -
230B ARG* 4.3 2.0 - - - +
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Residues in contact with GLU 357 (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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314A SER 5.5 1.1 - - - +
317A LEU* 3.3 29.8 - - + +
318A ARG* 3.3 33.0 + - - +
353A SER* 2.8 23.2 + - - +
354A ILE* 4.4 0.2 - - - -
356A LYS* 1.3 83.0 + - - +
358A ALA* 1.3 59.8 + - - +
360A TRP* 3.3 15.3 + - + +
361A THR* 2.9 32.6 + - - -
224B ARG* 2.7 28.3 + - - -
230B ARG* 3.0 18.4 - - - +
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Residues in contact with ALA 358 (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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317A LEU* 3.7 9.4 - - + +
343A LEU* 4.3 12.5 - - + +
346A LEU* 4.1 22.9 - - + -
347A LEU* 4.2 12.8 - - + -
354A ILE 2.9 17.4 + - - +
355A LYS* 3.7 5.6 - - - +
357A GLU* 1.3 78.0 - - - +
359A CYS* 1.3 58.2 + - - +
361A THR* 3.4 5.4 + - - -
362A ILE* 2.9 35.6 + - - +
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Residues in contact with CYS 359 (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* 3.6 20.2 - - - -
355A LYS 2.9 21.6 + - - -
356A LYS 3.2 9.2 + - - +
358A ALA* 1.3 77.6 - - - +
360A TRP* 1.3 57.8 + - - +
362A ILE* 3.3 7.2 + - - +
363A SER* 2.9 27.2 + - - -
385A LEU* 3.9 13.9 - - - -
388A ILE* 3.8 19.3 - - - -
396A THR* 4.4 3.6 - - - +
399A GLU* 3.4 18.8 - - + +
400A ALA* 3.7 15.9 - - - +
403A ALA* 4.1 4.5 - - - +
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Residues in contact with TRP 360 (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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318A ARG* 4.8 4.3 - - - -
321A GLY* 3.6 33.7 - - - -
322A ASN* 3.7 16.2 - - - -
325A THR* 4.1 11.2 - - + -
356A LYS 3.0 15.3 + - - +
357A GLU* 3.7 26.0 - - + +
358A ALA 3.3 0.2 - - - -
359A CYS* 1.3 75.3 - - - +
361A THR* 1.3 75.6 + - - +
363A SER* 2.5 23.0 + - - -
364A ASN* 3.2 30.7 + - - +
399A GLU* 3.7 27.1 - - + +
222B ARG* 3.9 13.8 - - - +
223B ARG* 4.3 3.4 - - - +
224B ARG* 4.1 38.6 - - + +
230B ARG* 3.7 28.0 - - - -
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Residues in contact with THR 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU* 3.7 11.7 + - + +
320A VAL* 4.6 8.7 - - + -
321A GLY* 3.4 20.9 - - - -
324A VAL* 3.6 23.7 - - + +
343A LEU* 4.0 27.8 - - + -
357A GLU 2.9 19.7 + - - -
358A ALA 3.6 5.4 - - - -
360A TRP* 1.3 82.0 - - - +
362A ILE* 1.3 62.4 + - - +
364A ASN* 3.1 14.2 + - - +
365A ILE* 3.2 15.2 + - + +
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Residues in contact with ILE 362 (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 LEU* 4.7 4.3 - - + -
343A LEU* 4.3 22.9 - - + -
347A LEU* 4.0 21.3 - - + -
358A ALA 2.9 21.3 + - - +
359A CYS* 3.6 4.7 - - - +
361A THR* 1.3 76.8 - - - +
363A SER* 1.3 57.6 + - - +
365A ILE* 2.9 9.2 + - - +
366A THR* 2.8 42.0 + - + +
376A VAL* 4.4 6.5 - - + -
381A ILE* 3.7 46.9 - - + -
385A LEU* 4.1 15.5 - - + -
403A ALA* 4.2 1.8 - - + -
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Residues in contact with SER 363 (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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359A CYS 2.9 11.0 + - - -
360A TRP* 2.5 27.0 + - - -
362A ILE* 1.3 76.9 - - - +
364A ASN* 1.3 59.6 + - - +
366A THR* 3.3 2.5 + - - -
367A ALA* 3.1 16.6 + - - +
399A GLU 4.2 1.3 - - - -
402A TRP* 3.9 8.5 - - - -
403A ALA* 3.5 35.6 - - - +
406A ASN* 3.1 27.3 + - - -
222B ARG* 3.5 14.9 + - - -
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Residues in contact with ASN 364 (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 GLY 4.6 2.6 + - - -
324A VAL* 3.5 29.5 - - + +
325A THR* 3.5 21.1 - - - +
331A THR* 4.9 6.4 + - - +
360A TRP* 3.2 35.5 + - - +
361A THR* 3.1 8.1 + - - +
362A ILE 3.1 0.8 - - - -
363A SER* 1.3 84.0 + - - +
365A ILE* 1.3 63.4 + - - +
367A ALA* 4.0 14.8 + - - +
368A GLY 4.2 4.0 + - - -
406A ASN* 5.4 0.9 + - - -
222B ARG* 3.3 33.5 + - - +
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Residues in contact with ILE 365 (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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324A VAL* 4.0 19.5 - - + -
331A THR* 4.1 7.4 - - - +
334A ILE* 5.2 2.2 - - + -
335A LEU* 3.5 46.7 - - + -
339A ALA* 5.8 0.2 - - + -
340A LEU* 3.9 15.9 - - + -
343A LEU* 4.0 17.9 - - + -
361A THR* 3.2 17.6 + - + +
362A ILE* 2.9 8.6 + - - +
364A ASN* 1.3 77.0 - - - +
366A THR* 1.3 57.2 + - - +
367A ALA 3.1 4.3 - - - -
368A GLY* 3.1 18.9 + - - -
372A GLN* 4.0 13.2 - - + +
373A ILE 4.6 0.9 + - - -
376A VAL* 3.7 22.2 - - + -
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Residues in contact with THR 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ILE* 2.8 27.1 + - + +
363A SER 3.3 8.7 + - - -
365A ILE* 1.3 72.2 - - - +
367A ALA* 1.3 56.7 + - - +
368A GLY 3.3 2.5 - - - -
373A ILE* 3.8 22.4 - - - +
376A VAL* 3.8 35.7 - - + -
382A PHE* 4.1 13.0 - - + -
403A ALA 2.7 27.1 + - - +
406A ASN* 3.4 21.9 - - - +
407A ALA* 3.5 9.9 + - - -
410A GLY* 5.6 0.3 - - - -
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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