Contacts of the helix formed by residues 348 - 364 (chain B) in PDB entry 3C39
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 ALA 348 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342B PHE* 3.5 32.8 - - + +
344B TRP 3.2 6.7 + - - +
345B GLU* 3.3 21.8 + - - +
347B PHE* 1.4 75.5 - - - +
349B ARG* 1.3 60.2 + - - +
350B GLY 3.4 2.7 - - - -
351B THR* 3.2 6.4 + - - +
352B LYS* 3.0 44.9 + - + +
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Residues in contact with ARG 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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286B VAL* 3.8 29.3 - - - +
314B ASP* 3.3 5.2 + - - +
315B CYS 6.1 0.2 - - - +
345B GLU* 4.4 17.2 + - - +
346B ALA* 3.6 25.1 + - - +
347B PHE* 4.6 0.2 - - - +
348B ALA* 1.3 74.5 - - - +
350B GLY* 1.3 56.7 + - - +
352B LYS* 4.1 6.9 - - + +
353B ALA* 2.8 36.7 + - - +
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Residues in contact with GLY 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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314B ASP* 3.0 23.4 + - - -
315B CYS* 3.7 21.7 + - - -
316B GLY 6.2 0.2 - - - -
320B SER* 4.1 9.3 + - - -
323B TYR* 5.7 1.2 - - - -
339B VAL* 3.7 8.5 - - - +
349B ARG* 1.3 75.4 - - - +
351B THR* 1.3 57.7 + - - +
353B ALA* 3.6 1.9 - - - +
354B LEU* 3.1 29.1 + - - +
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Residues in contact with THR 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ASP* 4.1 1.5 + - - -
335B TRP* 3.6 25.2 - - + -
338B PRO* 4.1 8.4 - - + +
339B VAL* 3.6 23.0 + - - +
340B GLY* 3.7 7.6 + - - -
342B PHE* 3.6 39.2 - - + +
348B ALA* 3.2 9.4 + - - -
350B GLY* 1.3 73.4 - - - +
352B LYS* 1.3 60.5 + - + +
354B LEU* 3.5 2.3 + - - -
355B MET* 3.0 28.1 + - + +
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Residues in contact with LYS 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B PHE* 5.6 3.8 - - + -
345B GLU* 2.9 30.5 + - - +
348B ALA* 3.0 40.8 + - + +
349B ARG* 4.1 6.3 - - + +
351B THR* 1.3 70.9 - - + +
353B ALA* 1.3 60.1 + - - +
355B MET* 3.2 9.4 + - - +
356B ASP* 2.9 37.2 + - - +
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Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B SER* 3.9 22.7 - - - +
349B ARG 2.8 23.5 + - - +
350B GLY 3.6 4.9 - - - +
352B LYS* 1.3 71.7 - - - +
354B LEU* 1.3 62.0 + - - +
356B ASP* 3.1 14.3 + - - +
357B GLU* 3.1 26.6 + - - +
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Residues in contact with LEU 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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210B ILE* 3.9 25.1 - - + -
234B ILE* 4.9 0.9 - - + -
320B SER* 5.3 0.6 + - - -
323B TYR* 4.1 29.6 - - + -
327B VAL* 3.8 28.5 - - + -
335B TRP* 3.7 26.5 - - + -
339B VAL* 3.7 31.0 - - + -
350B GLY 3.1 14.2 + - - +
351B THR* 3.7 0.7 - - - +
352B LYS 3.4 0.2 - - - -
353B ALA* 1.3 77.0 - - - +
355B MET* 1.3 58.5 + - - +
357B GLU* 3.1 8.1 + - + -
358B VAL* 2.9 32.8 + - + +
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Residues in contact with MET 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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335B TRP* 3.7 28.4 - - + -
351B THR* 3.0 18.4 + - + +
352B LYS* 3.2 12.5 + - - +
354B LEU* 1.3 77.1 - - - +
356B ASP* 1.3 59.8 + - - +
358B VAL* 3.2 3.5 + - - +
359B VAL* 2.8 41.9 + - + +
370B ILE* 3.7 32.3 - - + -
388B VAL* 4.6 14.4 - - - -
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Residues in contact with ASP 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 LYS* 2.9 24.1 + - - +
353B ALA* 3.1 12.7 + - - +
355B MET* 1.3 78.4 - - - +
357B GLU* 1.3 63.4 + - + +
359B VAL* 3.8 7.3 - - - +
360B LYS* 3.0 40.4 + - + +
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Residues in contact with GLU 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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320B SER 5.1 2.0 - - - +
324B ALA* 3.5 37.6 - - + +
327B VAL* 3.5 31.0 - - + +
328B THR* 5.3 2.3 + - - -
353B ALA* 3.1 14.8 + - + +
354B LEU* 3.1 11.7 + - + +
356B ASP* 1.3 77.0 - - - +
358B VAL* 1.3 57.3 + - - +
360B LYS* 3.0 35.1 + - - +
361B ALA 2.9 23.6 + - - -
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Residues in contact with VAL 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ILE* 4.3 11.0 - - + -
327B VAL* 4.4 6.5 - - + -
333B ILE* 4.5 11.0 - - + -
335B TRP* 4.1 17.0 - - + -
354B LEU* 2.9 29.7 + - + +
355B MET* 3.8 8.5 - - - +
357B GLU* 1.3 75.4 - - - +
359B VAL* 1.3 56.8 + - - +
361B ALA* 3.8 5.1 - - - +
362B THR* 2.6 34.0 + - - -
368B THR* 3.8 19.9 - - + +
370B ILE* 4.1 14.8 - - + -
388B VAL* 3.7 20.9 - - + -
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Residues in contact with VAL 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B MET* 2.8 30.0 + - + +
356B ASP* 3.8 7.4 - - - +
358B VAL* 1.3 76.6 - - - +
360B LYS* 1.3 65.0 - - + +
362B THR* 3.2 5.9 + - - -
363B SER* 3.1 29.6 + - - +
387B LYS* 3.7 56.4 - - + +
388B VAL* 4.1 10.1 - - + -
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Residues in contact with LYS 360 (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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356B ASP* 3.0 30.6 + - + +
357B GLU* 3.0 41.7 + - - +
359B VAL* 1.3 77.8 - - + +
361B ALA* 1.3 63.0 + - - +
363B SER* 3.5 9.4 + - - -
364B ARG* 3.4 21.7 + - - +
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Residues in contact with ALA 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B VAL* 3.7 19.1 - - + -
333B ILE* 4.5 2.0 - - + -
357B GLU 2.9 18.6 + - - +
358B VAL* 3.8 6.5 - - - +
359B VAL 3.2 0.2 - - - -
360B LYS* 1.3 74.2 - - - +
362B THR* 1.3 65.4 + - - +
364B ARG* 3.1 30.2 + - - +
366B CYS* 3.0 38.6 + - + +
368B THR* 4.6 0.2 - - + -
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Residues in contact with THR 362 (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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358B VAL 2.6 22.2 + - - -
359B VAL 3.3 7.0 - - - -
361B ALA* 1.3 76.5 - - - +
363B SER* 1.3 56.1 + - - +
365B GLY* 2.7 27.0 + - - -
366B CYS* 3.4 17.9 + - - +
368B THR* 2.7 24.8 + - - +
387B LYS 3.5 21.2 + - - +
388B VAL* 3.8 2.3 - - - -
389B SER* 3.8 16.2 - - - +
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Residues in contact with SER 363 (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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12A ASP* 5.5 6.3 - - - +
14A LYS* 4.6 19.6 + - - +
359B VAL* 3.1 17.9 + - - +
360B LYS* 3.6 13.3 - - - -
361B ALA 3.3 0.2 - - - -
362B THR* 1.3 77.2 - - - +
364B ARG* 1.3 58.6 - - - +
365B GLY 3.3 0.9 + - - -
387B LYS* 5.5 1.4 + - - +
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Residues in contact with ARG 364 (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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327B VAL* 2.9 21.2 + - - +
328B THR* 3.3 19.2 + - - +
330B ALA 2.8 30.7 + - - -
331B LYS* 4.1 24.2 + - - +
360B LYS 3.4 11.9 - - - +
361B ALA* 3.1 22.4 + - - +
362B THR 3.1 0.2 - - - -
363B SER* 1.3 77.7 - - - +
365B GLY* 1.3 54.6 + - - +
366B CYS* 3.4 22.5 - - - +
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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