Contacts of the helix formed by residues 343 - 357 (chain B) in PDB entry 3SN5
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 LEU 343 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B GLU* 3.3 25.8 - - + +
315B VAL* 5.3 2.2 - - - +
318B THR* 3.2 36.1 - - + +
335B LEU* 6.0 0.2 - - + -
339B GLU 3.7 4.9 - - - +
340B LEU* 3.5 32.1 + - + +
341B ASN 3.7 1.6 - - - -
342B ASP* 1.3 80.6 - - - +
344B PRO* 1.4 60.8 - - - +
345B VAL 3.4 0.3 + - - -
346B LEU* 3.4 17.2 + - + -
347B ASP* 2.9 31.5 + - - +
455B LYS* 3.8 12.8 - - + -
459B ILE* 3.7 28.9 - - + -
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Residues in contact with PRO 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU* 3.3 13.7 - - - +
342B ASP* 3.4 17.3 - - - +
343B LEU* 1.4 86.8 - - - +
345B VAL* 1.4 54.9 - - + +
347B ASP* 3.4 8.2 + - + +
348B SER* 2.9 30.3 + - - -
413B LEU* 3.4 23.6 - - + +
417B GLY 3.8 17.7 - - - +
418B LYS* 4.7 1.8 - - - -
419B THR* 3.9 18.7 + - - +
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Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ALA* 3.9 21.1 - - + +
311B ALA* 3.8 27.1 - - - +
314B GLU* 3.1 25.1 + - + +
344B PRO* 1.4 71.7 - - + +
346B LEU* 1.3 60.5 + - - +
348B SER* 3.2 4.3 + - - -
349B ILE* 3.0 42.1 + - + +
409B TYR* 4.3 9.6 - - + +
413B LEU* 4.0 21.3 - - + -
417B GLY 5.8 1.6 - - - +
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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
----------------------------------------------------------
301B MET* 4.6 4.9 - - - -
311B ALA* 4.0 26.5 - - + +
314B GLU* 3.0 14.7 + - + +
315B VAL* 4.0 14.1 - - + -
343B LEU* 3.9 26.7 - - + +
345B VAL* 1.3 74.7 - - - +
347B ASP* 1.4 57.1 + - - +
349B ILE* 3.2 8.5 + - + +
350B ILE* 2.9 37.0 + - + +
455B LYS* 4.3 20.4 - - + +
458B LEU* 4.1 24.0 - - + -
459B ILE* 3.9 28.9 - - + -
462B LEU* 4.7 0.7 - - + -
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Residues in contact with ASP 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A GLN* 5.4 3.8 + - - -
340B LEU 4.6 0.2 - - - +
341B ASN* 4.9 5.4 - - - +
343B LEU 2.9 21.7 + - - +
344B PRO* 3.5 8.8 - - + +
345B VAL 3.3 0.2 - - - -
346B LEU* 1.4 73.4 - - - +
348B SER* 1.3 57.4 + - - +
350B ILE* 3.4 5.3 + - - +
351B LYS* 2.9 59.4 + - - +
419B THR* 5.0 7.1 + - + +
451B ILE* 3.6 13.0 - - - +
455B LYS* 2.9 35.6 + - - +
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Residues in contact with SER 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B PRO 2.9 18.0 + - - -
345B VAL 3.4 4.7 - - - -
347B ASP* 1.3 76.0 - - - +
349B ILE* 1.4 51.1 + - - +
351B LYS* 3.4 1.8 + - - +
352B GLU* 2.9 36.0 + - - +
409B TYR 2.7 24.8 + - - -
411B ARG 3.6 1.0 + - - -
412B TYR* 3.0 39.7 + - - -
413B LEU* 3.6 17.8 - - - +
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Residues in contact with ILE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B SER* 3.8 26.7 - - - +
301B MET* 4.1 17.0 - - + -
307B ALA* 3.8 27.4 - - + +
311B ALA* 3.9 11.7 - - + -
345B VAL* 3.0 32.0 + - + +
346B LEU* 3.2 10.1 + - + +
348B SER* 1.4 73.6 - - - +
350B ILE* 1.4 54.1 + - - +
352B GLU 3.5 0.2 + - - -
353B SER* 2.8 38.2 + - - +
407B PHE* 3.7 18.4 - - + -
409B TYR* 4.1 21.5 - - + +
458B LEU* 4.9 8.3 - - + -
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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
----------------------------------------------------------
297B SER* 3.7 15.5 - - - +
346B LEU 2.9 24.3 + - - +
347B ASP* 3.9 3.8 - - - +
349B ILE* 1.4 73.9 - - - +
351B LYS* 1.3 56.3 + - + +
353B SER* 3.1 3.3 + - - -
354B LEU* 2.9 39.0 + - + +
434B TYR* 5.0 0.4 - - - +
451B ILE* 3.7 36.1 - - + +
454B ILE* 3.6 39.3 - - + -
455B LYS* 3.7 31.6 - - + +
458B LEU* 4.1 10.5 - - + -
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Residues in contact with LYS 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B ASP* 2.9 49.4 + - - +
348B SER 3.7 0.2 - - - +
350B ILE* 1.3 75.2 - - + +
352B GLU* 1.3 50.4 + - - +
354B LEU 3.2 1.2 + - - -
355B ARG* 2.8 33.1 + - - +
412B TYR* 3.5 41.0 - - + +
419B THR* 4.3 19.2 - - - +
433B TYR* 6.1 1.8 - - + -
434B TYR* 3.3 50.2 - - + +
451B ILE* 6.2 1.3 - - + -
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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
----------------------------------------------------------
348B SER 2.9 21.5 + - - +
351B LYS* 1.3 70.0 - - - +
353B SER* 1.3 63.2 + - - +
355B ARG* 2.6 44.6 + - - +
356B LEU* 3.4 24.1 + - - +
406B THR 3.2 2.1 - - - +
407B PHE* 3.3 29.1 - - + -
408B LYS 3.0 34.8 + - - +
409B TYR* 5.0 0.4 - - - -
411B ARG* 2.8 34.0 + - + +
412B TYR* 3.8 5.5 - - + -
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Residues in contact with SER 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA 4.9 1.1 - - - -
296B TRP* 3.6 15.3 + - - +
297B SER* 3.3 38.4 + - - -
300B GLN* 4.0 3.7 - - - +
349B ILE 2.8 22.2 + - - -
350B ILE 3.4 5.2 - - - -
352B GLU* 1.3 78.1 - - - +
354B LEU* 1.3 56.9 + - - +
356B LEU* 3.6 4.4 + - - +
357B SER* 2.7 31.5 + - - -
407B PHE* 3.5 15.4 - - - -
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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
----------------------------------------------------------
293B ALA* 3.6 35.7 - - + +
350B ILE* 2.9 31.3 + - + +
351B LYS 3.8 3.6 - - - +
353B SER* 1.3 77.4 - - - +
355B ARG* 1.4 58.5 + - - +
357B SER* 3.6 4.9 - - - +
358B SER* 2.8 37.5 + - - +
434B TYR* 3.5 21.3 - - - +
436B PRO* 3.9 25.4 - - + -
437B PHE* 4.0 20.9 - - + -
451B ILE* 4.6 0.4 - - + -
488B ILE* 3.8 15.0 - - + -
601B HEM 4.4 7.6 - - + -
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Residues in contact with ARG 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 LYS 2.8 20.2 + - - +
352B GLU* 2.6 46.2 + - - +
353B SER 3.4 0.4 - - - -
354B LEU* 1.4 72.4 - - - +
356B LEU* 1.3 71.8 + - - +
357B SER 3.8 0.2 + - - -
358B SER 4.4 3.3 + - - +
392B GLN* 5.4 0.9 - - - +
395B HIS* 2.7 80.9 + - + +
396B LEU* 3.9 10.9 - - - +
401B TYR* 3.8 19.3 - - + +
404B PRO* 2.8 36.5 + - - +
406B THR 3.3 10.9 + - - -
411B ARG* 3.7 9.8 - - - +
412B TYR* 3.5 22.7 - - - +
434B TYR* 4.5 4.7 - - + -
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B GLN* 3.7 25.8 - - - +
352B GLU* 3.4 16.2 + - - +
353B SER 4.0 4.0 - - - +
354B LEU 3.2 0.4 - - - -
355B ARG* 1.3 91.8 - - - +
357B SER* 1.4 58.4 + - - +
358B SER 3.8 0.4 - - - -
392B GLN* 4.1 7.4 + - - -
396B LEU* 4.1 14.3 - - + +
404B PRO 3.6 23.1 - - - +
405B LEU* 3.8 22.7 - - + +
407B PHE* 3.9 25.4 - - + +
479B LEU* 3.5 20.2 - - - +
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Residues in contact with SER 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B TRP* 3.7 32.1 - - - -
353B SER 2.7 25.0 + - - -
354B LEU* 3.2 4.9 + - - +
356B LEU* 1.4 77.8 - - - +
358B SER* 1.4 64.4 + - - +
359B ALA 3.5 0.5 + - - -
392B GLN* 4.8 1.3 - - - -
479B LEU* 4.3 10.5 - - - -
488B ILE* 3.5 18.2 - - - +
489B LEU* 2.9 36.8 + - - +
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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