Contacts of the helix formed by residues 350 - 370 (chain B) in PDB entry 3SF4
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 ASP 350 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312B ILE* 6.2 0.3 - - - +
345B SER* 3.0 17.8 + - - +
348B VAL* 3.4 15.0 + - + -
349B GLY* 1.3 73.9 - - - +
351B LYS* 1.3 58.8 + - - +
352B SER* 3.5 8.7 + - - -
353B GLY* 2.6 37.6 + - - -
354B GLU* 2.8 27.8 + - - +
30E ARG* 5.7 2.6 + - - -
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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
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349B GLY 3.0 9.7 + - - +
350B ASP* 1.3 74.7 + - - +
352B SER* 1.3 64.1 + - - +
354B GLU* 3.1 15.5 + - - +
355B LEU* 3.4 10.0 + - - +
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Residues in contact with SER 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ASP* 3.5 6.4 + - - -
351B LYS* 1.3 79.4 - - - +
353B GLY* 1.3 55.5 + - - +
355B LEU* 3.2 9.1 + - - +
356B THR* 2.7 37.7 + - - +
30E ARG* 5.3 9.3 + - - -
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Residues in contact with GLY 353 (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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319B TRP* 6.5 0.7 - - - -
341B HIS* 4.0 6.1 + - - -
345B SER* 3.5 10.3 + - - -
350B ASP* 2.6 35.9 + - - -
352B SER* 1.3 73.0 + - - +
354B GLU* 1.3 62.3 + - - +
356B THR* 3.7 9.5 - - - +
357B ALA* 3.1 25.1 + - - +
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Residues in contact with GLU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LEU* 3.7 8.0 - - + +
345B SER* 3.8 16.1 - - - -
346B ARG* 2.9 40.5 + - + +
350B ASP 2.8 17.9 + - - +
351B LYS* 3.1 9.0 + - - +
353B GLY* 1.3 76.9 - - - +
355B LEU* 1.3 59.6 + - - +
357B ALA* 3.3 3.3 + - - +
358B ARG* 2.8 53.1 + - - +
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Residues in contact with LEU 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 3.4 7.1 + - - +
352B SER* 3.2 12.2 + - - +
354B GLU* 1.3 78.8 - - - +
356B THR* 1.3 64.6 + - - +
358B ARG* 3.1 13.4 + - + +
359B LEU* 2.9 47.3 + - + +
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Residues in contact with THR 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B TRP* 3.9 33.3 + - + -
341B HIS* 4.2 2.8 - - + -
352B SER* 2.7 23.1 + - - +
353B GLY* 3.7 14.1 - - - +
355B LEU* 1.3 74.9 - - - +
357B ALA* 1.3 61.7 + - - +
359B LEU* 3.3 12.5 + - - +
360B ASN* 3.0 27.9 + - - -
26E ASP* 3.9 11.5 + - - -
30E ARG* 6.2 1.8 - - - +
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Residues in contact with ALA 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ALA 4.5 4.0 - - - +
341B HIS* 3.4 29.4 - - + +
342B LEU* 3.7 29.8 - - + +
345B SER* 4.0 1.3 - - - +
353B GLY 3.1 19.8 + - - +
354B GLU 3.6 4.7 - - - +
356B THR* 1.3 79.2 + - - +
358B ARG* 1.3 56.4 + - - +
360B ASN* 3.5 4.0 + - - +
361B LEU* 3.0 28.8 + - - +
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Residues in contact with ARG 358 (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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342B LEU* 3.6 18.1 - - + +
346B ARG* 2.7 45.6 - - - +
354B GLU* 2.8 41.4 + - - +
355B LEU* 3.1 16.1 + - + +
357B ALA* 1.3 74.8 - - - +
359B LEU* 1.3 61.4 + - - +
361B LEU* 3.2 5.3 + - - +
362B SER* 2.8 34.3 + - - -
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Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LEU* 2.9 44.1 + - + +
356B THR* 3.7 9.4 - - - +
358B ARG* 1.3 75.9 - - - +
360B ASN* 1.3 62.3 + - - +
362B SER* 3.2 7.7 + - - +
363B ASP* 3.0 31.0 + - - +
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Residues in contact with ASN 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B TRP* 3.8 16.3 + - - -
323B ASN* 4.5 9.6 + - - +
338B ALA* 4.8 8.3 - - + -
341B HIS* 5.0 1.8 + - - +
356B THR* 3.0 22.5 + - - +
357B ALA* 3.9 6.2 - - - +
359B LEU* 1.3 79.4 + - - +
361B LEU* 1.3 65.6 + - - +
363B ASP* 3.7 5.3 + - - +
364B LEU* 3.0 32.3 + - + +
26E ASP* 3.2 25.7 + - - +
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Residues in contact with LEU 361 (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 MET* 3.8 19.5 - - + -
338B ALA* 4.0 17.6 - - + +
339B GLU* 3.6 39.3 - - + -
342B LEU* 3.9 26.2 - - + -
357B ALA 3.0 18.1 + - - +
358B ARG* 3.2 4.2 + - - +
360B ASN* 1.3 75.9 - - - +
362B SER* 1.3 58.9 + - - +
364B LEU* 3.0 5.2 + - - +
365B GLN* 2.8 52.7 + - + +
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Residues in contact with SER 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ARG 2.8 20.2 + - - -
359B LEU* 3.2 12.5 + - - +
361B LEU* 1.3 73.8 - - - +
363B ASP* 1.3 59.8 + - - +
365B GLN* 3.1 18.8 + - - +
366B MET* 2.8 37.1 + - - +
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Residues in contact with ASP 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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359B LEU 3.0 21.4 + - - +
360B ASN* 3.7 7.1 + - - +
361B LEU 3.2 0.2 - - - -
362B SER* 1.3 76.7 + - - +
364B LEU* 1.3 67.3 + - - +
366B MET* 3.2 12.2 + - - +
367B VAL* 3.0 34.2 + - - +
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Residues in contact with LEU 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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322B GLY* 5.3 2.0 - - - +
326B THR* 3.9 18.4 - - + +
331B HIS* 3.7 32.5 - - + +
334B ALA* 3.6 36.3 - - + +
335B MET* 3.6 22.7 - - + +
338B ALA* 3.7 18.6 - - + -
360B ASN* 3.0 16.2 + - + +
361B LEU 3.0 8.1 + - - +
363B ASP* 1.3 80.2 - - + +
365B GLN* 1.3 63.3 + - - +
367B VAL* 3.1 9.1 + - + +
368B LEU 3.0 18.7 + - - -
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Residues in contact with GLN 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B MET* 4.3 17.4 - - - -
339B GLU* 6.3 0.4 - - - -
361B LEU* 2.8 42.3 + - + +
362B SER* 3.1 24.4 + - - +
364B LEU* 1.3 75.5 - - - +
366B MET* 1.3 56.3 + - + +
368B LEU* 3.4 3.7 + - - +
369B GLY* 2.7 32.4 + - - -
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Residues in contact with MET 366 (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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362B SER* 2.8 22.4 + - - +
363B ASP* 3.4 13.0 - - - +
365B GLN* 1.3 78.1 - - + +
367B VAL* 1.3 60.4 + - + +
369B GLY* 4.4 2.5 - - - +
370B LEU* 2.8 64.7 + - + +
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Residues in contact with VAL 367 (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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331B HIS* 3.7 33.9 - - + +
363B ASP* 3.0 31.2 + - - +
364B LEU* 3.1 12.8 + - + +
366B MET* 1.3 76.4 - - + +
368B LEU* 1.3 61.7 + - - +
370B LEU* 4.2 2.2 - - - +
371B SER* 2.8 30.6 + - - +
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Residues in contact with LEU 368 (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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331B HIS* 6.6 0.2 - - + -
335B MET* 4.0 28.7 - - + -
364B LEU 3.0 13.1 + - - +
365B GLN* 3.6 7.2 - - - +
367B VAL* 1.3 75.7 - - - +
369B GLY* 1.3 70.3 + - - +
371B SER* 2.9 21.0 + - - -
372B TYR* 3.6 26.5 - - + +
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Residues in contact with GLY 369 (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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365B GLN 2.7 20.7 + - - -
366B MET* 3.8 3.8 - - - -
368B LEU* 1.3 77.5 - - - +
370B LEU* 1.3 58.0 + - - +
371B SER 3.1 4.7 + - - -
372B TYR* 3.4 22.0 + - - +
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Residues in contact with LEU 370 (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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366B MET* 2.8 51.7 + - + +
367B VAL* 4.2 2.5 - - - +
369B GLY* 1.3 68.1 - - - -
371B SER* 1.3 56.1 + - - +
372B TYR 3.1 16.5 + - - +
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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