Contacts of the helix formed by residues 359 - 374 (chain B) in PDB entry 5C5B
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 SER 359 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265B ASP* 3.7 26.0 - - - -
267B ASP* 4.3 5.2 + - - -
340B TYR* 3.6 13.2 - - - +
357B ALA* 3.5 1.9 - - - +
358B GLU* 1.3 87.8 - - - +
360B ARG* 1.3 64.1 + - - +
361B LYS* 3.4 6.4 + - - +
362B GLU* 3.0 32.3 + - - +
363B ASN* 3.1 24.1 + - - +
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Residues in contact with ARG 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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265B ASP* 3.1 17.4 + - - +
267B ASP* 4.9 0.2 - - - +
268B VAL* 4.9 5.2 - - + +
271B PRO* 3.8 29.1 - - + +
273B ILE* 5.3 0.9 - - + -
340B TYR* 3.3 31.0 - - - +
359B SER* 1.3 70.3 - - - +
361B LYS* 1.3 56.2 + - - +
363B ASN* 3.2 14.6 + - - +
364B GLU* 2.9 79.6 + - + +
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Residues in contact with LYS 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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267B ASP* 3.4 32.9 + - + +
271B PRO* 4.3 9.2 - - + -
272B GLN* 3.3 21.2 + - + +
273B ILE* 4.3 10.8 - - + -
359B SER* 3.2 3.2 + - - +
360B ARG* 1.3 79.7 - - - +
362B GLU* 1.3 84.8 + - + +
364B GLU* 4.0 0.5 - - - +
365B GLU* 2.9 74.5 + - + +
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Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LYS* 2.5 36.6 + - - +
281B ALA 5.4 1.9 - - - +
284B LEU* 5.9 0.4 - - + -
357B ALA* 4.1 14.8 - - + -
358B GLU* 5.0 10.1 - - + +
359B SER* 3.0 23.3 + - - +
361B LYS* 1.3 98.7 - - + +
363B ASN* 1.3 60.2 + - - +
366B TRP* 2.9 43.2 + - + +
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Residues in contact with ASN 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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332B ALA* 4.4 8.1 - - - +
340B TYR* 3.3 34.1 - - + +
341B CYS 3.9 1.4 - - - -
342B PHE* 3.2 27.1 - - - +
357B ALA* 3.8 7.7 - - + +
359B SER 3.1 18.9 + - - +
360B ARG* 3.4 21.1 - - - +
362B GLU* 1.3 74.7 - - - +
364B GLU* 1.3 62.6 + - - +
366B TRP* 3.3 4.7 + - - +
367B ILE* 3.0 51.5 + - - +
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Residues in contact with GLU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ILE* 3.6 36.0 - - + +
360B ARG* 2.9 64.5 + - + +
361B LYS 4.0 0.7 - - - +
363B ASN* 1.3 80.7 + - - +
365B GLU* 1.3 59.2 + - - +
367B ILE* 3.3 10.4 + - - +
368B CYS* 2.9 39.4 + - - -
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Residues in contact with GLU 365 (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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272B GLN 3.5 0.7 - - - +
273B ILE* 3.4 21.5 - - + -
274B ASN* 2.6 30.0 + - - +
277B LEU* 3.5 26.3 - - + +
280B LYS* 3.6 19.6 + - - +
361B LYS* 2.9 57.8 + - - +
364B GLU* 1.3 73.0 - - - +
366B TRP* 1.3 60.7 + - - +
368B CYS* 3.9 5.6 - - - +
369B ALA* 2.9 30.3 + - - +
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Residues in contact with TRP 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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280B LYS* 3.4 48.6 - - + +
282B GLY* 3.9 17.0 - - - +
283B TYR 5.2 0.2 + - - -
284B LEU* 3.5 43.1 - - + +
302B PHE* 3.5 32.5 - - + -
304B THR* 3.9 14.8 - - + -
309B LEU* 3.8 21.8 - - + -
342B PHE* 3.7 18.4 - + + -
355B LEU* 6.3 0.2 - - + -
362B GLU* 2.9 34.9 + - + +
363B ASN 3.6 3.8 - - - +
365B GLU* 1.3 76.4 - - - +
367B ILE* 1.3 62.6 + - - +
369B ALA* 3.2 3.0 + - + +
370B ILE* 2.9 42.9 + - + +
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Residues in contact with ILE 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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330B VAL* 3.2 29.1 - - + +
331B MET* 4.8 1.6 - - - -
332B ALA* 3.7 26.0 - - + +
342B PHE* 3.9 23.1 - - + -
363B ASN* 3.0 40.5 + - - +
364B GLU* 3.5 14.6 - - - +
366B TRP* 1.3 74.8 - - - +
368B CYS* 1.3 62.1 + - - +
370B ILE* 5.0 0.2 - - - -
371B ASN* 2.9 43.2 + - - +
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Residues in contact with CYS 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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273B ILE* 5.0 3.6 - - - -
274B ASN 4.5 1.1 - - - +
275B ARG* 3.3 52.3 - - + +
277B LEU* 5.6 0.2 - - - -
364B GLU* 2.9 30.1 + - - +
365B GLU* 3.9 6.3 - - - +
367B ILE* 1.3 78.9 - - - +
369B ALA* 1.3 60.7 + - - +
371B ASN* 3.7 7.6 - - - +
372B ASN* 2.9 38.6 + - - +
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Residues in contact with ALA 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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277B LEU* 3.2 25.1 - - + +
278B ILE 5.0 0.4 - - - -
279B GLN 4.8 5.4 - - - +
280B LYS* 4.2 23.1 - - + +
304B THR* 5.4 4.0 - - + -
365B GLU 2.9 20.0 + - - +
366B TRP* 3.5 7.0 - - + +
368B CYS* 1.3 76.4 - - - +
370B ILE* 1.3 59.2 + - + +
372B ASN* 3.3 2.8 + - - +
373B ILE* 2.9 34.8 + - - +
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Residues in contact with ILE 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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304B THR* 5.5 0.7 - - + -
309B LEU* 4.8 4.3 - - + -
325B LEU* 3.6 42.4 - - + +
328B CYS* 5.8 1.6 - - + +
329B SER* 5.2 3.4 - - - -
330B VAL* 3.6 36.6 - - + +
342B PHE* 4.0 14.1 - - + -
344B ILE* 3.9 24.0 - - + -
355B LEU* 5.6 0.2 - - + -
366B TRP* 2.9 30.3 + - + +
369B ALA* 1.3 78.2 - - + +
371B ASN* 1.3 56.7 + - - +
373B ILE* 3.4 6.9 + - - +
374B SER* 3.0 27.2 + - - -
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Residues in contact with ASN 371 (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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329B SER* 5.0 3.5 + - - -
330B VAL* 3.4 26.2 + - - +
367B ILE* 2.9 38.5 + - - +
368B CYS* 3.7 9.0 - - - +
370B ILE* 1.3 75.7 - - - +
372B ASN* 1.3 64.7 - - - +
374B SER* 2.4 29.2 + - - +
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Residues in contact with ASN 372 (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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275B ARG* 2.8 37.0 + - - +
276B ASN* 3.3 14.6 - - - +
277B LEU 2.9 27.8 + - - +
278B ILE* 4.4 14.8 - - + +
368B CYS* 2.9 21.9 + - - +
369B ALA 3.6 0.2 - - - +
371B ASN* 1.3 75.2 - - - +
373B ILE* 1.3 68.3 + - - +
374B SER 3.4 3.1 + - - +
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Residues in contact with ILE 373 (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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278B ILE* 3.4 31.0 - - + +
304B THR* 3.8 28.0 - - + -
306B GLY 3.8 14.8 - - - +
307B GLY* 3.6 32.5 - - - +
325B LEU* 4.2 17.7 - - + -
326B ASP* 2.5 26.8 - - - +
369B ALA 2.9 22.3 + - - +
370B ILE* 3.7 5.8 - - - +
372B ASN* 1.3 78.7 - - - +
374B SER* 1.3 58.5 + - - +
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Residues in contact with SER 374 (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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325B LEU 3.6 8.1 - - - -
326B ASP* 3.0 30.5 - - - -
327B ASN* 5.1 0.4 - - - -
328B CYS 3.6 22.2 + - - -
370B ILE* 3.0 13.9 + - - -
371B ASN* 2.4 32.6 + - - +
372B ASN 3.2 3.0 - - - +
373B ILE* 1.3 83.6 - - - +
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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