Contacts of the helix formed by residues 270 - 288 (chain B) in PDB entry 4S15
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 MET 270 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B SER* 1.3 75.2 - - - +
271B ALA* 1.3 57.2 + - - +
273B LEU* 3.2 26.2 + - + +
274B GLU* 3.1 38.8 + - - +
455B HIS* 3.7 34.5 - - + +
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Residues in contact with ALA 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B SER* 3.2 8.5 + - - +
270B MET* 1.3 78.7 - - - +
272B GLU* 1.3 59.4 + - + +
274B GLU* 3.4 20.9 + - - +
275B HIS* 3.1 24.1 + - - +
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B SER* 3.3 35.0 + - - +
270B MET 3.2 0.4 - - - -
271B ALA* 1.3 76.9 - - + +
273B LEU* 1.3 61.1 + - + +
275B HIS* 3.7 8.8 - - - +
276B LEU* 3.0 27.9 + - - +
448B LYS* 5.6 4.0 + - - -
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B SER 3.3 12.6 + - - +
270B MET* 3.2 35.6 + - + +
272B GLU* 1.3 75.6 - - - +
274B GLU* 1.3 60.9 + - - +
276B LEU* 3.4 6.8 + - + +
277B ALA* 2.9 31.0 + - - +
448B LYS* 3.6 31.6 - - + +
451B LEU* 3.8 33.0 - - + +
452B ALA* 3.8 17.9 - - + +
455B HIS* 5.1 7.0 - - + -
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Residues in contact with GLU 274 (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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270B MET* 3.1 27.1 + - + +
271B ALA* 3.4 21.3 - - - +
273B LEU* 1.3 77.9 - - - +
275B HIS* 1.3 56.8 + - - +
277B ALA* 3.7 5.6 - - - +
278B GLN* 3.0 31.3 + - - +
455B HIS* 4.5 22.4 + - + +
459B LYS* 5.7 4.5 - - - +
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Residues in contact with HIS 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ALA 3.1 17.4 + - - +
272B GLU* 3.7 8.3 - - - +
274B GLU* 1.3 73.7 - - - +
276B LEU* 1.3 66.7 + - - +
278B GLN* 3.2 18.0 + - - +
279B ASN* 3.0 59.9 + - - -
342B ASP* 5.3 0.2 + - - -
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B GLU 3.0 18.1 + - - +
273B LEU* 3.8 7.2 - - + +
275B HIS* 1.3 77.0 - - - +
277B ALA* 1.3 64.3 + - - +
279B ASN* 3.2 9.3 + - + +
280B ILE* 3.0 45.3 + - + +
341B ILE* 6.1 1.6 - - + -
342B ASP* 5.5 15.7 - - + +
448B LYS* 3.6 43.1 - - + +
449B ILE* 3.9 14.4 - - + +
452B ALA* 4.3 6.5 - - + -
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU 2.9 18.6 + - - +
274B GLU* 3.7 6.7 - - - +
276B LEU* 1.3 76.8 - - - +
278B GLN* 1.3 58.0 + - - +
280B ILE* 4.0 1.0 - - - +
281B SER* 2.9 36.0 + - - +
422B LEU* 4.2 30.4 - - + +
452B ALA* 4.3 5.8 - - + +
455B HIS* 6.0 2.5 - - + -
456B VAL* 4.3 13.5 - - + -
459B LYS* 6.2 1.8 - - - +
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Residues in contact with GLN 278 (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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274B GLU 3.0 19.2 + - - +
275B HIS* 3.5 16.3 + - - +
276B LEU 3.2 0.2 - - - -
277B ALA* 1.3 77.8 - - - +
279B ASN* 1.3 65.5 + - - +
281B SER* 3.4 5.9 + - - -
282B LYS* 3.0 31.3 + - + +
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Residues in contact with ASN 279 (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 HIS* 3.0 56.0 + - - +
276B LEU* 3.2 8.7 + - + +
278B GLN* 1.3 82.7 - - - +
280B ILE* 1.3 64.5 + - + +
282B LYS* 3.4 11.8 + - - +
283B SER* 2.9 29.7 + - - -
340B ARG 5.7 2.0 - - - +
342B ASP* 3.3 26.6 + - - +
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Residues in contact with ILE 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 3.0 41.2 + - + +
277B ALA 4.1 0.2 - - - +
279B ASN* 1.3 74.5 - - + +
281B SER* 1.3 65.9 + - - +
283B SER* 3.3 6.9 + - - -
284B HIS* 3.0 22.2 + - - +
337B PHE* 3.9 8.1 - - + -
341B ILE* 4.8 17.0 - - + +
342B ASP 6.0 1.1 - - - +
421B ALA* 3.5 32.1 - - + +
422B LEU* 3.7 26.9 - - + +
425B ALA* 3.9 22.9 - - + -
449B ILE* 4.0 12.6 - - + -
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Residues in contact with SER 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA* 2.9 22.3 + - - +
278B GLN* 3.7 6.5 - - - -
279B ASN 3.3 0.2 - - - -
280B ILE* 1.3 78.6 - - - +
282B LYS* 1.3 56.3 + - - +
284B HIS* 3.3 3.8 + - - +
285B LEU* 2.9 29.7 + - - +
418B ASP* 3.0 43.4 + - - +
421B ALA* 3.9 9.8 - - - +
422B LEU* 5.3 1.2 - - - +
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Residues in contact with LYS 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B GLN* 3.0 19.5 + - + +
279B ASN* 3.7 11.7 - - - +
280B ILE 3.3 0.2 - - - -
281B SER* 1.3 73.4 - - - +
283B SER* 1.3 61.4 + - - +
285B LEU* 3.3 11.3 + - + +
286B GLU* 2.9 61.4 + - + +
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Residues in contact with SER 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ASN 2.9 18.5 + - - -
280B ILE* 3.3 7.1 + - - -
282B LYS* 1.3 76.3 - - - +
284B HIS* 1.3 60.7 + - - +
286B GLU* 3.5 11.0 + - - +
287B THR* 2.8 32.1 + - - +
337B PHE* 3.8 16.8 - - - -
340B ARG* 3.3 40.4 + - - +
341B ILE* 5.1 1.3 - - - -
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Residues in contact with HIS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE 3.0 7.1 + - - +
281B SER 3.6 4.7 + - - +
282B LYS 3.2 0.2 - - - -
283B SER* 1.3 74.5 - - - +
285B LEU* 1.3 68.7 + - - +
287B THR* 3.1 2.5 + - - -
288B CYS* 3.0 53.1 + - - -
337B PHE* 3.7 15.0 - + + -
367B ARG* 3.6 18.6 + - - -
370B ARG* 3.8 7.0 + - - -
417B GLU* 3.1 53.5 + - - +
420B ILE* 3.7 16.6 - - + +
421B ALA* 3.5 31.6 - - + +
424B SER* 5.1 2.5 - - - -
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Residues in contact with LEU 285 (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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281B SER 2.9 17.6 + - - +
282B LYS* 3.3 11.4 + - + +
284B HIS* 1.3 83.0 + - - +
286B GLU* 1.3 68.4 + - + +
287B THR 3.4 0.5 + - - -
288B CYS* 3.7 14.2 + - - +
291B LEU* 5.4 17.0 - - + +
417B GLU* 5.7 9.6 - - + +
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Residues in contact with GLU 286 (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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282B LYS* 2.9 55.3 + - + +
283B SER* 3.9 6.3 + - - +
284B HIS 3.2 0.2 - - - -
285B LEU* 1.3 82.6 - - + +
287B THR* 1.3 60.4 - - - +
288B CYS 3.6 3.7 - - - +
333B TYR* 5.6 0.7 - - - -
340B ARG* 3.1 37.0 + - - +
502C LEU* 4.7 5.4 - - - +
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Residues in contact with THR 287 (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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283B SER 2.8 21.1 + - - +
284B HIS 3.1 1.4 + - - -
286B GLU* 1.3 81.2 - - - +
288B CYS* 1.3 61.9 + - - +
333B TYR* 3.3 31.6 - - - +
336B GLU* 3.9 11.2 - - + -
337B PHE* 3.4 24.9 - - - +
340B ARG* 4.0 22.9 - - - +
367B ARG* 2.9 35.5 + - - -
502C LEU* 4.2 5.2 - - + -
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Residues in contact with CYS 288 (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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284B HIS* 3.0 61.5 + - - +
285B LEU* 3.7 11.8 + - - +
286B GLU 3.6 3.4 - - - +
287B THR* 1.3 79.6 - - - +
289B GLN* 1.3 62.7 - - - +
290B TYR* 3.8 10.1 - - - +
291B LEU* 5.7 4.2 - - + +
333B TYR* 4.3 4.1 - - - -
367B ARG* 4.2 3.1 - - - -
370B ARG* 3.7 15.0 - - - +
417B GLU* 4.5 0.2 - - - -
602B GOL 3.1 22.0 - - - +
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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