Contacts of the helix formed by residues 269 - 288 (chain A) 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 SER 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A MET* 1.3 65.1 + - - +
271A ALA* 3.7 8.8 + - - +
272A GLU* 3.2 48.6 + - - +
273A LEU* 3.2 27.0 + - - +
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Residues in contact with MET 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A SER* 1.3 74.9 - - - +
271A ALA* 1.3 61.8 + - - +
273A LEU* 3.2 17.9 + - + +
274A GLU* 3.0 37.6 + - - +
455A HIS* 3.5 43.3 - - + +
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A SER* 3.2 9.3 - - - +
270A MET* 1.3 79.5 - - - +
272A GLU* 1.3 56.8 + - + +
274A GLU* 3.1 13.8 + - - +
275A HIS* 2.9 51.7 + - + +
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Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A SER* 3.2 34.8 + - - +
271A ALA* 1.3 77.7 - - + +
273A LEU* 1.3 59.5 + - + +
275A HIS* 3.5 12.2 + - + +
276A LEU* 3.0 27.4 + - - +
448A LYS* 4.5 15.2 + - - -
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A SER 3.2 16.6 + - - +
270A MET* 3.6 27.4 - - + +
272A GLU* 1.3 75.0 - - + +
274A GLU* 1.3 60.8 + - - +
276A LEU* 3.4 6.8 + - + +
277A ALA* 3.0 29.1 + - - +
448A LYS* 3.4 39.3 - - + +
451A LEU* 4.0 33.0 - - + +
452A ALA* 4.0 16.3 - - + +
455A HIS* 5.3 7.2 - - + -
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Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A MET* 3.0 30.5 + - - +
271A ALA* 3.1 14.3 + - - +
273A LEU* 1.3 75.4 - - - +
275A HIS* 1.3 68.7 + - + +
277A ALA* 3.4 6.8 + - - +
278A GLN* 3.0 23.4 + - - +
455A HIS* 4.1 23.8 + - + +
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Residues in contact with HIS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ALA* 2.9 39.2 + - + +
272A GLU* 3.8 11.5 - - + +
274A GLU* 1.3 78.5 + - + +
276A LEU* 1.3 67.2 + - - +
278A GLN* 3.1 16.0 + - - +
279A ASN* 2.9 24.3 + - - +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A GLU 3.0 17.7 + - - +
273A LEU* 3.6 8.1 - - + +
274A GLU 3.3 0.2 - - - -
275A HIS* 1.3 77.2 - - - +
277A ALA* 1.3 62.5 + - - +
279A ASN* 3.3 11.0 + - + +
280A ILE* 3.1 41.2 + - + +
341A ILE* 5.5 3.6 - - + -
343A GLY* 6.0 2.2 - - - +
445A LEU* 4.5 17.7 - - + -
448A LYS* 3.7 46.0 - - + +
449A ILE* 3.8 10.5 - - + +
452A ALA* 4.6 4.9 - - + -
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A LEU 3.0 17.4 + - - +
274A GLU* 3.8 7.0 - - - +
276A LEU* 1.3 76.8 - - - +
278A GLN* 1.3 58.9 + - - +
280A ILE* 3.8 1.0 - - - +
281A SER* 2.8 33.1 + - - -
418A ASP* 6.5 0.9 - - + -
422A LEU* 4.2 32.0 - - + +
452A ALA* 4.5 5.6 - - + +
455A HIS* 6.5 0.7 - - + -
456A VAL* 4.5 11.7 - - + -
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Residues in contact with GLN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A GLU 3.0 17.9 + - - +
275A HIS* 3.5 16.0 - - - +
277A ALA* 1.3 75.2 - - - +
279A ASN* 1.3 65.1 + - - +
281A SER* 3.7 5.3 - - - -
282A LYS* 2.9 55.5 + - + +
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Residues in contact with ASN 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A HIS 2.9 11.7 + - - +
276A LEU* 3.6 14.9 - - + +
278A GLN* 1.3 78.0 - - - +
280A ILE* 1.3 58.5 + - - +
282A LYS* 4.0 4.5 - - - +
283A SER* 3.1 25.6 + - - -
340A ARG 3.2 18.1 + - - -
341A ILE* 3.6 9.9 - - - +
342A ASP* 3.0 43.0 + - - +
343A GLY 4.7 0.3 + - - -
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Residues in contact with ILE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A LEU* 3.1 27.4 + - + +
277A ALA 4.0 2.7 - - - +
279A ASN* 1.3 75.1 - - - +
281A SER* 1.3 62.4 + - - +
283A SER* 3.4 6.3 + - - -
284A HIS* 3.0 27.4 + - - +
337A PHE* 3.7 6.2 - - + -
341A ILE* 4.1 24.0 - - + -
421A ALA* 3.4 35.0 - - + +
422A LEU* 3.7 24.9 - - + +
425A ALA* 3.8 14.6 - - + -
449A ILE* 3.8 26.5 - - + -
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Residues in contact with SER 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ALA 2.8 20.7 + - - -
278A GLN* 3.7 7.2 + - - +
280A ILE* 1.3 78.5 - - - +
282A LYS* 1.3 61.1 + - - +
284A HIS* 3.4 3.5 + - - +
285A LEU* 3.1 36.0 + - - +
418A ASP* 2.7 37.4 + - - +
421A ALA* 4.0 10.8 - - - -
422A LEU* 5.8 0.4 - - - +
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Residues in contact with LYS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A GLN* 2.9 50.0 + - + +
279A ASN* 4.1 4.0 - - - +
281A SER* 1.3 77.6 - - - +
283A SER* 1.3 66.2 + - - +
285A LEU* 3.3 9.6 + - + +
286A GLU* 3.0 45.2 + - + +
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Residues in contact with SER 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ASN 3.1 18.9 + - - -
280A ILE 3.7 5.4 - - - -
282A LYS* 1.3 77.2 - - - +
284A HIS* 1.3 55.3 + - - +
286A GLU* 3.4 5.6 + - - +
287A THR* 2.7 35.3 + - - +
337A PHE* 2.7 37.7 + - - -
340A ARG* 3.2 29.7 - - - +
341A ILE* 4.3 3.4 - - - -
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Residues in contact with HIS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ILE 3.0 8.9 + - - +
281A SER 3.6 3.3 + - - +
282A LYS 3.2 0.2 - - - -
283A SER* 1.3 77.0 - - - +
285A LEU* 1.3 70.7 + - - +
287A THR* 3.0 3.3 + - - -
288A CYS* 2.9 52.1 + - - -
337A PHE* 3.6 14.3 - + + -
367A ARG* 3.6 18.0 + - + -
370A ARG* 3.7 11.7 + - - -
417A GLU* 3.0 51.3 + - - +
420A ILE* 3.9 9.3 - - + +
421A ALA* 3.4 32.7 - - + +
424A SER* 5.3 2.5 - - - -
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A SER* 3.1 27.8 + - - +
282A LYS* 3.3 9.6 + - + +
284A HIS* 1.3 84.8 - - - +
286A GLU* 1.3 63.0 + - + +
287A THR 3.4 0.3 + - - -
288A CYS* 3.8 13.1 + - + +
291A LEU* 6.0 6.6 - - + +
370A ARG* 5.7 0.4 - - - +
417A GLU* 3.9 34.8 - - + +
418A ASP* 5.1 3.4 - - - +
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Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A LYS* 3.0 38.1 + - + +
283A SER* 3.8 4.9 - - - +
284A HIS 3.2 0.4 - - - -
285A LEU* 1.3 77.9 - - + +
287A THR* 1.3 59.7 + - - +
288A CYS 3.6 2.9 - - - +
333A TYR* 5.6 0.7 - - - -
340A ARG* 3.0 42.2 + - - +
502D LEU* 4.9 5.7 - - - +
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Residues in contact with THR 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A SER 2.7 22.7 + - - +
284A HIS 3.0 1.0 + - - -
286A GLU* 1.3 82.5 - - - +
288A CYS* 1.3 62.5 + - - +
333A TYR* 3.3 34.4 - - - +
336A GLU* 3.8 17.5 - - + +
337A PHE* 3.4 23.9 - - - +
340A ARG* 4.1 16.2 - - - +
367A ARG* 2.9 35.4 + - - -
502D LEU* 4.6 2.7 - - + -
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Residues in contact with CYS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A HIS* 2.9 55.5 + - - +
285A LEU* 3.8 11.3 + - + +
286A GLU 3.6 2.8 - - - +
287A THR* 1.3 79.2 + - - +
289A GLN* 1.3 65.1 + - - +
290A TYR* 3.4 4.8 + - - +
333A TYR* 4.5 2.6 - - - -
367A ARG* 4.2 3.8 - - - -
370A ARG* 3.4 25.4 - - - +
417A GLU* 4.3 0.4 - - - +
602A GOL 3.3 18.4 - - - +
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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