Contacts of the helix formed by residues 316 - 336 (chain B) in PDB entry 1SXP
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 316 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312B GLU 3.2 17.2 + - - -
313B LEU 3.4 8.7 - - - +
315B HIS* 1.3 87.9 - - - +
317B ASP* 1.3 62.0 + - - +
318B VAL* 3.8 6.2 + - - +
319B LEU* 2.9 30.5 + - - +
320B ARG* 3.0 16.3 + - - +
352B PG4 3.8 3.1 - - - -
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Residues in contact with ASP 317 (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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315B HIS 3.5 4.9 + - - -
316B SER* 1.3 73.9 - - - +
318B VAL* 1.3 60.7 + - + +
320B ARG* 3.0 25.2 + - - +
321B LYS* 2.9 61.6 + - - +
352B PG4 3.2 29.6 + - - +
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B SER* 3.1 5.7 - - - +
317B ASP* 1.3 79.7 - - + +
319B LEU* 1.3 62.2 + - - +
321B LYS* 4.0 5.7 - - - +
322B GLU* 3.1 25.9 + - + +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ARG* 3.9 28.9 - - - +
309B ARG* 5.8 3.1 - - - -
312B GLU* 3.9 40.6 - - + +
313B LEU* 4.0 14.6 - - + -
316B SER* 2.9 24.1 + - - +
318B VAL* 1.3 78.7 - - - +
320B ARG* 1.3 62.9 + - - +
322B GLU* 3.5 7.0 + - - +
323B MET* 3.1 33.0 + - - +
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Residues in contact with ARG 320 (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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178B THR 5.9 1.2 + - - -
180B LYS* 3.4 27.4 - - - +
251B ILE* 4.0 30.5 - - + -
277B ASP* 4.0 5.5 + - - -
279B VAL* 3.8 18.8 - - + +
313B LEU* 3.6 18.4 - - + +
316B SER 3.0 16.4 + - - +
317B ASP* 3.0 21.4 + - - +
318B VAL 3.2 0.2 - - - -
319B LEU* 1.3 77.7 - - - +
321B LYS* 1.3 81.5 + - - +
323B MET* 3.3 3.6 + - - +
324B LEU* 2.8 51.1 + - - +
352B PG4 3.3 24.7 + - - -
355B GOL 5.2 1.6 + - - -
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Residues in contact with LYS 321 (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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177B PRO* 5.6 5.5 - - - +
317B ASP* 2.9 41.3 + - - +
318B VAL* 4.1 5.6 - - - +
320B ARG* 1.3 98.3 - - - +
322B GLU* 1.3 57.4 + - - +
324B LEU* 4.1 2.2 - - - -
325B SER* 2.8 27.2 + - - -
355B GOL 3.0 44.3 + - - +
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Residues in contact with GLU 322 (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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297B ARG* 3.0 40.0 + - - -
318B VAL* 3.1 22.1 + - + +
319B LEU* 3.8 10.8 - - - +
320B ARG 3.2 0.4 - - - -
321B LYS* 1.3 74.8 - - - +
323B MET* 1.3 66.8 + - - +
325B SER* 2.8 23.5 + - - +
326B ILE* 2.9 24.1 + - + +
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Residues in contact with MET 323 (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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279B VAL* 3.8 19.5 - - + -
281B LEU* 4.5 2.9 - - + -
297B ARG* 3.7 50.5 - - + +
298B PHE* 3.2 50.5 - - + -
309B ARG* 5.0 5.2 - - - -
313B LEU* 4.0 22.9 - - + -
319B LEU* 3.1 32.8 + - + +
320B ARG 3.7 3.4 - - - +
322B GLU* 1.3 78.2 - - - +
324B LEU* 1.3 62.6 + - - +
326B ILE* 3.2 4.6 + - - -
327B GLN* 3.0 19.8 + - - +
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Residues in contact with LEU 324 (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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276B SER 4.2 2.5 - - - +
277B ASP* 3.1 49.6 - - - +
278B ALA 3.7 23.1 - - - +
279B VAL* 3.8 11.4 - - + +
320B ARG* 2.8 33.3 + - - +
321B LYS* 3.6 5.8 - - - +
323B MET* 1.3 78.8 - - - +
325B SER* 1.3 61.4 + - - +
327B GLN* 3.3 13.8 + - - +
328B HIS* 3.0 37.6 + - + +
355B GOL 3.5 21.8 - - - -
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Residues in contact with SER 325 (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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321B LYS 2.8 15.6 + - - -
322B GLU* 2.8 23.4 + - - +
324B LEU* 1.3 76.3 - - - +
326B ILE* 1.3 59.5 + - - +
328B HIS* 3.6 3.0 + - - +
329B ASP* 3.0 27.9 + - - +
355B GOL 3.8 20.8 - - - -
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Residues in contact with ILE 326 (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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293B ILE* 4.4 11.4 - - + -
295B ASP* 3.7 9.4 - - + +
297B ARG* 3.3 30.5 - - - +
298B PHE* 4.1 15.7 - - + -
322B GLU* 2.9 32.7 + - + +
323B MET* 3.2 8.3 + - - +
325B SER* 1.3 78.5 - - - +
327B GLN* 1.3 61.2 + - - +
329B ASP* 3.2 7.4 + - + +
330B ILE* 3.0 33.6 + - + +
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Residues in contact with GLN 327 (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 THR 3.5 0.8 + - - -
274B MET* 2.9 46.5 + - + +
276B SER 4.0 0.2 + - - -
278B ALA 3.1 21.2 + - - -
279B VAL* 3.5 5.0 - - - +
280B MET* 2.8 37.0 + - + +
293B ILE* 5.0 3.4 - - + -
298B PHE* 3.7 18.7 - - + -
323B MET 3.0 11.0 + - - +
324B LEU* 3.4 17.5 - - - +
326B ILE* 1.3 78.0 - - - +
328B HIS* 1.3 71.4 + - + +
330B ILE* 3.4 6.8 + - - +
331B LEU* 3.0 26.3 + - - +
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Residues in contact with HIS 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 4.3 30.8 - - + +
175B SER 4.7 8.9 + - - -
274B MET 3.3 19.9 + - - -
275B ALA 4.1 7.6 + - - -
276B SER 3.1 29.2 + - - -
277B ASP* 4.9 3.0 + - - -
324B LEU* 3.0 24.2 + - + +
325B SER* 4.0 4.3 - - - +
327B GLN* 1.3 84.7 - - + +
329B ASP* 1.3 65.7 + - - +
331B LEU* 3.5 4.9 + - - +
332B ASN* 3.1 30.8 + - - +
355B GOL 3.1 26.2 + - - +
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Residues in contact with ASP 329 (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 SER 3.0 19.3 + - - +
326B ILE* 3.2 8.7 + - + +
328B HIS* 1.3 79.1 - - - +
330B ILE* 1.3 66.5 + - - +
332B ASN* 3.5 6.2 + - - +
333B LYS* 3.1 52.2 + - - +
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Residues in contact with ILE 330 (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 MET* 4.4 11.0 - - + -
292B ILE 3.7 23.6 - - - +
293B ILE* 4.1 21.5 - - + -
294B ASN* 5.7 3.1 - - + +
326B ILE* 3.0 22.8 + - + +
327B GLN* 3.8 6.3 - - - +
328B HIS 3.3 0.2 - - - -
329B ASP* 1.3 84.8 - - - +
331B LEU* 1.3 69.0 + - - +
333B LYS* 3.2 24.1 + - + +
334B THR* 3.3 15.0 + - - +
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Residues in contact with LEU 331 (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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167B ILE* 3.7 23.1 - - + -
172B PHE* 3.9 5.2 - - + -
174B LEU* 3.7 19.7 - - + -
271B TRP* 4.4 3.8 - - + +
274B MET* 3.1 31.8 - - + +
275B ALA* 3.7 36.6 - - + +
327B GLN 3.0 14.3 + - - +
328B HIS* 3.7 6.3 - - - +
330B ILE* 1.3 76.4 - - - +
332B ASN* 1.3 57.8 + - - +
334B THR* 2.9 22.6 + - - -
335B ARG* 2.9 34.7 + - + -
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Residues in contact with ASN 332 (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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174B LEU* 4.2 21.9 - - - +
328B HIS* 3.1 17.8 + - - +
329B ASP* 3.9 6.4 - - - +
331B LEU* 1.3 79.8 - - - +
333B LYS* 1.3 66.0 + - - +
335B ARG* 3.4 39.4 - - - +
336B ALA* 2.9 24.4 + - - +
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Residues in contact with LYS 333 (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 ASP* 3.1 40.4 + - - +
330B ILE* 3.7 19.8 - - + +
331B LEU 3.2 0.4 - - - -
332B ASN* 1.3 77.8 - - + +
334B THR* 1.3 63.0 + - - +
336B ALA* 3.5 16.7 + - - +
337B LYS* 3.7 20.3 - - - +
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Residues in contact with THR 334 (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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164B GLN* 3.7 21.2 - - - +
167B ILE* 3.6 22.7 - - + -
168B HIS* 3.8 5.9 - - - -
271B TRP* 3.8 24.7 - - + -
330B ILE* 3.3 13.9 + - - +
331B LEU 2.9 10.0 + - - -
333B LYS* 1.3 80.0 - - - +
335B ARG* 1.3 61.9 + - - +
337B LYS* 3.1 28.3 + - + +
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Residues in contact with ARG 335 (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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167B ILE* 3.3 22.0 + - + +
168B HIS* 4.0 8.2 + - - +
169B MET 5.3 1.6 + - - -
170B ASN 5.7 1.2 + - - -
172B PHE* 3.2 53.9 + - - +
174B LEU* 5.4 2.4 - - - +
331B LEU* 2.9 27.9 + - + +
332B ASN* 3.2 33.5 + - - +
334B THR* 1.3 72.3 - - - +
336B ALA* 1.3 55.7 + - - +
337B LYS 3.0 5.8 - - - -
338B LYS* 2.9 28.2 + - - +
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Residues in contact with ALA 336 (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 ASN 2.9 17.3 + - - +
333B LYS* 3.5 10.5 - - - +
334B THR 3.2 0.4 - - - -
335B ARG* 1.3 75.9 - - - +
337B LYS* 1.3 59.9 + - + +
338B LYS* 3.2 3.6 + - - +
339B ALA* 4.9 2.1 + - - +
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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
------------------------------------------------------------
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