Contacts of the helix formed by residues 316 - 336 (chain A) in PDB entry 1SXQ
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A GLU* 2.9 15.2 + - - -
313A LEU 3.3 10.0 - - - +
315A HIS* 1.3 84.7 - - - +
317A ASP* 1.3 63.5 + - - +
318A VAL* 3.6 9.9 + - - +
319A LEU* 3.0 29.2 + - - +
320A ARG 3.1 16.5 + - - -
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Residues in contact with ASP 317 (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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313A LEU 4.2 2.4 + - - -
314A LYS 5.1 1.2 + - - -
315A HIS 4.0 3.0 + - - -
316A SER* 1.3 72.9 - - - +
318A VAL* 1.3 60.0 + - + +
320A ARG* 2.8 37.9 + - - +
321A LYS* 2.9 60.7 + - - +
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Residues in contact with VAL 318 (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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316A SER* 3.0 8.0 - - - +
317A ASP* 1.3 80.6 - - + +
319A LEU* 1.3 58.6 + - - +
321A LYS* 3.4 6.7 + - - +
322A GLU* 2.9 30.4 + - + +
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ARG* 3.4 34.1 - - - +
309A ARG* 5.8 3.4 - - - -
312A GLU* 3.3 44.4 - - + +
313A LEU* 4.0 20.2 - - + -
316A SER* 3.0 22.8 + - - +
318A VAL* 1.3 77.6 - - - +
320A ARG* 1.3 64.9 + - - +
322A GLU* 3.1 10.4 + - - +
323A MET* 2.9 37.3 + - + +
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Residues in contact with ARG 320 (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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177A PRO* 6.4 0.4 - - - +
180A LYS* 3.9 22.3 - - - +
251A ILE* 3.8 37.4 - - + +
277A ASP* 4.2 4.2 + - - -
279A VAL* 3.7 19.8 - - + +
313A LEU* 3.8 25.5 - - + +
316A SER 3.1 12.4 + - - +
317A ASP* 2.8 34.3 + - - +
319A LEU* 1.3 78.5 - - - +
321A LYS* 1.3 75.3 + - - +
323A MET 3.4 0.3 + - - -
324A LEU* 3.0 53.8 + - - +
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Residues in contact with LYS 321 (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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317A ASP* 2.9 44.0 + - - +
318A VAL* 3.9 4.9 - - - +
320A ARG* 1.3 92.6 - - - +
322A GLU* 1.3 67.9 + - - +
324A LEU* 3.4 9.7 + - + +
325A SER* 3.0 24.6 + - - -
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Residues in contact with GLU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ARG* 2.9 42.8 + - - -
318A VAL* 2.9 21.1 + - + +
319A LEU* 3.1 12.3 + - - +
321A LYS* 1.3 77.6 - - - +
323A MET* 1.3 61.4 + - - +
325A SER* 3.3 7.3 + - - -
326A ILE* 3.0 35.9 + - + +
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Residues in contact with MET 323 (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 VAL* 3.8 18.4 - - + -
281A LEU* 4.7 2.7 - - + -
297A ARG* 3.3 53.2 - - + +
298A PHE* 3.3 46.0 - - + -
309A ARG* 5.4 3.8 - - - -
313A LEU* 4.0 18.6 - - + -
319A LEU* 2.9 40.8 + - + +
320A ARG 3.9 3.1 - - - +
322A GLU* 1.3 75.7 - - - +
324A LEU* 1.3 64.9 + - - +
326A ILE* 3.2 3.1 + - - -
327A GLN* 2.9 20.9 + - - +
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Residues in contact with LEU 324 (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 SER 4.0 4.5 - - - +
277A ASP* 3.4 47.1 - - - +
278A ALA 3.6 24.2 - - - +
279A VAL* 3.7 8.7 - - + +
320A ARG* 3.0 38.5 + - - +
321A LYS* 3.7 9.2 - - + +
323A MET* 1.3 76.2 - - - +
325A SER* 1.3 63.1 + - - +
327A GLN* 3.4 15.6 - - + +
328A HIS* 2.9 40.1 + - + +
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Residues in contact with SER 325 (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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321A LYS 3.0 17.4 + - - -
322A GLU* 3.5 7.6 - - - -
323A MET 3.2 0.2 - - - -
324A LEU* 1.3 77.4 - - - +
326A ILE* 1.3 56.6 + - - +
328A HIS* 3.4 7.2 + - - +
329A ASP* 3.0 42.1 + - - -
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Residues in contact with ILE 326 (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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293A ILE* 4.3 13.0 - - + -
295A ASP* 3.7 10.1 - - + +
297A ARG* 3.2 30.7 - - - +
298A PHE* 4.0 17.3 - - + -
322A GLU* 3.0 27.6 + - + +
323A MET* 3.5 9.4 - - - +
325A SER* 1.3 77.2 - - - +
327A GLN* 1.3 64.1 + - - +
329A ASP* 3.3 7.6 + - - +
330A ILE* 3.0 28.4 + - + +
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Residues in contact with GLN 327 (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 THR 3.4 7.9 + - - -
274A MET* 3.1 40.1 + - + +
276A SER 3.9 1.8 + - - -
278A ALA 3.0 24.7 + - - -
279A VAL* 3.5 5.0 - - - -
280A MET* 2.9 28.0 + - + +
293A ILE* 3.7 27.1 - - + -
298A PHE* 3.5 12.8 - - + -
323A MET 2.9 12.3 + - - +
324A LEU* 3.4 24.1 - - - +
326A ILE* 1.3 76.7 - - - +
328A HIS* 1.3 62.5 + - - +
330A ILE* 3.5 0.8 + - - -
331A LEU* 3.0 22.3 + - - +
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Residues in contact with HIS 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 4.0 29.6 - - + +
175A SER 4.3 12.4 + - - -
274A MET 3.1 17.5 + - - -
275A ALA 3.8 10.1 - - - -
276A SER 3.0 29.0 + - - -
277A ASP* 4.9 3.8 + - - -
324A LEU* 2.9 37.0 + - + +
325A SER* 3.7 7.6 - - - +
327A GLN* 1.3 79.0 - - - +
329A ASP* 1.3 66.0 + - - +
331A LEU* 3.3 7.1 + - - +
332A ASN* 3.1 27.4 + - - +
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Residues in contact with ASP 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A SER* 3.0 31.1 + - - +
326A ILE* 3.3 6.3 + - - +
328A HIS* 1.3 75.5 - - - +
330A ILE* 1.3 69.0 + - + +
332A ASN* 3.2 10.8 + - - +
333A LYS* 3.0 30.1 + - + +
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Residues in contact with ILE 330 (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 TRP* 6.1 0.7 - - + -
274A MET* 4.4 7.4 - - + -
292A ILE 3.5 23.8 - - - +
293A ILE* 4.2 20.4 - - + -
294A ASN 5.8 1.8 - - - +
326A ILE* 3.0 27.8 + - + +
327A GLN* 3.8 6.3 - - - +
329A ASP* 1.3 77.8 - - + +
331A LEU* 1.3 64.7 + - - +
333A LYS* 3.1 28.1 + - + +
334A THR* 3.4 9.8 + - - +
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Residues in contact with LEU 331 (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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167A ILE* 4.3 9.5 - - + +
172A PHE* 3.8 12.1 - - + -
174A LEU* 4.2 4.5 - - + -
271A TRP* 4.1 15.9 - - + +
274A MET* 3.5 21.1 - - + +
275A ALA* 3.4 45.5 - - + +
327A GLN 3.0 17.6 + - - +
328A HIS* 3.5 7.0 - - - +
329A ASP 3.2 0.2 - - - -
330A ILE* 1.3 77.9 - - - +
332A ASN* 1.3 61.6 + - - +
334A THR* 3.0 21.7 + - - -
335A ARG* 3.0 39.6 + - + +
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Residues in contact with ASN 332 (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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172A PHE* 4.9 1.2 - - - -
174A LEU* 3.9 17.6 - - - +
328A HIS 3.1 16.9 + - - +
329A ASP* 3.2 12.3 + - - +
331A LEU* 1.3 77.0 - - - +
333A LYS* 1.3 65.8 + - + +
334A THR 3.2 0.2 - - - -
335A ARG* 3.2 42.8 - - - +
336A ALA* 3.0 22.9 + - - +
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Residues in contact with LYS 333 (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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329A ASP* 3.0 17.9 + - + +
330A ILE* 3.1 23.3 + - + +
332A ASN* 1.3 76.2 - - + +
334A THR* 1.3 62.7 + - - +
336A ALA* 3.4 19.2 - - - +
337A LYS* 3.7 23.2 + - - +
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Residues in contact with THR 334 (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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164A GLN* 3.3 33.2 - - - +
167A ILE* 3.5 16.4 - - + -
168A HIS* 3.6 8.3 - - - -
271A TRP* 3.8 18.7 - - + -
330A ILE* 3.4 7.9 + - - +
331A LEU 3.0 9.4 + - - -
333A LYS* 1.3 75.9 - - - +
335A ARG* 1.3 66.0 + - - +
336A ALA 3.1 1.8 - - - -
337A LYS* 3.0 25.7 + - + +
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Residues in contact with ARG 335 (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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167A ILE* 3.1 32.3 + - + +
168A HIS* 4.0 9.1 + - - +
169A MET 4.9 4.0 + - - -
170A ASN 5.8 1.2 + - - -
172A PHE* 3.2 39.8 + - - +
173A GLN* 5.6 0.4 - - - +
174A LEU* 5.7 1.0 - - - +
331A LEU* 3.0 31.8 + - + +
332A ASN* 3.2 35.4 + - - +
334A THR* 1.3 77.1 - - - +
336A ALA* 1.3 62.8 + - - +
338A LYS* 3.1 22.0 + - - +
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Residues in contact with ALA 336 (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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332A ASN 3.0 11.9 + - - +
333A LYS* 3.4 15.9 - - - +
335A ARG* 1.3 77.4 - - - +
337A LYS* 1.3 58.7 + - + +
338A LYS* 3.2 4.4 + - - +
339A ALA* 4.9 1.9 + - - +
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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