Contacts of the helix formed by residues 320 - 342 (chain B) in PDB entry 4D1Q
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 ASN 320 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B SER* 4.6 3.4 + - - -
274B LEU* 3.2 26.8 - - - +
318B ARG 3.7 0.8 + - - -
319B TRP* 1.3 75.6 - - - +
321B SER* 1.3 62.1 + - - +
322B THR* 3.5 4.2 + - - -
323B TYR* 3.2 28.3 + - - +
324B THR* 2.9 19.2 + - + -
364B LEU* 3.7 10.4 + - - +
367B PHE* 4.1 3.3 - - - +
368B GLU* 3.0 55.8 + - - +
371B PHE* 3.9 21.0 - - + -
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Residues in contact with SER 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B SER* 5.7 0.3 + - - -
313B SER 5.1 0.9 - - - +
314B GLU* 3.5 36.7 + - - +
315B CYS 4.4 6.1 - - - -
316B PRO* 3.9 10.5 + - - +
318B ARG* 3.2 23.2 + - - -
319B TRP 3.1 2.5 - - - -
320B ASN* 1.3 74.4 + - - +
322B THR* 1.3 66.1 + - - +
324B THR* 3.1 17.2 + - - -
325B MET* 3.3 13.7 + - - +
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Residues in contact with THR 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 5.7 1.2 - - - +
278B PHE* 3.7 31.6 - - + -
288B ILE* 3.8 33.4 - - + -
314B GLU* 3.8 24.2 + - - +
320B ASN* 4.5 2.6 + - - -
321B SER* 1.3 80.8 + - - +
323B TYR* 1.3 58.6 + - - +
325B MET* 3.2 5.0 + - - +
326B LEU* 2.8 40.7 + - + +
364B LEU* 4.5 3.4 - - - +
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Residues in contact with TYR 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ASN* 3.2 21.0 + - - +
321B SER 3.2 0.6 - - - -
322B THR* 1.3 76.5 + - - +
324B THR* 1.3 90.3 + - + +
325B MET 2.9 0.9 + - - -
326B LEU* 3.0 4.7 + - - +
327B ARG* 2.8 69.4 + - + +
361B VAL* 3.7 13.2 - - + -
364B LEU* 3.4 40.4 - - + +
365B ASP* 2.6 39.7 + - - -
368B GLU* 3.1 38.6 - - + +
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Residues in contact with THR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LYS* 4.2 12.8 - - + +
313B SER 6.1 0.9 - - - -
319B TRP 4.7 3.0 + - - +
320B ASN 2.9 16.1 + - - -
321B SER* 3.1 9.8 + - - -
323B TYR* 1.3 93.3 - - + +
325B MET* 1.3 59.7 + - - +
327B ARG* 3.8 3.6 - - - +
328B SER* 3.3 21.5 + - - -
368B GLU* 4.7 9.0 - - - +
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Residues in contact with MET 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE* 4.5 6.1 - - - +
291B CYS* 3.3 35.7 - - + +
292B LYS* 3.9 21.8 - - - +
295B VAL* 4.5 5.4 - - + -
312B LYS 3.0 28.9 - - - +
313B SER* 4.3 15.4 + - - -
314B GLU* 4.3 19.1 - - + +
321B SER 3.3 10.6 + - - +
322B THR* 3.2 9.8 + - - +
323B TYR 2.9 1.4 + - - -
324B THR* 1.3 75.8 - - - +
326B LEU* 1.3 84.9 + - + +
327B ARG 3.2 1.3 - - - -
328B SER* 2.6 20.7 + - - -
329B ILE* 3.4 9.2 + - + +
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE* 4.9 12.1 - - + -
291B CYS* 3.8 21.1 - - + -
322B THR* 2.8 39.6 + - + +
323B TYR* 3.8 4.7 - - - +
325B MET* 1.3 92.0 - - + +
327B ARG* 1.3 65.6 + - - +
329B ILE* 2.9 16.8 + - - +
330B LEU* 3.0 12.8 + - - +
357B ILE* 4.1 18.0 - - + +
360B MET* 4.2 34.1 - - + -
361B VAL* 4.1 15.5 - - + -
364B LEU* 5.1 5.2 - - + -
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Residues in contact with ARG 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B TYR* 2.8 59.9 + - + +
324B THR* 3.8 5.6 - - - +
326B LEU* 1.3 75.8 - - - +
328B SER* 1.3 63.8 + - - +
330B LEU* 3.1 7.1 + - - +
331B ASP* 2.9 50.2 + - - +
361B VAL* 4.2 9.3 - - + +
493G SER* 2.8 52.7 + - - -
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Residues in contact with SER 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B SER* 5.3 2.5 - - - -
310B SER 3.9 8.7 - - - -
311B LEU* 3.7 6.9 - - - +
312B LYS* 3.0 40.8 + - - -
324B THR 3.3 10.7 + - - -
325B MET 2.6 22.5 + - - -
327B ARG* 1.3 80.6 - - - +
329B ILE* 1.3 60.1 + - - +
331B ASP* 4.8 4.0 - - - -
332B ASN* 2.9 32.6 + - - +
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Residues in contact with ILE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B CYS* 3.4 54.3 - - + +
294B ILE* 4.3 13.7 - - + -
295B VAL* 4.6 4.7 - - + -
311B LEU* 4.1 22.9 - - + -
325B MET* 4.1 11.0 - - + +
326B LEU 2.9 9.9 + - - +
328B SER* 1.3 81.5 + - - +
330B LEU* 1.3 57.4 + - + +
332B ASN 3.0 3.6 + - - -
333B TRP* 2.7 63.0 + - + -
336B VAL* 4.6 8.4 - - + +
349B ILE* 6.1 0.2 - - + -
352B ILE* 5.3 1.1 - - + -
357B ILE* 4.9 2.9 - - + -
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU 3.0 9.5 + - - +
327B ARG* 3.4 10.1 - - - +
329B ILE* 1.3 76.8 - - - +
331B ASP* 1.3 65.8 + - - +
332B ASN 3.2 1.0 + - - -
333B TRP* 3.3 34.3 + - + +
354B LYS* 4.7 9.0 + - + -
357B ILE* 3.2 28.9 - - + -
358B GLN* 3.5 43.4 - - - +
361B VAL* 3.3 35.0 - - + -
493G SER* 5.5 0.7 - - - +
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Residues in contact with ASP 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B SER* 5.3 3.1 - - - +
327B ARG* 2.9 57.1 + - - +
328B SER* 4.2 5.7 - - - +
330B LEU* 1.3 78.5 - - - +
332B ASN* 1.3 67.0 + - - +
333B TRP 3.5 0.2 - - - -
335B SER* 5.3 0.3 + - - -
493G SER* 4.1 9.0 + - - -
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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
----------------------------------------------------------
307B LEU* 3.6 23.4 - - + +
308B ARG* 3.8 13.3 + - - +
309B SER* 3.1 39.9 + - - +
310B SER 4.7 0.6 + - - -
311B LEU* 4.3 4.0 - - + +
328B SER* 2.9 24.5 + - - +
329B ILE 3.0 4.3 + - - -
331B ASP* 1.3 84.0 - - - +
333B TRP* 1.3 66.3 + - - +
334B GLU 3.4 2.5 - - - -
335B SER* 3.0 16.7 + - - -
336B VAL* 2.9 31.1 + - + +
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Residues in contact with TRP 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 ILE* 2.7 42.1 + - + -
330B LEU* 3.3 26.8 + - + +
331B ASP 3.5 0.4 - - - -
332B ASN* 1.3 76.0 - - - +
334B GLU* 1.3 69.0 + - - +
336B VAL* 3.0 7.7 + - + +
337B ILE* 2.7 47.7 + - + +
349B ILE* 3.7 32.1 - - + -
352B ILE* 3.8 31.6 - - + -
354B LYS* 3.2 60.2 - - + +
357B ILE* 4.8 2.9 - - + -
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Residues in contact with GLU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ASN 3.1 1.0 + - - -
333B TRP* 1.3 92.9 - - - +
335B SER* 1.3 69.3 + - - +
336B VAL 2.8 1.4 + - - -
337B ILE* 2.9 34.5 + - + +
338B GLN* 3.0 16.9 + - - +
354B LYS* 4.3 7.9 + - - -
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ARG 5.7 1.1 - - - -
307B LEU* 4.3 21.3 - - - -
308B ARG* 5.5 1.6 + - - +
331B ASP 5.3 0.2 + - - -
332B ASN* 3.2 24.4 + - - -
334B GLU* 1.3 77.7 - - - +
336B VAL* 1.3 55.3 + - - +
338B GLN* 3.4 8.3 - - - +
339B ILE* 3.0 32.5 + - - +
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Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 4.5 9.4 - - + -
298B PHE* 3.7 20.2 - - + -
307B LEU* 4.6 8.7 - - + -
311B LEU* 4.6 7.9 - - + -
329B ILE* 4.6 9.0 - - + +
332B ASN* 2.9 34.2 + - + +
333B TRP* 3.9 8.1 - - + +
334B GLU 2.8 0.8 + - - -
335B SER* 1.3 75.3 - - - +
337B ILE* 1.3 66.4 + - - +
338B GLN 3.2 1.1 - - - -
339B ILE* 3.8 4.8 - - - +
340B LEU* 3.0 42.2 + - + +
349B ILE* 4.2 12.3 - - + -
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Residues in contact with ILE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B TRP* 2.7 35.8 + - + +
334B GLU* 2.9 33.8 + - + +
336B VAL* 1.3 72.4 - - - +
338B GLN* 1.3 66.0 + - + +
340B LEU* 3.8 3.7 - - - +
341B SER* 2.9 37.2 + - - -
346B THR* 4.6 4.8 - - + +
349B ILE* 3.4 35.7 - - + -
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Residues in contact with GLN 338 (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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306B ARG* 6.0 1.6 - - - +
334B GLU 3.0 17.3 + - - +
335B SER* 3.4 9.2 - - - +
337B ILE* 1.3 82.9 - - + +
339B ILE* 1.3 70.8 + - + +
341B SER* 3.4 4.8 - - - -
342B GLU* 3.0 48.1 + - - +
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Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PHE* 4.0 15.7 - - + -
303B LEU* 3.7 29.4 - - + -
306B ARG* 4.2 37.9 - - + +
307B LEU* 3.4 30.3 - - + -
335B SER* 3.0 20.8 + - - +
336B VAL* 3.8 4.3 - - - +
337B ILE 3.4 0.2 - - - -
338B GLN* 1.3 83.1 - - + +
340B LEU* 1.3 64.5 + - + +
341B SER 3.2 0.5 + - - -
342B GLU* 3.3 19.5 + - + +
343B ALA* 3.3 13.5 + - + +
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 4.0 11.0 - - + -
297B TYR* 4.3 15.5 - - + -
298B PHE* 3.8 23.3 - - + -
303B LEU* 5.9 0.2 - - + -
336B VAL* 3.0 29.0 + - + +
337B ILE* 3.9 3.4 - - - +
339B ILE* 1.3 81.4 - - + +
341B SER* 1.3 61.1 + - - +
343B ALA* 3.4 5.3 + - + -
344B GLY 3.4 2.3 + - - -
345B GLU* 2.9 52.1 + - + +
346B THR* 3.4 6.6 + - + -
348B ARG* 4.0 19.3 - - + -
349B ILE* 3.9 27.8 - - + -
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Residues in contact with SER 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ILE 2.9 19.2 + - - -
338B GLN* 3.4 6.3 - - - -
340B LEU* 1.3 70.8 - - - +
342B GLU* 1.3 54.0 + - - +
343B ALA 2.5 19.1 + - - -
344B GLY* 2.6 18.2 + - - -
346B THR* 3.3 24.2 + - - +
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Residues in contact with GLU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ARG* 3.2 32.2 + - - +
338B GLN* 3.0 31.3 + - - +
339B ILE* 3.3 15.5 + - + +
341B SER* 1.3 75.7 + - - +
343B ALA* 1.3 56.2 + - + +
344B GLY 3.6 0.4 - - - -
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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
------------------------------------------------------------
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