Contacts of the helix formed by residues 327 - 344 (chain B) in PDB entry 5YDJ
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 327 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B PHE* 3.8 20.1 + - - +
326B GLY* 1.3 72.6 - - - +
328B ALA* 1.3 65.2 + - - +
329B GLY 3.2 2.7 - - - -
330B LEU* 3.1 23.6 + - + +
331B PHE* 3.0 34.3 + - + -
452B VAL 4.7 0.2 - - - +
453B PRO* 3.4 5.9 - - - +
454B VAL* 2.6 52.0 + - - +
456B ASP* 3.3 17.7 + - - -
459B PHE* 4.2 9.7 - - + +
460B LEU* 4.6 3.4 - - - +
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Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PHE 3.8 15.7 - - - +
207B ARG 3.7 22.9 - - - +
208B HIS* 3.8 13.5 - - + -
209B PRO* 4.1 0.5 - - - +
310B ARG* 3.7 14.1 - - - +
314B LEU 4.5 1.3 - - - +
315B GLY 3.2 14.2 + - - +
326B GLY 3.2 3.6 + - - -
327B ASN* 1.3 76.6 - - - +
329B GLY* 1.3 52.5 + - - +
331B PHE* 3.2 3.6 + - - +
332B ASP* 2.8 39.7 + - - +
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Residues in contact with GLY 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TYR* 3.6 5.2 - - - +
310B ARG 3.6 22.4 - - - -
315B GLY* 2.8 16.5 + - - -
316B PHE* 3.8 9.4 - - - -
327B ASN 3.2 0.4 - - - -
328B ALA* 1.3 73.1 - - - +
330B LEU* 1.3 56.2 + - - +
332B ASP* 3.3 15.4 + - - +
333B GLN* 3.1 29.9 + - - +
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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
----------------------------------------------------------
281B PHE* 4.9 1.6 - - + -
316B PHE* 3.8 23.9 - - + -
327B ASN* 3.1 28.7 + - + +
329B GLY* 1.3 73.7 - - - +
331B PHE* 1.3 61.3 + - - +
333B GLN* 3.4 25.3 + - - +
334B ASN* 2.9 26.9 + - - +
365B SER* 4.0 24.7 - - - +
368B LEU* 4.0 10.1 - - + -
369B HIS* 4.1 0.7 - - - -
453B PRO* 3.9 16.6 - - + -
459B PHE* 3.9 42.1 - - + -
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Residues in contact with PHE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LEU* 4.3 21.3 - - + -
458A ALA* 4.1 5.6 - - + -
208B HIS* 3.2 44.2 - + + -
209B PRO* 3.7 18.4 - - + +
327B ASN* 3.0 27.5 + - + -
328B ALA 3.2 6.9 + - - +
330B LEU* 1.3 74.8 - - - +
332B ASP* 1.3 58.9 + - - +
334B ASN* 3.5 10.8 + - + +
335B LEU* 3.0 29.3 + - - +
374B LEU* 3.3 34.3 - - + -
456B ASP* 3.7 15.9 - - - -
458B ALA* 3.9 7.2 - - + -
459B PHE* 3.7 22.4 - + + -
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Residues in contact with ASP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B TYR* 3.3 28.6 - - + +
209B PRO* 3.1 27.6 - - - +
256B LEU* 3.5 10.0 - - - +
309B TYR* 4.2 7.0 - - + -
310B ARG* 3.0 53.3 + - - +
328B ALA 2.8 16.4 + - - +
329B GLY* 3.3 9.1 - - - +
330B LEU 3.3 0.2 - - - -
331B PHE* 1.3 75.9 - - - +
333B GLN* 1.3 58.2 + - - +
335B LEU* 3.4 1.4 + - - +
336B ALA* 2.9 24.6 + - - +
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Residues in contact with GLN 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE* 3.4 16.6 - - + +
281B PHE* 5.2 0.2 - - - -
307B LEU* 3.8 12.7 - - + +
309B TYR* 3.3 43.9 - - + -
329B GLY 3.1 11.7 + - - +
330B LEU* 3.5 16.5 - - - +
332B ASP* 1.3 76.3 - - - +
334B ASN* 1.3 60.5 + - - +
336B ALA* 3.3 7.7 + - - +
337B LEU* 2.8 33.3 + - - +
365B SER* 3.1 33.2 + - - -
369B HIS* 2.8 28.1 + - - +
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Residues in contact with ASN 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ARG* 5.7 1.2 - - - +
374A LEU* 4.6 11.9 - - - +
330B LEU 2.9 17.2 + - - +
331B PHE* 3.5 14.9 + - + +
332B ASP 3.3 0.2 - - - -
333B GLN* 1.3 75.8 - - - +
335B LEU* 1.3 57.1 + - - +
337B LEU* 3.3 8.2 + - - +
338B ARG* 3.1 47.6 + - - +
369B HIS* 4.0 6.7 - - - -
374B LEU* 3.5 29.8 + - - +
375B SER* 3.4 24.1 + - - -
378B LEU* 3.7 2.6 - - - +
459B PHE* 4.2 9.3 - - + -
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ASP* 4.6 7.4 - - - +
196B TYR* 3.5 28.5 - - + +
197B ALA* 4.0 4.0 - - + -
209B PRO* 3.9 24.0 - - + +
210B ARG 3.9 17.9 - - - +
211B PRO* 4.0 20.4 - - + -
331B PHE 3.0 18.6 + - - +
332B ASP 3.7 3.4 - - - +
334B ASN* 1.3 75.2 - - - +
336B ALA* 1.3 60.6 + - - +
338B ARG* 3.2 37.2 + - + +
339B TRP* 3.0 26.6 + - - +
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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
----------------------------------------------------------
196B TYR* 3.9 16.1 - - + -
258B ILE* 3.8 20.6 - - + +
274B LEU* 5.9 0.2 - - - -
307B LEU* 3.8 24.7 - - + -
332B ASP 2.9 17.9 + - - +
333B GLN* 3.4 6.1 - - - +
335B LEU* 1.3 78.2 - - - +
337B LEU* 1.3 61.2 + - - +
339B TRP* 3.3 5.3 + - - +
340B VAL* 3.2 27.1 + - - +
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 4.1 19.5 - - + -
276B ILE* 5.2 4.0 - - + -
307B LEU* 5.1 6.1 - - + -
333B GLN 2.8 21.0 + - - +
334B ASN 3.5 7.6 - - - +
335B LEU 3.3 0.2 - - - -
336B ALA* 1.3 72.0 - - - +
338B ARG* 1.3 58.6 + - - +
340B VAL* 3.4 6.7 + - + +
341B ARG* 3.0 27.9 + - - +
354B VAL* 5.2 3.4 - - + -
356B LEU* 3.5 27.8 - - + -
369B HIS* 3.8 32.8 - - + +
375B SER* 4.0 14.4 - - - -
378B LEU* 3.8 26.5 - - + +
379B PHE* 4.3 11.9 - - + -
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Residues in contact with ARG 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ARG* 3.5 35.9 - - - +
373A ALA 4.3 2.8 + - - -
374A LEU* 2.7 53.6 + - - +
377A ASP* 4.0 19.5 + - - +
378A LEU* 4.4 10.4 - - - +
334B ASN* 3.1 27.8 + - - +
335B LEU* 3.2 35.7 + - + +
337B LEU* 1.3 73.0 - - - +
339B TRP* 1.3 63.7 + - - +
341B ARG* 3.6 6.2 + - - +
342B ASP* 3.2 34.5 + - - +
374B LEU 6.0 0.2 - - - -
378B LEU* 3.7 22.2 - - + -
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Residues in contact with TRP 339 (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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170B THR* 4.1 14.8 - - + +
171B ASP* 4.5 10.1 + - - -
172B LYS* 6.4 0.9 - - + +
194B ILE* 3.6 38.5 - - + +
195B PRO 4.5 3.8 + - - -
196B TYR* 4.2 19.1 - - + -
215B TRP* 5.9 2.2 - - - -
258B ILE* 3.8 22.7 - - + -
260B VAL* 4.0 17.0 - - + -
335B LEU* 3.0 13.1 + - + +
336B ALA* 3.4 9.2 - - - +
337B LEU 3.3 0.4 - - - -
338B ARG* 1.3 73.9 - - - +
340B VAL* 1.3 78.9 + - + +
342B ASP* 3.1 2.6 + - - -
343B ASN* 2.7 66.9 + - + +
344B ILE* 4.7 4.3 - - + -
347B PHE* 3.5 28.5 - + - -
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ILE* 4.6 3.6 - - + -
272B VAL* 4.3 7.6 - - + -
274B LEU* 3.6 33.2 - - + -
305B VAL* 3.8 16.8 - - + -
307B LEU* 6.5 0.2 - - + -
336B ALA 3.2 13.9 + - - +
337B LEU* 3.4 6.7 + - + +
339B TRP* 1.3 94.2 - - + +
341B ARG* 1.3 61.8 + - - +
344B ILE* 3.1 51.6 + - + +
354B VAL* 4.2 16.6 - - + -
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Residues in contact with ARG 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASP* 4.0 22.0 + - - +
342A ASP* 2.8 40.8 + - - +
337B LEU 3.0 16.8 + - - +
338B ARG* 3.8 7.2 - - - +
340B VAL* 1.3 80.4 - - - +
342B ASP* 1.3 66.8 + - - +
343B ASN 3.6 0.2 + - - -
344B ILE 4.7 0.5 + - - -
345B HIS 5.5 0.2 + - - -
351B PRO* 3.8 49.5 + - + +
352B SER* 5.1 3.4 - - - +
354B VAL* 5.8 0.9 - - - -
377B ASP* 3.6 20.2 + - - -
378B LEU* 3.8 34.7 + - - +
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Residues in contact with ASP 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ARG* 3.5 35.4 + - - +
342A ASP* 4.9 5.2 - - - +
377A ASP* 4.0 13.9 - - - +
171B ASP* 3.3 23.1 - - + +
338B ARG* 3.2 17.5 + - - +
339B TRP* 3.1 2.5 + - - -
341B ARG* 1.3 84.5 - - - +
343B ASN* 1.3 62.8 + - - +
345B HIS* 5.6 1.7 - - - +
346B ARG* 3.5 18.0 + - - +
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Residues in contact with ASN 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B THR* 3.4 12.4 - - + -
171B ASP* 3.1 47.0 + - - -
339B TRP* 2.7 68.5 + - + +
341B ARG 3.4 0.2 - - - -
342B ASP* 1.3 82.3 - - - +
344B ILE* 1.3 58.2 + - - +
345B HIS* 3.2 4.0 - - - -
346B ARG* 2.9 40.0 + - - +
347B PHE* 3.5 7.8 - - + -
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Residues in contact with ILE 344 (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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260B VAL* 4.1 17.0 - - + -
272B VAL* 3.9 29.2 - - + -
303B ILE* 3.8 13.5 - - + -
305B VAL* 3.5 29.2 - - + -
339B TRP* 4.7 4.7 - - + -
340B VAL* 3.1 38.1 + - + +
341B ARG 4.7 0.4 + - - -
343B ASN* 1.3 75.9 - - - +
345B HIS* 1.3 61.9 + - - +
346B ARG 3.2 0.4 - - - -
347B PHE* 3.3 17.8 + - + +
348B GLY 3.3 0.3 + - - -
349B GLY* 2.9 33.1 + - - +
351B PRO* 4.1 17.0 - - + -
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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
------------------------------------------------------------
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