Contacts of the helix formed by residues 322 - 340 (chain B) in PDB entry 3V6R
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 322 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ALA* 5.9 3.3 - - - +
320B ALA* 4.2 2.2 - - - +
321B ASP* 1.3 76.0 + - - +
323B GLU* 1.3 59.4 + - - +
324B HIS* 3.9 6.7 - - - -
325B ASN* 3.5 32.1 + - - +
326B LYS* 3.0 30.0 + - - +
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Residues in contact with GLU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B SER* 1.3 72.4 - - - +
324B HIS* 1.4 56.8 + - - +
326B LYS* 3.6 6.7 + - - +
327B LEU* 3.1 29.5 + - - +
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Residues in contact with HIS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LYS* 5.7 1.2 + - - -
382A GLU* 3.7 46.1 + - - +
383A ARG* 5.4 0.7 - - - -
384A GLU* 3.7 20.3 + - + +
163B HIS* 5.8 2.2 - - + -
164B GLU* 4.8 12.6 - - - -
322B SER* 3.9 6.0 - - - -
323B GLU* 1.4 77.6 - - - +
325B ASN* 1.4 69.7 + - - +
327B LEU* 3.3 15.1 + - + +
328B LYS* 2.9 64.0 + - + +
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Residues in contact with ASN 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ALA 5.2 7.5 + - - +
163B HIS* 3.5 23.4 + - + +
319B PRO* 3.5 44.4 - - - +
320B ALA* 4.2 5.0 - - - +
322B SER* 3.5 28.8 + - - +
324B HIS* 1.4 87.7 + - - +
326B LYS* 1.3 59.3 + - - +
328B LYS* 4.1 3.4 - - - -
329B ALA* 3.1 22.7 + - - +
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Residues in contact with LYS 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ASP* 4.9 6.5 - - - +
319B PRO 5.2 0.9 - - - -
320B ALA* 5.7 3.8 - - + +
322B SER 3.0 18.6 + - - +
323B GLU* 3.9 10.5 - - - +
325B ASN* 1.3 74.8 - - - +
327B LEU* 1.4 63.8 + - - +
329B ALA* 3.3 7.6 + - - +
330B SER* 3.1 22.1 + - - -
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLU* 6.1 0.7 - - - +
323B GLU* 3.1 19.8 + - + +
324B HIS* 3.5 16.2 - - + +
326B LYS* 1.4 76.3 - - - +
328B LYS* 1.4 57.3 + - - +
330B SER* 3.3 11.9 + - - -
331B GLN* 3.0 56.7 + - + +
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Residues in contact with LYS 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLU* 3.1 39.2 + - - -
163B HIS* 3.4 35.0 - - + +
164B GLU* 5.8 2.2 - - - +
167B SER* 6.1 0.6 - - - -
324B HIS* 2.9 41.8 + - + +
325B ASN 3.8 0.7 - - - +
326B LYS 3.3 0.2 - - - -
327B LEU* 1.4 75.5 - - + +
329B ALA* 1.3 58.0 + - - +
331B GLN* 2.7 29.0 + - - +
332B ALA* 2.9 23.0 + - - +
357B PRO 3.4 14.3 + - - -
358B TYR* 3.4 35.4 + - + +
361B VAL* 4.3 3.4 - - - +
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Residues in contact with ALA 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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163B HIS* 3.6 8.7 - - - +
315B ASP* 4.1 14.6 - - - +
318B PHE* 3.7 37.4 - - + -
319B PRO 5.0 1.1 - - - +
325B ASN 3.1 17.5 + - - +
326B LYS* 3.3 6.5 + - - +
328B LYS* 1.3 73.0 - - - +
330B SER* 1.4 59.0 + - - +
332B ALA* 3.7 1.4 - - - +
333B ARG* 3.0 36.9 + - - +
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Residues in contact with SER 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ASP* 5.3 0.6 + - - -
326B LYS 3.1 13.1 + - - -
327B LEU* 3.4 17.7 - - - -
329B ALA* 1.4 76.4 - - - +
331B GLN* 1.4 55.2 + - - +
333B ARG* 4.0 16.8 + - - +
334B ASP* 3.3 25.8 + - - +
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Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLU* 4.9 3.8 + - - -
327B LEU* 3.0 40.6 + - + +
328B LYS* 2.7 45.6 + - - +
329B ALA 3.2 0.2 - - - -
330B SER* 1.4 75.0 - - - +
332B ALA* 1.4 58.9 + - - +
334B ASP* 3.2 5.9 + - - +
335B LEU* 3.0 23.7 + - - +
356B HIS* 3.3 16.7 - - + -
357B PRO* 3.5 29.7 - - + +
358B TYR* 4.0 11.4 - - + -
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Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B MET* 4.6 0.2 - - + -
253B MET* 3.3 23.6 - - + +
318B PHE* 3.7 28.0 - - + -
328B LYS 2.9 17.4 + - - +
329B ALA 3.4 1.3 + - - +
331B GLN* 1.4 73.5 - - - +
333B ARG* 1.3 56.3 + - - +
335B LEU* 3.2 2.6 + - - -
336B LEU* 3.0 26.6 + - - +
358B TYR* 3.6 28.2 - - + +
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Residues in contact with ARG 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B PHE* 3.9 18.4 - - + +
310B PRO* 3.7 35.4 - - - +
313B PHE* 2.8 33.6 + - + +
314B PRO* 3.6 1.4 - - - +
315B ASP* 3.3 45.7 + - - +
318B PHE* 4.2 12.2 - - + -
329B ALA 3.0 17.5 + - - +
330B SER* 4.0 22.5 + - - +
332B ALA* 1.3 75.1 - - - +
334B ASP* 1.4 57.1 + - - +
336B LEU* 3.2 11.9 + - - +
337B SER* 2.9 27.9 + - - -
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Residues in contact with ASP 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B SER 3.3 13.9 + - - +
331B GLN* 3.2 11.8 + - - +
333B ARG* 1.4 76.3 - - - +
335B LEU* 1.3 62.2 + - - +
337B SER* 2.9 24.5 + - - -
338B LYS* 2.9 38.2 + - - +
356B HIS* 2.8 24.6 + - - +
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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
----------------------------------------------------------
170B LEU* 5.0 0.7 - - + -
174B LEU* 5.6 1.3 - - + -
253B MET* 3.9 22.9 - - + -
331B GLN 3.0 8.0 + - - +
332B ALA* 3.2 8.0 + - - +
334B ASP* 1.3 73.2 - - - +
336B LEU* 1.3 59.8 + - - +
338B LYS* 3.2 3.1 + - - +
339B MET* 3.0 58.2 + - + +
348B ILE* 4.4 14.1 - - + -
353B ALA* 4.5 8.5 - - + -
356B HIS* 3.8 37.9 + - + -
358B TYR* 4.2 6.1 - - + -
359B ILE* 3.7 33.7 - - + -
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Residues in contact with LEU 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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250B GLY* 3.5 26.7 - - - +
253B MET* 3.7 22.4 - - + -
254B GLY* 3.6 17.3 - - - +
257B VAL* 4.4 15.7 - - + -
309B PHE* 3.8 3.4 - - + -
313B PHE* 3.9 37.9 - - + -
318B PHE* 4.8 1.8 - - + -
332B ALA 3.0 21.9 + - - +
333B ARG* 3.2 10.3 + - - +
335B LEU* 1.3 76.8 - - - +
337B SER* 1.4 56.1 + - - +
338B LYS 3.1 0.2 - - - -
339B MET* 4.7 2.9 - - - -
340B LEU* 2.8 47.2 + - + +
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Residues in contact with SER 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B PHE* 3.6 39.6 - - - -
333B ARG 2.9 14.0 + - - -
334B ASP* 2.9 26.4 + - - -
336B LEU* 1.4 74.7 - - - +
338B LYS* 1.4 59.3 + - - +
341B VAL* 3.3 18.2 - - - +
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ASP* 2.9 40.8 + - - +
335B LEU* 3.2 8.9 + - - +
336B LEU 3.1 0.8 - - - -
337B SER* 1.4 81.8 + - - +
339B MET* 1.4 57.4 + - - +
340B LEU 3.7 0.2 - - - -
341B VAL* 3.5 13.7 - - - +
346B LYS 4.5 2.9 - - - +
347B ARG* 3.6 1.4 - - - -
348B ILE* 3.0 57.8 + - + +
356B HIS* 4.2 12.6 - - + -
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Residues in contact with MET 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 5.3 0.9 - - + -
174B LEU* 5.0 2.7 - - - -
246B ILE* 3.8 27.8 - - + +
247B TRP* 4.0 9.7 - - - -
249B VAL* 4.0 25.1 - - + +
250B GLY* 3.7 27.8 - - - +
253B MET* 3.5 32.1 - - - -
335B LEU* 3.0 36.6 + - + +
336B LEU* 4.1 2.0 - - + +
338B LYS* 1.4 73.9 - - - +
340B LEU* 1.4 60.6 + - - +
341B VAL 3.1 8.0 + - - -
347B ARG* 3.4 19.9 + - - +
348B ILE* 3.7 16.8 - - + -
353B ALA* 5.0 4.5 - - - -
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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
----------------------------------------------------------
247B TRP* 4.1 16.6 - - + +
250B GLY* 3.6 33.4 - - - +
251B CYS* 3.6 10.1 - - - +
262B LEU* 3.5 29.2 - - + -
263B PHE* 4.0 17.5 - - + -
279B LEU* 4.0 19.4 - - + +
309B PHE* 3.4 26.5 - - + -
313B PHE* 3.9 16.2 - - + -
336B LEU* 2.8 32.2 + - + +
339B MET* 1.4 67.6 - - - +
341B VAL* 1.4 60.9 + - - +
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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