Contacts of the helix formed by residues 322 - 334 (chain B) in PDB entry 5M64
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 322 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278B LYS* 3.6 5.4 - - - +
321B GLN* 1.3 77.3 + - + +
323B ARG* 1.3 88.4 + - - +
324B THR* 2.8 21.0 + - - +
325B GLN* 3.1 24.6 - - - +
326B VAL* 3.0 20.4 + - - +
104M SER* 2.8 48.2 + - - +
105M SER* 3.9 1.0 - - - +
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Residues in contact with ARG 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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278B LYS* 3.1 30.2 - - - +
279B ALA* 4.2 8.6 - - - +
280B LEU 5.2 0.7 - - - +
281B CYS* 3.6 25.3 + - - +
282B HIS* 3.1 48.6 + - - +
283B THR 4.0 0.6 - - - +
284B SER* 3.5 35.6 + - - +
322B ASN* 1.3 92.8 - - - +
324B THR* 1.3 73.7 + - + +
326B VAL* 3.8 4.8 - - - +
327B LEU* 2.9 30.8 + - - +
102M SER* 5.4 8.7 + - - +
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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
----------------------------------------------------------
322B ASN* 2.8 27.2 + - + +
323B ARG* 1.3 92.9 - - + +
325B GLN* 1.3 68.1 + - - +
327B LEU* 3.2 6.5 + - - +
328B GLN* 2.9 34.7 + - - +
104M SER 4.1 2.3 + - - -
105M SER* 4.3 20.3 - - - +
107M ASN* 5.0 2.2 + - - -
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Residues in contact with GLN 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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319B HIS 3.0 25.6 - - - +
320B LEU* 3.5 20.2 - - + +
321B GLN* 3.1 11.4 + - - +
322B ASN* 3.1 16.4 + - - +
324B THR* 1.3 80.6 + - - +
326B VAL* 1.3 65.5 + - - +
328B GLN* 3.2 10.2 + - - +
329B TYR* 3.0 19.2 + - - +
104M SER* 2.7 36.5 + - - +
107M ASN* 3.0 38.5 - - - +
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B MET* 3.2 39.0 - - + +
278B LYS* 3.4 25.8 - - + +
279B ALA* 3.7 13.0 - - + -
313B PHE* 5.1 2.9 - - + -
320B LEU* 3.6 31.4 - - + -
322B ASN 3.0 18.8 + - - +
323B ARG* 3.9 7.6 - - - +
325B GLN* 1.3 76.6 - - - +
327B LEU* 1.3 56.0 + - - +
329B TYR* 3.3 4.0 + - - +
330B LEU* 3.0 26.7 + - + +
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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
----------------------------------------------------------
279B ALA* 3.8 20.1 - - - +
323B ARG 2.9 19.4 + - - +
324B THR* 3.6 4.9 - - - +
326B VAL* 1.3 73.8 - - - +
328B GLN* 1.3 61.6 + - - +
330B LEU* 3.7 9.8 - - + +
331B GLY 3.0 24.1 + - - -
346B ASP 3.2 21.4 - - - +
347B LEU* 3.6 18.2 - - + +
350B GLY* 3.5 23.1 - - - +
351B GLN* 3.5 24.0 - - + +
354B LEU* 4.0 12.1 - - + -
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Residues in contact with GLN 328 (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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324B THR* 2.9 21.2 + - - +
325B GLN* 3.2 14.6 + - - +
327B LEU* 1.3 78.2 - - - +
329B TYR* 1.3 57.8 + - - +
332B ASP* 2.9 29.6 + - - +
346B ASP* 2.9 47.2 + - - +
347B LEU* 3.4 26.9 - - - +
107M ASN* 3.2 27.9 - - - +
108M LEU* 3.3 16.6 - - - +
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Residues in contact with TYR 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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275B MET* 3.7 30.5 - - + -
316B ARG* 4.0 23.9 + - - -
317B TYR* 5.3 15.3 - + - -
320B LEU* 4.7 14.6 - - + -
325B GLN 3.0 15.2 + - - +
326B VAL 3.3 5.4 + - - +
328B GLN* 1.3 73.6 - - - +
330B LEU* 1.3 60.9 + - - +
332B ASP* 3.6 10.9 - - + +
333B LYS* 3.0 46.0 + - + +
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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
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271B VAL* 5.6 0.2 - - + -
275B MET* 3.4 50.5 - - + +
276B ILE* 4.1 18.2 - - + -
279B ALA* 3.6 20.4 - - + -
326B VAL 3.0 17.9 + - - +
327B LEU* 3.7 15.7 - - + +
329B TYR* 1.3 77.2 - - - +
331B GLY* 1.3 56.6 + - - +
333B LYS* 5.1 0.2 - - - -
334B PHE* 2.9 56.5 + - + +
350B GLY* 4.7 5.2 - - - +
353B VAL* 5.7 3.1 - - + -
354B LEU* 4.2 13.7 - - + -
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Residues in contact with GLY 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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327B LEU 3.0 16.4 + - - -
328B GLN 3.8 1.8 - - - -
330B LEU* 1.3 76.3 - - - +
332B ASP* 1.3 56.1 + - - +
334B PHE* 4.0 2.7 - - - -
335B ARG* 3.1 35.7 + - - +
346B ASP* 3.8 14.1 - - - -
349B VAL* 3.7 20.0 - - - +
350B GLY* 3.8 6.6 - - - -
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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
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328B GLN 2.9 18.0 + - - +
329B TYR* 3.6 14.4 - - + +
330B LEU 3.1 0.2 - - - -
331B GLY* 1.3 77.5 - - - +
333B LYS* 1.3 65.4 + - - +
335B ARG* 3.6 18.9 + - - +
346B ASP* 4.8 6.4 - - + +
109M ARG* 3.7 40.7 + - - +
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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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275B MET* 6.3 0.7 - - + -
329B TYR* 3.0 36.0 + - + +
330B LEU* 5.1 0.4 - - + -
332B ASP* 1.3 78.6 - - - +
334B PHE* 1.3 77.5 + - + +
335B ARG 3.4 2.7 + - - -
336B VAL* 5.0 4.5 + - - +
337B VAL* 5.6 0.9 + - - +
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Residues in contact with PHE 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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262B PHE* 4.7 17.7 - + - -
269B TYR* 3.8 37.0 - + + -
270B LEU 6.1 0.7 - - - -
271B VAL* 5.8 7.4 - - + -
275B MET* 5.7 3.6 - - + -
330B LEU* 2.9 45.3 + - + +
331B GLY* 3.6 4.3 - - - -
333B LYS* 1.3 93.7 - - + +
335B ARG* 1.3 62.1 + - - +
336B VAL 3.5 2.5 - - - +
337B VAL* 3.3 34.3 - - + +
338B PHE* 4.9 1.7 + + - -
349B VAL* 3.8 14.9 - - - +
353B VAL* 4.4 20.1 - - + +
357B ILE* 5.5 5.8 - - + -
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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
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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