Contacts of the helix formed by residues 322 - 334 (chain B) in PDB entry 6Q3W
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 CYS 322 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B VAL* 4.5 1.6 - - - -
229B HIS* 5.6 6.7 - - + -
321B SER* 1.3 79.2 + - - +
323B PRO* 1.3 78.9 - - + +
324B GLU* 3.1 22.1 + - - +
325B LEU* 3.1 22.9 + - - -
326B ASP* 2.9 27.4 + - - -
348B PHE* 4.0 9.2 - - + -
349B GLY* 3.5 28.3 - - - -
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Residues in contact with PRO 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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322B CYS* 1.3 87.4 - - + +
324B GLU* 1.3 65.7 + - - +
326B ASP* 3.3 9.3 + - + +
327B GLN* 2.8 32.7 + - - +
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Residues in contact with GLU 324 (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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225B SER* 4.2 3.1 - - - -
227B VAL* 3.8 29.6 - - + +
322B CYS* 3.4 23.1 - - - +
323B PRO* 1.3 83.1 - - - +
325B LEU* 1.3 63.6 + - - +
327B GLN* 3.2 5.2 + - - +
328B LEU* 2.9 29.6 + - - +
372B TYR* 3.6 33.5 - - + +
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Residues in contact with LEU 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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225B SER* 4.5 4.5 - - - +
311B HIS* 4.4 0.2 - - - -
321B SER* 3.5 22.9 - - - +
322B CYS* 3.1 16.6 + - - +
324B GLU* 1.3 77.9 - - - +
326B ASP* 1.3 58.1 + - - +
328B LEU* 3.3 6.1 + - - +
329B VAL* 2.9 35.7 + - - +
343B MET* 3.7 25.8 - - + -
344B THR 5.9 0.2 - - - +
347B GLY* 4.4 1.3 - - - -
348B PHE 4.2 3.4 - - - +
349B GLY* 3.4 39.7 - - - +
350B GLY 3.7 15.5 - - - +
351B CYS 3.8 9.2 - - - +
352B THR* 3.7 21.7 - - + +
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Residues in contact with ASP 326 (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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311B HIS* 2.9 20.6 + - - +
315B ARG* 3.3 33.1 - - - +
321B SER* 2.8 18.4 + - - -
322B CYS* 2.9 25.1 + - - +
323B PRO* 3.6 7.6 - - + +
325B LEU* 1.3 75.2 - - - +
327B GLN* 1.3 63.7 - - - +
329B VAL* 3.2 3.6 + - - +
330B GLU* 3.0 23.9 + - - +
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Residues in contact with GLN 327 (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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323B PRO 2.8 18.6 + - - +
324B GLU* 3.7 4.0 - - - +
326B ASP* 1.3 74.5 - - - +
328B LEU* 1.3 57.4 + - - +
330B GLU* 3.5 6.0 + - - +
331B ALA* 3.0 29.0 + - + +
371B HIS 3.6 24.7 + - - +
372B TYR* 3.3 12.4 - - + -
373B GLY* 3.1 25.6 + - - +
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Residues in contact with LEU 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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223B THR* 4.0 16.8 - - + +
225B SER* 3.6 39.7 - - - +
324B GLU 2.9 19.1 + - - +
325B LEU* 3.6 4.9 - - - +
327B GLN* 1.3 75.4 - - - +
329B VAL* 1.3 63.7 + - - +
331B ALA* 3.5 4.6 + - - +
332B ALA* 3.1 23.7 + - - +
352B THR* 3.9 27.2 + - + +
368B ILE* 3.7 27.8 - - + +
372B TYR* 3.5 35.2 - - + -
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Residues in contact with VAL 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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308B VAL* 5.8 1.3 - - + -
311B HIS* 3.5 42.8 - - + +
325B LEU 2.9 20.3 + - - +
326B ASP 3.6 4.7 - - - +
328B LEU* 1.3 74.7 - - - +
330B GLU* 1.3 64.9 + - - +
332B ALA* 3.3 3.3 + - - +
333B LEU* 3.1 37.3 + - + +
341B SER* 3.8 22.6 - - - +
342B ARG* 3.8 21.8 - - - +
343B MET 3.9 0.4 - - - +
352B THR* 4.0 7.4 - - + -
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Residues in contact with GLU 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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326B ASP 3.0 16.7 + - - +
327B GLN* 3.9 6.1 - - + +
329B VAL* 1.3 78.2 - - - +
331B ALA* 1.3 63.5 + - - +
333B LEU* 3.3 10.1 + - - +
334B ALA* 3.2 21.7 + - - +
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Residues in contact with ALA 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 GLN 3.0 19.3 + - - +
328B LEU* 3.7 8.1 - - + +
329B VAL 3.3 0.2 - - - -
330B GLU* 1.3 76.3 - - - +
332B ALA* 1.3 61.9 - - - +
334B ALA* 3.3 11.8 + - - +
335B VAL* 3.5 4.3 - - - +
367B HIS* 3.4 23.1 + - - +
368B ILE* 4.2 24.7 - - + +
371B HIS* 4.2 21.8 - - + +
372B TYR* 5.9 0.4 - - + -
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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
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328B LEU 3.1 17.7 + - - +
329B VAL 3.7 4.5 - - - +
330B GLU 3.3 0.2 - - - -
331B ALA* 1.3 76.8 - - - +
333B LEU* 1.3 57.5 + - - +
335B VAL* 3.0 19.5 + - - +
338B VAL* 3.2 22.4 - - + +
341B SER* 3.9 20.6 - - - +
352B THR* 6.1 0.2 - - - +
354B THR* 3.9 17.0 - - + +
368B ILE* 3.9 21.7 - - + +
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Residues in contact with LEU 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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308B VAL* 3.8 35.0 - - + -
329B VAL* 3.1 32.5 + - + +
330B GLU* 3.3 9.4 + - - +
332B ALA* 1.3 76.0 - - - +
334B ALA* 1.3 61.3 + - - +
335B VAL 3.1 5.3 + - - +
338B VAL* 4.2 10.3 - - + +
339B TYR 5.1 1.6 - - - +
340B GLY* 4.0 8.3 - - - -
341B SER* 3.7 26.7 - - - +
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Residues in contact with ALA 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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330B GLU 3.2 11.1 + - - +
331B ALA* 3.5 11.9 - - - +
332B ALA 3.1 0.8 - - - -
333B LEU* 1.3 77.3 - - - +
335B VAL* 1.3 60.3 + - - +
336B PRO* 3.6 8.5 - - - +
367B HIS* 4.0 18.8 + - + +
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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