Contacts of the helix formed by residues 320 - 333 (chain B) in PDB entry 4CQ8
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
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318B THR* 3.2 17.1 - - - +
319B VAL* 1.4 83.4 - - + +
321B ILE* 1.3 66.4 + - - +
322B VAL* 3.2 30.2 + - - +
323B ASP* 3.2 38.9 + - - +
362B ASN* 5.5 1.3 + - - +
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Residues in contact with ILE 321 (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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314B LYS* 3.9 32.9 - - + +
318B THR* 4.3 0.4 - - - +
319B VAL 3.8 4.6 + - - -
320B ASN* 1.3 75.0 + - - +
322B VAL* 1.4 59.4 + - + +
324B ASP* 3.0 7.6 + - - +
325B LEU* 3.0 45.3 + - + +
342B ASN 4.5 3.8 - - - +
343B VAL* 4.1 19.3 - - + -
351B LEU* 3.7 28.5 - - + -
354B ASN* 3.7 30.3 - - - +
363B ILE* 3.8 18.4 - - + -
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Residues in contact with VAL 322 (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 21.4 + - - +
321B ILE* 1.4 75.1 - - + +
323B ASP* 1.4 58.0 + - - +
325B LEU* 3.8 9.9 - - + +
326B LYS* 2.9 53.8 + - + +
362B ASN* 3.8 23.8 - - - +
363B ILE* 3.9 29.2 - - + -
366B SER* 3.7 22.9 - - - +
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Residues in contact with ASP 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B THR* 4.9 3.2 - - + +
319B VAL* 5.9 1.2 - - - +
320B ASN* 3.2 36.8 + - - +
322B VAL* 1.4 74.7 - - - +
324B ASP* 1.3 63.3 + - - +
326B LYS* 3.8 17.0 + - - +
327B TYR* 3.1 27.7 + - - +
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Residues in contact with ASP 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PRO* 3.4 30.6 - - + +
253B ARG* 5.0 1.7 + - - -
313B GLY 3.8 11.4 - - - +
314B LYS* 3.4 4.3 - - + -
315B ASN* 2.8 23.6 + - - +
318B THR* 2.7 39.1 + - + +
321B ILE 3.0 9.8 + - - +
323B ASP* 1.3 78.7 - - - +
325B LEU* 1.3 63.5 + - - +
327B TYR* 3.4 1.1 + - - +
328B CYS* 3.1 28.6 + - - -
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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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312B ILE* 3.8 43.4 - - + +
313B GLY* 4.0 13.0 - - - +
321B ILE* 3.0 33.8 + - + +
322B VAL* 3.8 13.2 - - + +
324B ASP* 1.3 73.5 - - - +
326B LYS* 1.3 58.7 + - + +
328B CYS* 3.2 5.2 + - - +
329B ILE* 3.0 34.2 + - - +
341B ILE* 4.1 10.8 - - + -
363B ILE* 3.7 31.9 - - + +
367B VAL* 3.9 21.8 - - + -
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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
----------------------------------------------------------
322B VAL* 2.9 42.7 + - + +
323B ASP* 3.8 15.1 + - - +
325B LEU* 1.3 73.6 - - + +
327B TYR* 1.3 65.3 + - - +
329B ILE* 3.3 4.1 + - + +
330B ASN* 2.9 31.7 + - - +
366B SER* 4.7 10.7 - - - +
367B VAL* 6.3 0.2 - - + -
370B GLU* 3.3 43.7 - - + +
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Residues in contact with TYR 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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252B PRO* 3.5 40.3 + - + -
283B CYS* 4.1 12.3 - - + -
284B ASP* 2.6 36.4 + - - -
323B ASP 3.1 17.8 + - - +
324B ASP* 3.6 5.4 - - - +
325B LEU 3.4 0.2 - - - -
326B LYS* 1.3 76.8 - - - +
328B CYS* 1.4 62.1 + - - +
330B ASN* 3.4 6.8 + - - +
331B LYS* 3.2 22.7 + - + +
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Residues in contact with CYS 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ILE* 4.3 10.8 - - + -
251B THR 4.1 3.8 - - - -
252B PRO* 3.9 25.6 - - - -
283B CYS* 3.7 23.8 - - - -
312B ILE* 3.6 32.5 - - + -
313B GLY 4.6 1.6 - - - -
324B ASP 3.1 16.6 + - - +
325B LEU 3.2 6.3 + - - +
327B TYR* 1.4 76.0 - - - +
329B ILE* 1.3 59.8 + - - +
331B LYS* 3.1 1.0 + - - +
332B ILE* 2.8 37.0 + - - +
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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
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312B ILE* 4.0 12.1 - - + -
325B LEU 3.0 30.5 + - - +
326B LYS* 3.3 4.9 + - + +
328B CYS* 1.3 73.5 - - - +
330B ASN* 1.3 61.2 + - - +
332B ILE* 5.1 0.4 - - - -
333B GLY* 2.9 32.9 + - - +
334B ARG 4.6 0.2 + - - -
339B ILE* 4.8 7.6 - - + -
367B VAL* 3.7 44.2 - - + +
370B GLU* 3.8 19.5 - - + +
371B ILE* 3.7 39.0 - - + +
374B LEU* 4.0 12.5 - - + +
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Residues in contact with ASN 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LYS* 2.9 26.1 + - - +
327B TYR* 3.9 6.8 - - - +
329B ILE* 1.3 74.4 - - - +
331B LYS* 1.3 59.4 + - - +
370B GLU* 2.7 35.8 + - - +
373B ASN* 6.1 0.2 - - - +
374B LEU* 3.6 26.4 - - + +
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Residues in contact with LYS 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B CYS* 3.6 18.2 - - - +
284B ASP* 2.8 43.3 + - - +
287B THR* 3.4 35.5 - - - +
288B GLU* 4.5 11.1 + - - -
291B ILE* 5.9 0.7 - - - -
327B TYR* 3.2 13.4 + - + +
328B CYS 3.1 1.6 + - - -
330B ASN* 1.3 80.1 - - - +
332B ILE* 1.3 59.3 + - - +
333B GLY 3.7 0.4 - - - -
334B ARG* 5.2 2.4 + - - +
335B TYR* 3.6 20.1 - - - -
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Residues in contact with ILE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ILE* 4.4 0.2 - - + -
250B ILE* 3.9 24.7 - - + -
283B CYS* 4.4 1.8 - - - -
286B VAL* 4.2 11.2 - - + -
287B THR* 3.4 38.4 - - + +
290B LEU* 3.8 28.3 - - + -
310B VAL* 3.9 29.4 - - + -
312B ILE* 4.8 1.8 - - + -
328B CYS 2.8 23.8 + - - +
331B LYS* 1.3 72.5 - - - +
333B GLY* 1.3 64.5 + - - +
334B ARG 3.3 2.9 - - - -
335B TYR* 3.0 17.9 + - + -
336B ALA* 3.5 7.3 + - - +
339B ILE* 4.5 7.0 - - + -
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Residues in contact with GLY 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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328B CYS 3.8 0.2 + - - -
329B ILE* 2.9 23.5 + - - -
331B LYS 3.7 0.2 - - - -
332B ILE* 1.3 78.8 - - - +
334B ARG* 1.3 59.8 + - - +
335B TYR 3.2 1.0 + - - -
336B ALA* 3.3 9.4 + - - +
339B ILE* 4.3 17.5 - - - -
374B LEU* 4.3 6.5 - - - -
416B TRP* 4.3 4.0 - - - -
424B PRO* 3.5 26.2 - - - +
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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