Contacts of the helix formed by residues 317 - 328 (chain A) in PDB entry 3CQ6
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 ASP 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A PHE* 4.0 1.6 - - - -
316A SER* 1.3 80.4 - - - +
318A GLN* 1.3 67.3 + - - +
319A HIS* 3.1 21.6 + - - +
320A ALA* 3.0 23.3 + - + +
321A ALA* 3.0 17.0 + - - +
366A LEU 2.8 14.3 + - - +
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Residues in contact with GLN 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A PHE* 3.8 15.9 - - + +
316A SER 4.2 0.4 + - - -
317A ASP* 1.3 73.1 + - - +
319A HIS* 1.3 66.4 + - - +
321A ALA* 3.5 3.0 - - - +
322A TRP* 2.7 29.1 + - - +
334A ASP* 2.9 33.5 - - - +
336A GLY* 5.2 2.1 - - - -
337A ILE 3.5 8.4 + - - +
338A ALA* 3.6 21.0 - - - +
339A GLY* 3.1 24.1 - - - +
340A HIS 3.5 22.7 - - - +
341A LEU* 3.5 14.0 - - + +
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Residues in contact with HIS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A ASP* 3.1 11.0 + - - +
318A GLN* 1.3 85.0 + - - +
320A ALA* 1.3 56.1 + - - +
322A TRP* 3.1 31.0 + + - +
323A GLN* 2.9 62.6 + - + +
334A ASP* 3.5 23.1 - - + +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A ASP* 3.0 29.5 + - + +
319A HIS* 1.3 77.6 + - - +
321A ALA* 1.3 62.7 + - - +
323A GLN* 3.3 16.0 + - - +
324A ALA* 3.0 18.4 + - - +
366A LEU* 3.5 26.9 - - + +
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Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A PHE* 3.4 50.7 - - + -
317A ASP 3.0 8.0 + - - +
318A GLN 3.5 7.9 - - - +
320A ALA* 1.3 75.3 - - - +
322A TRP* 1.3 63.7 + - - +
324A ALA* 3.2 4.7 + - - +
325A PHE* 3.1 26.6 + - + -
341A LEU* 4.0 5.2 - - + -
361A ILE* 4.8 2.7 - - + -
366A LEU* 3.8 14.9 - - + +
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Residues in contact with TRP 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PRO* 3.7 27.1 - - + -
26A LEU* 4.2 4.0 - - + -
318A GLN 2.7 17.1 + - - +
319A HIS* 3.2 40.8 - + - +
321A ALA* 1.3 74.5 - - - +
323A GLN* 1.3 79.2 + - + +
325A PHE* 3.2 7.2 + - - +
326A LEU* 3.0 48.2 + - + +
330A VAL 4.8 0.4 - - - +
331A LEU* 3.8 18.1 - - + +
332A ILE* 3.0 36.5 + - + -
333A ARG 4.4 0.2 - - - -
334A ASP* 4.0 9.6 - - + -
341A LEU* 3.7 13.6 - - + +
404A PO4 2.4 30.3 + - - -
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Residues in contact with GLN 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A HIS* 2.9 40.0 + - + +
320A ALA* 3.3 16.5 + - - +
322A TRP* 1.3 93.5 - - + +
324A ALA* 1.3 56.5 + - - +
326A LEU* 3.3 8.9 + - + +
327A ASP* 2.8 39.4 + - - +
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A ALA 3.0 13.1 + - - +
321A ALA 3.2 9.8 + - - +
323A GLN* 1.3 77.2 - - - +
325A PHE* 1.3 59.8 + - - +
327A ASP* 3.5 6.5 + - - +
328A ARG* 2.9 48.2 + - - +
361A ILE* 3.9 14.1 - - + -
364A LEU* 4.7 3.6 - - + -
366A LEU* 3.8 18.4 - - + -
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Residues in contact with PHE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A TYR* 4.6 1.6 - - - -
312A PHE* 4.1 15.3 - + - -
315A PHE* 4.6 4.5 - + - -
321A ALA 3.1 27.5 + - - -
322A TRP 3.2 6.5 + - - +
324A ALA* 1.3 72.6 - - - +
326A LEU* 1.3 63.3 + - - +
328A ARG* 3.0 14.2 + - - +
329A GLY 3.2 0.3 + - - -
330A VAL* 2.9 39.1 + - + +
332A ILE* 3.8 26.0 - - + +
341A LEU* 4.2 5.6 - - + -
354A PHE* 3.4 39.5 - + - -
357A ALA* 3.9 9.6 - - + -
358A ALA* 3.7 27.1 - - + -
361A ILE* 3.3 30.5 - - + -
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.7 39.7 - - + -
28A VAL* 4.3 19.1 - - + +
322A TRP* 3.0 34.5 + - + +
323A GLN* 3.5 12.6 - - + +
325A PHE* 1.3 76.5 - - - +
327A ASP* 1.3 61.4 + - - +
329A GLY* 2.9 20.3 + - - -
330A VAL 3.1 8.2 + - - +
331A LEU* 4.2 12.8 - - + -
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Residues in contact with ASP 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A GLN* 2.8 28.3 + - - +
324A ALA* 3.7 9.7 - - - +
325A PHE 3.3 0.2 - - - -
326A LEU* 1.3 77.1 - - - +
328A ARG* 1.3 65.7 + - + +
329A GLY 3.3 1.4 + - - -
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Residues in contact with ARG 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A ALA* 2.9 36.6 + - - +
325A PHE 3.0 9.8 + - - +
327A ASP* 1.3 83.0 - - - +
329A GLY* 1.3 60.0 + - - +
330A VAL* 3.4 7.6 + - - +
357A ALA* 3.9 31.8 - - + +
360A GLU* 2.9 39.0 + - - +
361A ILE* 4.1 11.8 - - - +
364A LEU* 3.8 25.2 - - - +
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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