Contacts of the helix formed by residues 319 - 332 (chain B) in PDB entry 3DL2
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 319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B GLY* 1.3 72.3 - - - -
320B ASN* 1.3 58.5 + - - +
321B LEU 3.4 2.2 - - - +
322B ASP* 3.5 6.2 + - - +
323B SER* 2.9 30.1 + - - -
345B VAL* 3.3 39.9 - - + +
346B ILE 4.1 8.1 - - - -
347B GLY 4.0 10.1 - - - -
348B GLU 4.3 1.8 - - - -
349B GLN* 3.8 30.5 - - - -
410B SER 3.5 3.4 - - - -
428B SER* 2.9 25.1 + - - +
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Residues in contact with ASN 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ILE* 3.0 16.7 + - + +
319B CYS* 1.3 74.3 - - - +
321B LEU* 1.3 66.1 - - - +
323B SER* 3.3 5.0 + - - -
324B GLN* 3.0 45.0 + - - +
393B SER* 3.6 30.1 + - - -
397B MET* 3.6 30.0 - - + +
409B HIS* 2.9 32.1 + - - +
410B SER* 3.0 14.0 + - - +
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ASP* 3.5 14.1 - - + +
228A ILE* 6.0 0.7 - - + -
317B ILE 4.6 1.2 + - - -
318B GLY 5.3 0.6 + - - -
320B ASN* 1.3 78.0 - - - +
322B ASP* 1.3 63.7 + - - +
324B GLN* 3.4 5.9 + - + +
325B ARG* 3.0 55.6 + - + +
385B GLN* 3.6 36.3 - - + +
389B SER* 4.0 38.6 - - - +
390B VAL* 4.1 10.1 - - + +
393B SER* 4.1 19.5 + - - +
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Residues in contact with ASP 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B CYS* 3.5 11.2 + - - +
321B LEU* 1.3 77.8 - - - +
323B SER* 1.3 52.4 + - - +
325B ARG* 3.5 2.0 + - - +
326B LEU* 2.8 36.2 + - - +
345B VAL* 3.7 24.4 - - + +
349B GLN* 2.7 27.9 - - - +
353B LYS* 3.0 37.4 + - - +
380B LEU* 3.7 19.4 - - + +
385B GLN* 3.5 15.5 + - - -
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Residues in contact with SER 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B CYS 2.9 22.5 + - - -
320B ASN* 3.7 5.2 - - - -
321B LEU 3.2 0.2 - - - -
322B ASP* 1.3 72.3 - - - +
324B GLN* 1.3 66.4 + - - +
326B LEU* 3.8 2.0 - - - +
327B GLN* 3.1 32.7 + - - +
344B TRP* 3.8 25.1 - - - +
345B VAL* 2.9 36.6 + - - +
410B SER* 3.4 10.1 - - - -
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Residues in contact with GLN 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ILE* 3.8 31.3 - - + +
320B ASN* 3.0 40.6 + - - +
321B LEU* 3.9 7.1 - - + +
323B SER* 1.3 77.3 - - - +
325B ARG* 1.3 61.8 + - - +
327B GLN* 3.9 10.7 - - - +
328B TYR* 3.1 23.4 + - - +
344B TRP* 6.3 2.0 - - + -
393B SER* 4.5 11.6 - - - -
396B ASP* 2.9 31.4 + - - +
407B LYS* 3.7 12.9 - - - +
409B HIS* 3.8 6.1 + - - -
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Residues in contact with ARG 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A MET* 3.5 25.5 - - + +
225A ASP* 2.7 43.8 + - - +
228A ILE* 3.9 9.9 - - + -
321B LEU* 3.0 35.8 + - + +
322B ASP* 4.8 1.7 + - - +
324B GLN* 1.3 75.2 - - - +
326B LEU* 1.3 60.0 + - - +
328B TYR* 3.1 3.0 + - - +
329B ILE* 2.8 36.0 + - + +
380B LEU* 3.5 24.3 + - + +
383B LYS* 3.9 16.5 + - - +
384B GLY 2.8 28.7 + - - -
385B GLN* 3.5 15.6 - - - +
389B SER* 3.5 15.4 + - - -
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ASP 2.8 22.1 + - - +
323B SER 3.3 4.7 + - - +
325B ARG* 1.3 73.2 - - - +
327B GLN* 1.3 57.5 + - - +
329B ILE* 3.4 8.4 + - + +
330B ILE* 3.1 31.8 + - + +
343B VAL* 3.8 34.5 - - + -
345B VAL* 3.7 24.0 - - + +
355B LEU* 3.9 16.2 - - + -
376B ALA* 3.6 44.9 - - + +
377B MET* 3.8 9.0 - - + +
380B LEU* 4.2 11.0 - - + +
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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 SER 3.1 20.3 + - - +
324B GLN* 3.9 11.1 - - - +
326B LEU* 1.3 75.8 - - - +
328B TYR* 1.3 58.6 + - - +
330B ILE* 4.0 2.8 - - - +
331B THR* 3.0 35.0 + - - +
341B LYS* 3.3 35.6 - - - +
343B VAL* 2.7 32.3 + - + +
344B TRP* 3.3 39.1 - - - -
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Residues in contact with TYR 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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224A MET* 3.5 31.8 - - + -
227A GLU* 4.2 35.2 - - + +
228A ILE* 3.7 27.1 - - + -
324B GLN 3.1 14.7 + - - +
325B ARG 3.1 7.9 + - - +
327B GLN* 1.3 72.5 - - - +
329B ILE* 1.3 58.2 + - - +
332B ASN* 2.7 69.4 + - + +
333B VAL* 3.4 16.3 + - + -
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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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224A MET* 4.3 12.1 - - - -
325B ARG* 2.8 29.1 + - + +
326B LEU* 3.6 6.1 - - - +
328B TYR* 1.3 73.4 - - - +
330B ILE* 1.3 58.4 + - - +
333B VAL* 3.1 18.4 + - + -
334B LEU* 2.8 31.6 + - + +
376B ALA* 4.0 19.7 - - + +
379B LEU* 3.7 34.5 - - + -
380B LEU* 3.8 40.2 - - + +
383B LYS* 4.4 11.7 - - - -
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Residues in contact with ILE 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 LEU* 3.1 16.0 + - + +
327B GLN* 4.0 3.8 - - - +
328B TYR 3.3 0.2 - - - -
329B ILE* 1.3 75.4 - - - +
331B THR* 1.3 64.0 + - - +
334B LEU* 3.6 7.4 - - - +
335B LYS 3.3 5.2 + - - -
336B ALA* 2.9 46.7 + - + +
338B THR* 4.3 20.0 - - + +
343B VAL* 3.6 31.4 - - + -
355B LEU* 6.3 0.2 - - + -
357B TRP* 3.9 20.2 - - + -
372B LEU* 4.3 13.5 - - + +
373B SER* 5.7 1.3 - - - -
376B ALA* 3.7 26.0 - - + -
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Residues in contact with THR 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 18.4 + - - +
330B ILE* 1.3 79.3 - - - +
332B ASN* 1.3 76.7 + - - +
335B LYS* 3.2 20.6 - - - +
336B ALA 4.4 8.9 + - - +
338B THR* 5.8 2.9 - - - +
341B LYS* 4.8 9.9 + - - -
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Residues in contact with ASN 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B TYR* 2.7 64.8 + - + +
331B THR* 1.3 92.1 - - - +
333B VAL* 1.3 64.3 + - - +
334B LEU 3.5 0.2 - - - -
335B LYS* 3.7 18.2 - - - +
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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