Contacts of the helix formed by residues 319 - 332 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A GLY* 1.3 74.8 - - - -
320A ASN* 1.3 57.9 + - - +
321A LEU 3.4 2.5 - - - +
322A ASP* 3.9 4.9 - - - +
323A SER* 2.9 30.5 + - - -
345A VAL* 3.2 41.3 - - + +
346A ILE 4.0 8.1 - - - -
347A GLY 4.0 10.5 - - - -
348A GLU 4.3 1.1 - - - -
349A GLN* 3.8 30.1 - - - +
410A SER* 3.5 3.8 - - - -
428A SER* 2.9 23.6 + - - +
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Residues in contact with ASN 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 ILE* 3.0 17.2 + - + +
318A GLY 3.4 0.2 - - - -
319A CYS* 1.3 73.4 - - - +
321A LEU* 1.3 64.0 + - - +
323A SER* 3.3 4.4 + - - -
324A GLN* 3.0 44.0 + - - +
393A SER* 3.6 35.5 + - - +
397A MET* 3.6 23.9 - - + +
409A HIS* 2.9 34.0 + - - +
410A SER 2.9 15.3 + - - +
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Residues in contact with LEU 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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317A ILE* 4.6 1.2 + - + -
318A GLY 5.3 0.8 + - - -
319A CYS 3.4 0.2 - - - -
320A ASN* 1.3 76.1 - - - +
322A ASP* 1.3 66.8 + - - +
324A GLN* 3.4 6.2 + - + +
325A ARG* 3.0 54.9 + - + +
385A GLN* 3.5 35.9 - - + +
389A SER* 4.0 38.6 - - - +
390A VAL* 4.1 12.6 - - + -
393A SER* 4.1 19.4 + - - +
225B ASP* 3.6 13.5 - - + +
228B ILE* 6.1 0.4 - - + -
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Residues in contact with ASP 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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319A CYS* 3.5 10.6 - - - +
320A ASN 3.4 0.2 - - - -
321A LEU* 1.3 76.6 - - - +
323A SER* 1.3 57.9 + - - +
325A ARG* 3.5 1.8 + - - +
326A LEU* 2.8 31.2 + - - +
345A VAL* 3.7 25.4 - - + +
349A GLN* 2.8 29.9 + - - +
353A LYS* 3.1 37.4 + - - +
380A LEU* 3.6 19.1 - - + +
385A GLN* 3.4 14.7 + - - +
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Residues in contact with SER 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 CYS 2.9 23.6 + - - -
320A ASN* 3.7 5.4 - - - -
321A LEU 3.2 0.4 - - - -
322A ASP* 1.3 71.9 - - - +
324A GLN* 1.3 62.2 + - - +
326A LEU* 3.3 3.1 + - - +
327A GLN* 3.0 37.1 + - - +
343A VAL 4.6 0.2 - - - +
344A TRP* 3.9 25.5 - - - +
345A VAL* 2.9 34.8 + - - +
410A SER* 3.4 9.6 - - - -
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Residues in contact with GLN 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 ASN* 3.0 30.3 + - - +
321A LEU* 4.0 6.5 - - + +
323A SER* 1.3 75.7 - - - +
325A ARG* 1.3 63.2 + - + +
327A GLN* 3.6 11.2 + - - +
328A TYR* 3.1 22.7 + - - +
344A TRP* 6.3 1.8 - - + -
393A SER* 4.6 9.2 - - - -
396A ASP* 2.8 33.7 + - - +
407A LYS* 3.6 13.9 - - - +
409A HIS* 3.8 15.6 + - - -
228B ILE* 3.7 31.9 - - + +
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Residues in contact with ARG 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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321A LEU* 3.0 36.7 + - + +
322A ASP* 4.8 1.7 + - - +
324A GLN* 1.3 73.5 - - - +
326A LEU* 1.3 54.6 + - - +
328A TYR* 3.1 3.3 + - - +
329A ILE* 2.8 41.0 + - + +
380A LEU* 3.5 23.0 + - + +
383A LYS* 3.8 25.0 + - - +
384A GLY 2.8 30.3 + - - -
385A GLN* 3.6 14.3 - - - +
386A ARG 5.0 0.2 - - - +
389A SER* 3.4 15.4 + - - -
224B MET* 4.2 15.3 - - - +
225B ASP* 2.7 43.2 + - - +
228B ILE* 3.9 9.4 - - + -
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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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322A ASP 2.8 22.1 + - - +
323A SER* 3.3 4.5 + - - +
325A ARG* 1.3 71.5 - - - +
327A GLN* 1.3 61.3 + - - +
329A ILE* 3.4 8.0 + - + +
330A ILE* 3.1 27.1 + - + +
343A VAL* 3.7 28.0 - - + +
344A TRP 4.7 2.5 - - - -
345A VAL* 3.7 20.9 - - + -
355A LEU* 3.8 24.7 - - + -
376A ALA* 3.6 45.5 - - + +
377A MET* 3.8 8.1 - - + +
380A LEU* 4.2 11.1 - - + +
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Residues in contact with GLN 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 SER 3.0 21.3 + - - +
324A GLN* 3.8 11.5 - - - +
326A LEU* 1.3 75.8 - - - +
328A TYR* 1.3 56.3 + - - +
330A ILE* 3.6 3.8 + - - +
331A THR* 3.1 34.8 + - - +
342A GLU* 4.0 14.8 + - + +
343A VAL* 2.7 42.2 + - + +
344A TRP* 3.3 37.4 - - - -
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Residues in contact with TYR 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 GLN 3.1 14.4 + - - +
325A ARG 3.1 7.9 + - - +
327A GLN* 1.3 73.4 - - - +
329A ILE* 1.3 58.5 + - - +
331A THR* 4.8 0.2 - - - -
332A ASN* 2.7 70.2 + - + +
333A VAL* 4.0 8.7 - - + -
224B MET* 3.6 42.7 - - + -
227B GLU* 4.2 34.9 + - + +
228B ILE* 3.7 25.1 - - + -
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Residues in contact with ILE 329 (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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325A ARG 2.8 27.3 + - - +
326A LEU* 3.5 7.0 - - - +
327A GLN 3.4 0.2 - - - -
328A TYR* 1.3 72.8 - - - +
330A ILE* 1.3 58.9 + - - +
333A VAL* 3.1 14.1 + - + +
334A LEU* 2.8 30.7 + - + +
376A ALA* 3.9 20.9 - - + +
379A LEU* 3.7 33.4 - - + -
380A LEU* 3.8 41.7 - - + +
383A LYS* 4.3 11.2 - - - -
224B MET* 4.0 18.6 - - + -
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Residues in contact with ILE 330 (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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326A LEU* 3.1 15.3 + - + +
327A GLN* 4.0 3.8 - - - +
329A ILE* 1.3 75.4 - - - +
331A THR* 1.3 62.5 + - - +
334A LEU* 3.7 5.9 - - - +
335A LYS 3.3 5.0 + - - -
336A ALA* 2.9 40.8 + - + +
338A THR* 3.4 26.9 - - + +
343A VAL* 3.6 31.2 - - + -
355A LEU* 6.4 0.7 - - + -
357A TRP* 3.8 21.3 - - + -
372A LEU* 4.4 14.1 - - + +
373A SER* 5.6 1.6 - - - -
376A ALA* 3.7 24.2 - - + -
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Residues in contact with THR 331 (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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327A GLN* 3.1 18.4 + - - +
328A TYR* 4.8 0.2 - - - -
330A ILE* 1.3 81.3 - - - +
332A ASN* 1.3 75.5 + - - +
335A LYS* 3.3 20.1 - - - +
336A ALA 4.6 7.0 + - - +
338A THR* 5.5 2.8 + - - -
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Residues in contact with ASN 332 (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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328A TYR* 2.7 63.1 + - + +
331A THR* 1.3 94.5 - - - +
333A VAL* 1.3 64.5 + - - +
334A LEU 3.5 0.2 - - - -
335A LYS* 3.6 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