Contacts of the helix formed by residues 318 - 336 (chain A) in PDB entry 2DFS
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 SER 318 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A GLY 3.1 10.1 + - - -
317A ILE* 1.4 70.4 - - - +
319A ASP* 1.3 56.9 + - - +
320A SER* 2.8 23.0 + - - -
321A TYR* 2.7 43.1 + - - +
322A GLN 2.9 9.9 + - - -
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Residues in contact with ASP 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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309A ARG* 5.7 3.5 + - - -
313A THR* 4.3 13.2 + - - +
317A ILE 3.5 0.9 + - - +
318A SER* 1.3 73.5 - - - +
320A SER* 1.3 60.0 + - - +
322A GLN* 3.4 29.9 + - - +
323A MET* 3.2 30.0 + - - +
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Residues in contact with SER 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A SER* 2.8 27.0 + - - -
319A ASP* 1.3 78.9 - - - +
321A TYR* 1.3 61.0 + - - -
323A MET* 3.9 5.8 + - - +
324A GLY* 3.4 14.4 + - - -
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Residues in contact with TYR 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ILE* 3.8 18.4 - - + -
318A SER* 2.7 30.8 + - - +
320A SER* 1.3 77.4 + - - +
322A GLN* 1.4 62.8 + - - +
324A GLY* 3.0 12.0 + - - +
325A ILE* 3.1 17.2 + - - +
414A TRP* 3.3 34.8 - + + -
418A HIS* 5.6 5.6 - + - -
587A LYS* 2.7 30.9 + - + +
588A LEU* 4.0 26.2 - - + +
591A GLU* 2.6 26.1 + - - -
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Residues in contact with GLN 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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309A ARG* 3.5 31.1 + - - +
312A CYS* 3.5 26.4 - - + +
313A THR* 3.1 26.7 + - - +
317A ILE* 3.4 24.4 + - + +
318A SER 2.9 8.8 + - - +
319A ASP* 3.4 30.8 + - - +
321A TYR* 1.4 74.1 - - - +
323A MET* 1.4 62.8 + - + +
325A ILE* 3.1 22.4 + - - +
326A PHE* 3.1 31.8 + - + -
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Residues in contact with MET 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLU* 3.5 40.8 - - + +
274A PHE* 4.3 19.3 - - + -
276A THR* 5.5 2.0 - - - +
277A LEU* 4.5 16.9 - - + +
309A ARG* 5.4 4.5 - - - -
319A ASP 3.2 15.5 + - - +
320A SER* 4.0 7.0 - - - +
321A TYR 3.4 0.2 - - - -
322A GLN* 1.4 76.9 - - + +
324A GLY* 1.4 56.2 + - - +
326A PHE* 4.1 7.7 - - + +
327A ARG* 3.0 34.1 + - - +
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Residues in contact with GLY 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A SER 3.4 8.9 + - - -
321A TYR* 3.0 11.7 + - - -
323A MET* 1.4 77.6 - - - +
325A ILE* 1.3 60.3 + - - +
327A ARG* 4.5 0.4 - - - -
328A ILE* 3.2 27.5 + - - +
586A PHE* 3.6 20.0 - - - -
588A LEU* 3.7 13.5 - - - -
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Residues in contact with ILE 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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206A ILE* 6.0 0.7 - - + -
261A ILE* 6.1 0.4 - - + -
312A CYS* 5.2 8.3 - - - -
317A ILE* 4.3 21.1 - - + -
321A TYR 3.1 13.9 + - - +
322A GLN* 3.1 9.4 + - - +
324A GLY* 1.3 74.0 - - - +
326A PHE* 1.3 73.4 + - + +
328A ILE* 3.2 5.4 + - - +
329A LEU* 3.1 34.4 + - + +
411A LEU* 3.9 16.3 - - + +
414A TRP* 4.2 21.5 - - + -
415A ILE* 4.0 37.7 - - + -
588A LEU* 4.3 7.4 - - + -
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Residues in contact with PHE 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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261A ILE* 4.4 12.6 - - + -
265A LEU* 3.9 6.3 - - + +
274A PHE* 3.6 26.9 - + + -
277A LEU* 3.5 19.2 - - + +
305A MET* 3.6 20.9 - - + -
308A THR* 5.4 3.4 - - + -
309A ARG* 3.8 33.9 - - + -
312A CYS* 5.4 6.5 - - - -
322A GLN* 3.1 42.3 + - + +
323A MET* 4.1 11.0 - - - +
325A ILE* 1.3 87.1 - - + +
327A ARG* 1.3 56.3 + - - +
329A LEU* 3.4 16.5 + - + +
330A ALA* 2.9 29.6 + - - +
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Residues in contact with ARG 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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276A THR* 2.9 39.2 + - - +
277A LEU* 4.3 13.3 - - + +
278A ARG* 4.5 3.6 - - - +
323A MET 3.0 20.7 + - - +
324A GLY* 3.7 4.9 - - - +
326A PHE* 1.3 74.1 - - - +
328A ILE* 1.4 63.3 + - - +
330A ALA* 3.5 6.3 + - - +
331A GLY* 3.1 17.7 + - - -
362A ASP* 3.9 6.9 + - - -
363A LEU* 3.0 59.9 + - - +
364A MET* 5.0 1.2 - - - +
585A LYS* 6.0 3.8 - - - +
586A PHE* 3.7 23.6 - - + -
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Residues in contact with ILE 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 GLY 3.2 3.3 + - - +
325A ILE 3.2 8.5 + - - +
327A ARG* 1.4 72.9 - - - +
329A LEU* 1.4 58.1 + - - +
331A GLY* 3.1 3.8 + - - -
332A ILE* 3.0 27.4 + - + +
364A MET* 4.5 13.4 - - + +
407A ILE* 3.5 31.0 - - + -
411A LEU* 3.9 17.3 - - + -
586A PHE* 3.3 25.8 - - + -
588A LEU* 3.9 28.9 - - + -
589A LEU* 4.2 13.5 - - + -
592A LEU* 3.8 23.1 - - + -
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Residues in contact with LEU 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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206A ILE* 5.7 3.4 - - + -
261A ILE* 3.6 35.0 - - + -
262A PHE* 3.8 16.2 - - + -
265A LEU* 4.2 12.6 - - + -
325A ILE* 3.1 31.3 + - + +
326A PHE* 3.7 12.8 - - + +
328A ILE* 1.4 74.0 - - - +
330A ALA* 1.4 56.0 + - - +
332A ILE* 3.3 10.2 + - + +
333A LEU* 3.0 32.0 + - - +
408A TYR* 3.8 32.5 - - + -
411A LEU* 4.0 16.6 - - + -
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Residues in contact with ALA 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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265A LEU* 4.0 8.6 - - + +
277A LEU* 3.8 31.4 - - + +
279A LEU* 4.6 4.3 - - + -
326A PHE 2.9 17.8 + - - +
327A ARG 3.6 2.5 - - - +
329A LEU* 1.4 73.5 - - - +
331A GLY* 1.3 57.7 + - - +
333A LEU* 3.3 8.2 + - - +
334A HIS* 2.9 34.0 + - - -
363A LEU* 3.6 18.6 - - + -
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Residues in contact with GLY 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 ARG 3.1 9.7 + - - -
328A ILE 3.1 8.2 + - - -
330A ALA* 1.3 74.0 - - - +
332A ILE* 1.3 57.7 + - - +
334A HIS* 4.4 2.2 - - - -
335A LEU* 2.8 27.2 + - - +
360A PHE* 3.2 30.4 - - - -
363A LEU* 3.6 14.5 - - - +
364A MET* 5.1 4.0 - - - -
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Residues in contact with ILE 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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249A VAL* 4.6 10.3 - - + -
262A PHE* 4.6 8.7 - - + -
287A TYR* 3.2 41.4 - - + -
328A ILE* 3.0 18.2 + - + +
329A LEU* 3.3 17.7 + - + +
331A GLY* 1.3 73.3 - - - +
333A LEU* 1.3 62.2 + - - +
335A LEU* 3.5 7.7 + - - +
336A GLY 3.2 6.6 + - - -
364A MET* 6.0 0.7 - - + -
404A ALA* 4.0 17.9 - - + +
407A ILE* 3.9 36.8 - - + -
408A TYR* 4.1 30.1 - - + +
411A LEU* 5.1 1.1 - - + -
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Residues in contact with LEU 333 (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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262A PHE* 3.6 33.9 - - + +
265A LEU* 4.3 10.8 - - + -
266A CYS* 4.4 15.5 - - - -
279A LEU* 3.7 25.1 - - + -
285A PHE* 3.4 39.2 - - + +
286A HIS 5.4 0.2 + - - -
287A TYR* 4.5 13.0 - - + -
288A THR* 3.8 22.2 - - + -
329A LEU 3.0 16.9 + - - +
330A ALA* 3.5 8.1 - - - +
332A ILE* 1.3 75.9 - - - +
334A HIS* 1.3 60.6 + - + +
336A GLY* 3.4 12.8 + - - -
337A ASN* 3.9 2.6 + - - +
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Residues in contact with HIS 334 (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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277A LEU 3.6 13.0 + - - -
278A ARG 3.4 21.6 + - - -
279A LEU* 5.0 0.9 - - + -
284A TYR* 4.9 8.5 - + - -
285A PHE* 3.5 29.4 - + - -
330A ALA* 2.9 31.2 + - - +
331A GLY* 4.0 3.6 - - - +
333A LEU* 1.3 70.7 - - + +
335A LEU* 1.4 64.8 + - - +
337A ASN* 3.1 12.3 + - - +
338A VAL* 3.7 2.3 + - - +
356A PRO* 3.6 39.2 + - - +
359A ILE* 3.5 45.0 - - + +
360A PHE* 4.3 9.9 - - + +
363A LEU* 4.8 0.7 - - + -
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Residues in contact with LEU 335 (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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287A TYR* 4.6 0.7 - - - +
331A GLY 2.8 21.7 + - - +
332A ILE* 3.5 8.5 - - - +
333A LEU 3.4 0.2 - - - -
334A HIS* 1.4 69.7 - - - +
336A GLY* 1.3 62.8 + - - +
338A VAL* 3.2 32.0 + - + +
360A PHE* 3.8 42.5 - - + -
375A LEU* 4.8 17.3 - - + -
400A ARG* 3.6 34.5 - - + +
403A LEU* 4.2 19.5 - - + -
404A ALA* 4.3 17.5 - - + +
407A ILE* 4.7 5.2 - - + -
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Residues in contact with GLY 336 (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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286A HIS* 3.1 27.4 - - - +
287A TYR* 3.3 35.4 - - - -
332A ILE 3.2 7.7 + - - -
333A LEU 3.4 5.1 + - - -
334A HIS 3.2 1.8 - - - -
335A LEU* 1.3 76.7 - - - +
337A ASN* 1.3 60.6 + - - +
338A VAL 3.4 0.4 - - - -
400A ARG* 3.2 10.5 + - - -
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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
------------------------------------------------------------
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