Contacts of the helix formed by residues 306 - 326 (chain X) in PDB entry 3FEW
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 VAL 306 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231X TYR* 3.9 17.7 - - + -
302X ILE* 3.0 21.2 + - + +
304X SER 3.5 0.2 - - - -
305X ASP* 1.3 86.0 - - - +
307X LEU* 1.3 62.3 + - + +
308X ASN 3.4 1.3 - - - -
309X LYS* 3.4 3.0 + - - +
310X ALA* 3.0 29.1 + - - +
399X ALA* 3.7 21.1 - - + -
400X PHE* 4.6 9.0 - - + -
443X ALA* 3.4 34.8 - - + +
444X VAL* 3.9 15.0 - - + -
447X GLY* 4.4 8.7 - - - -
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Residues in contact with LEU 307 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293X TYR* 6.0 0.2 - - - +
302X ILE* 3.2 18.2 + - + +
303X GLN* 3.7 35.0 - - - +
306X VAL* 1.3 75.5 - - - +
308X ASN* 1.3 61.0 + - - +
310X ALA* 3.5 3.3 + - + -
311X ALA* 3.0 29.2 + - - +
340X VAL* 3.4 33.9 - - + +
341X LYS* 4.2 4.1 - - - +
343X PHE* 3.8 11.4 - - + -
344X GLN* 3.9 26.9 - - - +
443X ALA* 3.8 34.5 - - + +
446X LEU* 5.1 2.5 - - + -
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Residues in contact with ASN 308 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303X GLN* 2.9 45.7 + - - +
304X SER* 3.7 21.0 + - - +
307X LEU* 1.3 74.6 - - - +
309X LYS* 1.3 59.6 + - + +
311X ALA* 3.4 7.6 + - - +
312X GLU* 3.0 40.9 + - + +
341X LYS* 3.6 17.8 - - - +
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Residues in contact with LYS 309 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304X SER 3.6 18.4 - - - +
305X ASP* 3.4 22.0 - - - +
306X VAL 3.4 6.7 + - - +
307X LEU 3.2 0.4 - - - -
308X ASN* 1.3 75.6 - - + +
310X ALA* 1.3 66.4 + - - +
312X GLU* 3.1 28.6 + - - +
313X VAL* 3.0 27.0 + - - +
396X ILE* 3.4 47.0 + - + -
397X SER* 4.7 4.3 - - - -
400X PHE* 4.6 3.8 - - + -
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Residues in contact with ALA 310 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306X VAL* 3.0 18.9 + - + +
307X LEU* 4.5 1.3 - - + -
309X LYS* 1.3 74.6 - - - +
311X ALA* 1.3 57.8 + - - +
313X VAL* 3.2 9.3 + - - +
314X ILE* 3.0 34.9 + - - +
340X VAL* 3.7 19.3 - - + -
400X PHE* 5.3 2.1 - - + -
446X LEU 4.8 0.4 - - - +
447X GLY* 4.0 26.5 - - - +
450X SER* 4.4 12.3 - - - +
451X ALA* 5.7 1.1 - - - -
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Residues in contact with ALA 311 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307X LEU 3.0 19.2 + - - +
308X ASN* 3.5 7.0 - - - +
310X ALA* 1.3 73.8 - - - +
312X GLU* 1.3 64.4 + - + +
314X ILE 3.3 1.3 + - - +
315X SER* 2.9 23.0 + - - -
337X ALA* 3.4 39.2 - - + +
340X VAL* 3.9 3.5 - - - +
341X LYS* 3.9 20.0 - - + +
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Residues in contact with GLU 312 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308X ASN* 3.0 28.0 + - - +
309X LYS* 3.1 33.7 + - - +
311X ALA* 1.3 75.4 - - + +
313X VAL* 1.3 59.0 + - + +
315X SER* 3.2 9.3 + - - -
316X ASP* 3.1 34.6 + - - +
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Residues in contact with VAL 313 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309X LYS* 3.0 20.4 + - + +
310X ALA* 3.6 8.5 - - - +
311X ALA 3.2 0.2 - - - -
312X GLU* 1.3 75.9 - - + +
314X ILE* 1.3 64.7 + - + +
315X SER 3.2 0.9 + - - -
316X ASP* 3.4 10.9 + - - +
317X ILE* 3.2 27.6 + - + +
396X ILE* 4.8 12.8 - - + -
450X SER 4.2 3.4 - - - +
451X ALA* 4.1 26.9 - - + +
454X GLY* 3.9 28.9 - - - -
458X LEU* 5.3 5.8 - - + -
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Residues in contact with ILE 314 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310X ALA 3.0 16.9 + - - +
311X ALA* 3.7 6.1 - - - +
313X VAL* 1.3 75.4 - - + +
315X SER* 1.3 61.7 + - - +
317X ILE* 3.6 12.6 + - + +
318X GLY* 3.2 16.3 + - - -
333X ALA* 3.6 27.4 - - + +
336X ILE* 4.1 13.5 - - + -
337X ALA* 3.9 13.2 - - + +
340X VAL* 4.8 11.9 - - + -
450X SER* 3.4 34.8 - - - +
474X LEU* 4.4 24.5 - - + -
478X VAL* 4.4 8.3 - - + -
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Residues in contact with SER 315 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311X ALA 2.9 14.2 + - - -
312X GLU* 3.4 13.2 - - - -
313X VAL 3.1 0.2 - - - -
314X ILE* 1.3 74.5 - - - +
316X ASP* 1.3 59.3 + - - +
318X GLY* 2.8 22.7 + - - -
319X ASN* 3.2 17.1 + - - +
333X ALA* 5.2 1.1 - - - -
334X ARG* 3.1 37.0 + - - +
337X ALA* 4.0 7.0 - - - +
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Residues in contact with ASP 316 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312X GLU* 3.1 21.7 + - - +
313X VAL* 3.4 12.0 + - - +
315X SER* 1.3 75.7 - - - +
317X ILE* 1.3 57.1 + - - +
319X ASN* 3.1 15.2 + - - +
320X LYS* 2.9 27.0 + - - +
458X LEU* 4.0 24.6 - - + +
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Residues in contact with ILE 317 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313X VAL* 3.2 25.2 + - + +
314X ILE* 3.7 15.0 - - + +
315X SER 3.2 0.4 - - - -
316X ASP* 1.3 75.8 - - - +
318X GLY* 1.3 57.7 + - - +
320X LYS* 4.2 5.8 - - - -
321X VAL* 2.8 42.8 + - + +
329X TYR* 3.7 21.8 - - + +
333X ALA* 6.0 0.7 - - + -
450X SER 4.9 0.2 - - - +
454X GLY* 3.5 32.3 - - - -
457X ALA* 4.4 8.1 - - + -
458X LEU* 4.2 14.4 - - + -
471X GLY* 5.3 1.6 - - - -
474X LEU* 3.7 29.8 - - + -
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Residues in contact with GLY 318 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314X ILE 3.2 4.6 + - - -
315X SER 2.8 11.8 + - - -
317X ILE* 1.3 79.1 - - - +
319X ASN* 1.3 57.8 + - - -
322X GLY* 3.1 17.0 + - - -
329X TYR* 4.1 6.1 - - - -
330X LYS* 3.2 21.6 - - - +
333X ALA* 3.5 27.8 - - - +
334X ARG* 6.0 1.8 - - - -
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Residues in contact with ASN 319 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315X SER* 3.2 9.3 + - - +
316X ASP* 3.1 15.5 + - - +
318X GLY* 1.3 80.0 - - - +
320X LYS* 1.3 67.6 + - - +
323X ASP* 3.2 29.3 + - - +
330X LYS* 4.7 15.8 - - - +
334X ARG* 3.3 26.7 + - - +
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Residues in contact with LYS 320 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316X ASP 2.9 13.2 + - - +
317X ILE* 3.6 7.2 - - - +
319X ASN* 1.3 79.2 - - - +
321X VAL* 1.3 69.9 + - + +
323X ASP* 3.6 8.6 + - - +
324X TYR* 3.5 30.5 + - + -
457X ALA* 3.6 16.6 - - + +
458X LEU* 3.8 35.1 + - + +
460X LEU 2.7 31.0 + - - -
467X VAL* 4.5 13.0 - - + -
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Residues in contact with VAL 321 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317X ILE* 2.8 30.9 + - + +
320X LYS* 1.3 77.0 - - + +
322X GLY* 1.3 59.5 + - - +
324X TYR* 3.0 19.0 + - - +
325X LEU* 3.0 38.2 + - + +
329X TYR* 3.5 15.7 - - + -
457X ALA* 5.5 2.9 - - + -
467X VAL* 4.0 27.6 - - + +
468X GLY* 4.3 4.0 - - - -
470X VAL* 5.2 3.6 - - + -
471X GLY* 3.8 26.0 - - - +
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Residues in contact with GLY 322 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318X GLY 3.1 23.5 + - - -
319X ASN 4.0 0.2 - - - -
320X LYS 3.4 0.4 - - - -
321X VAL* 1.3 77.3 - - - +
323X ASP* 1.3 59.3 + - - +
325X LEU 4.7 0.4 - - - -
326X GLY* 2.7 46.0 + - - +
329X TYR* 4.0 6.5 - - - -
330X LYS* 3.8 11.4 - - - -
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Residues in contact with ASP 323 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319X ASN* 3.2 16.4 + - - +
320X LYS* 3.7 10.1 - - - +
321X VAL 3.2 0.4 - - - -
322X GLY* 1.3 75.9 - - - +
324X TYR* 1.3 68.4 + - + +
325X LEU 3.7 0.2 + - - -
326X GLY 4.8 0.5 + - - -
330X LYS* 3.8 17.7 + - - +
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Residues in contact with TYR 324 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320X LYS* 3.5 34.2 + - + -
321X VAL* 3.0 7.7 + - - +
323X ASP* 1.3 83.2 - - + +
325X LEU* 1.3 65.5 + - + +
464X ALA* 3.8 35.6 - - + +
465X ILE* 5.9 1.6 - - - -
467X VAL* 4.0 29.2 - - + -
468X GLY* 5.3 6.8 - - - +
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Residues in contact with LEU 325 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321X VAL* 3.0 35.5 + - + +
323X ASP 3.3 0.4 - - - -
324X TYR* 1.3 84.1 - - + +
326X GLY* 1.3 64.4 + - - +
328X ALA* 5.0 2.8 + - - +
329X TYR* 3.7 23.4 + - + +
468X GLY* 4.2 16.4 - - - +
472X ILE* 3.5 32.5 - - + -
494X ILE* 5.0 12.7 - - + +
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Residues in contact with GLY 326 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322X GLY* 2.7 27.9 + - - +
323X ASP 4.7 1.0 + - - -
325X LEU* 1.3 76.2 - - - +
327X ASP* 1.3 57.8 + - - -
328X ALA* 3.2 9.4 + - - -
329X TYR* 3.5 8.3 + - - +
330X LYS* 3.5 7.7 + - - -
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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