Contacts of the helix formed by residues 304 - 323 (chain E) in PDB entry 1PQ3
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 304 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302E ALA* 3.5 8.7 - - - +
303E THR* 1.3 85.3 - - - +
305E GLU* 1.3 78.2 + - - +
306E GLU* 3.0 28.0 - - - +
307E GLU* 3.3 10.9 + - - +
308E ALA* 3.3 18.0 + - - +
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Residues in contact with GLU 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E THR 4.9 0.3 - - - +
304E SER* 1.3 85.9 - - - +
306E GLU* 1.3 57.8 + - - +
308E ALA* 3.3 8.6 + - - +
309E LYS* 3.0 34.4 + - - +
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Residues in contact with GLU 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304E SER* 3.0 22.9 - - - +
305E GLU* 1.3 77.8 + - - +
307E GLU* 1.3 83.6 + - - +
309E LYS* 3.1 7.7 + - - +
310E THR* 2.7 48.2 + - - +
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Residues in contact with GLU 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E PRO* 3.6 33.5 - - + +
262E ALA* 4.9 0.2 - - - -
301E LEU 5.2 0.2 - - - +
302E ALA* 3.9 8.9 - - + -
303E THR* 2.8 40.6 + - - -
304E SER* 3.3 20.3 + - - +
306E GLU* 1.3 95.5 + - - +
308E ALA* 1.3 63.2 + - - +
310E THR* 3.2 6.2 + - - -
311E THR* 3.1 27.1 + - - -
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Residues in contact with ALA 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ALA* 5.8 0.7 - - - +
262E ALA* 4.2 7.3 - - - +
297E VAL* 5.7 1.2 - - - +
299E PRO* 4.1 22.3 - - + +
302E ALA* 3.5 19.7 - - + +
304E SER 3.3 5.3 + - - +
305E GLU* 3.4 11.9 - - - +
306E GLU 3.2 0.4 - - - -
307E GLU* 1.3 81.2 - - - +
309E LYS* 1.3 61.7 + - - +
311E THR* 3.3 3.5 + - - -
312E ALA* 3.1 23.0 + - - +
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Residues in contact with LYS 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ALA* 6.1 2.5 - - + -
305E GLU* 3.0 18.8 + - - +
306E GLU* 3.6 10.1 - - - +
308E ALA* 1.3 73.2 - - - +
310E THR* 1.3 65.5 + - - +
312E ALA* 3.4 7.6 + - + +
313E ASN* 2.9 47.9 + - - +
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Residues in contact with THR 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E THR 5.1 2.9 - - - +
259E LEU* 3.6 23.6 - - + +
261E PRO* 4.9 4.0 - - + -
306E GLU* 2.7 36.8 + - - +
307E GLU* 3.4 9.6 - - - -
309E LYS* 1.3 72.9 - - - +
311E THR* 1.3 56.6 + - - +
313E ASN* 3.3 8.1 + - - +
314E LEU* 2.9 27.6 + - + +
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Residues in contact with THR 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E ILE* 3.9 24.8 - - + +
259E LEU 4.4 3.6 - - - -
260E ALA* 4.0 10.5 - - + -
261E PRO* 3.3 7.6 - - - +
262E ALA* 3.0 49.3 + - + +
297E VAL* 4.2 11.0 - - + -
307E GLU 3.1 10.6 + - - -
308E ALA 3.7 2.9 - - - -
310E THR* 1.3 75.2 - - - +
312E ALA* 1.3 60.2 + - - +
314E LEU* 3.0 8.2 + - - +
315E ALA* 2.9 28.2 + - - +
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Residues in contact with ALA 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ALA* 3.8 35.9 - - + +
49E ILE* 4.4 2.8 - - - +
52E ALA* 3.8 10.3 - - + -
297E VAL* 4.9 7.3 - - + +
308E ALA 3.1 16.4 + - - +
309E LYS* 3.7 7.9 - - + +
310E THR 3.4 0.2 - - - -
311E THR* 1.3 76.2 - - - +
313E ASN* 1.3 62.2 + - - +
315E ALA* 3.1 9.6 + - - +
316E VAL* 3.1 25.3 + - - +
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Residues in contact with ASN 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ALA* 3.6 22.3 - - - +
309E LYS* 2.9 40.6 + - - +
310E THR* 3.6 7.1 - - - +
312E ALA* 1.3 76.5 - - - +
314E LEU* 1.3 63.7 + - - +
316E VAL* 3.2 7.7 + - - +
317E ASP* 2.9 33.2 + - - +
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Residues in contact with LEU 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E ILE* 4.4 2.2 - - + -
255E PHE* 3.5 48.0 - - + -
259E LEU* 3.4 34.1 - - + +
260E ALA* 3.9 7.4 - - + -
273E TYR* 3.5 36.1 - - + -
277E MET* 5.4 0.7 - - + -
310E THR* 2.9 14.5 + - + +
311E THR* 3.0 10.3 + - - +
313E ASN* 1.3 76.1 - - - +
315E ALA* 1.3 64.3 + - - +
317E ASP* 3.3 5.9 + - + +
318E VAL* 3.2 21.7 + - + +
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Residues in contact with ALA 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ILE* 3.9 20.9 - - + -
252E ILE* 3.9 12.1 - - + +
294E LEU* 3.7 26.9 - - + +
297E VAL* 4.3 4.5 - - + -
311E THR 2.9 11.4 + - - +
312E ALA 3.3 10.1 - - - +
314E LEU* 1.3 77.4 - - - +
316E VAL* 1.3 63.1 + - - +
318E VAL* 3.2 6.2 + - - +
319E ILE* 3.1 28.2 + - - +
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Residues in contact with VAL 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ILE* 3.6 31.2 - - + +
52E ALA* 3.6 13.9 - - + +
54E LEU* 4.0 22.2 - - + +
57E ARG* 3.3 40.6 - - + +
312E ALA 3.1 13.6 + - - +
313E ASN* 3.2 8.5 + - - +
315E ALA* 1.3 77.4 - - - +
317E ASP* 1.3 56.7 + - - +
319E ILE* 3.3 9.3 + - - +
320E ALA* 2.8 27.4 + - - +
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Residues in contact with ASP 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E ARG* 2.5 37.9 + - - +
273E TYR* 2.6 31.2 + - + -
277E MET* 3.5 18.6 - - - -
313E ASN* 2.9 22.4 + - - +
314E LEU* 3.6 9.4 - - - +
315E ALA 3.2 0.2 - - - -
316E VAL* 1.3 77.1 - - - +
318E VAL* 1.3 53.1 + - - +
320E ALA* 3.8 0.5 - - - +
321E SER* 2.7 39.0 + - - -
325E GLN* 4.2 3.8 - - - +
268F VAL* 5.1 2.3 - - - +
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Residues in contact with VAL 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E PHE* 3.7 33.9 - - + -
252E ILE* 5.3 0.2 - - + -
255E PHE* 3.3 40.8 - - + -
276E GLY 5.1 0.4 - - - +
277E MET* 3.4 14.3 - - + +
280E ALA* 3.7 6.2 - - + +
292E LEU* 5.3 2.9 - - + -
294E LEU* 3.9 16.4 - - + -
314E LEU 3.2 10.8 + - - +
315E ALA* 3.2 9.2 + - - +
317E ASP* 1.3 79.0 - - - +
319E ILE* 1.3 57.8 + - - +
322E SER* 2.8 38.7 + - - +
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Residues in contact with ILE 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ILE* 4.3 7.4 - - + -
54E LEU* 3.8 29.6 - - + -
58E LEU* 4.5 4.7 - - + -
114E VAL* 4.1 17.7 - - + -
116E LEU* 3.8 28.7 - - + -
292E LEU* 4.2 11.2 - - + -
294E LEU* 4.1 22.7 - - + -
315E ALA 3.1 15.8 + - - +
316E VAL 3.7 4.5 - - - +
318E VAL* 1.3 73.9 - - - +
320E ALA* 1.3 66.5 + - - +
322E SER* 3.0 14.6 + - - -
323E PHE* 3.2 36.3 - - + -
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Residues in contact with ALA 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E LEU* 5.3 0.6 - - + +
57E ARG* 4.0 21.5 - - + +
58E LEU* 4.4 8.5 - - + +
61E LEU* 3.4 15.4 - - + +
316E VAL* 2.8 22.0 + - + +
317E ASP 3.8 0.2 - - - +
319E ILE* 1.3 73.4 - - - +
321E SER* 1.3 57.5 + - - +
323E PHE 3.0 15.8 + - - -
324E GLY 3.3 1.2 + - - -
325E GLN* 3.0 44.1 + - + +
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Residues in contact with SER 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277E MET* 3.6 27.5 + - - +
280E ALA* 3.6 13.5 - - - +
281E GLU* 3.3 29.8 + - - +
284E HIS* 3.9 2.4 - - - +
317E ASP 2.7 22.9 + - - -
318E VAL 3.8 3.1 - - - -
320E ALA* 1.3 74.4 - - - +
322E SER* 1.3 60.1 + - - +
323E PHE 3.4 0.3 + - - -
324E GLY* 3.6 7.3 + - - -
325E GLN* 3.7 21.3 + - - +
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Residues in contact with SER 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E LEU* 3.8 11.6 - - - +
280E ALA* 3.4 22.6 - - - +
283E ILE* 5.4 0.7 - - - -
284E HIS* 3.2 19.3 + - - +
289E LEU* 3.6 22.1 - - - +
292E LEU* 3.5 28.4 - - - +
318E VAL* 2.8 23.0 + - - +
319E ILE 3.0 7.1 + - - -
321E SER* 1.3 76.3 - - - +
323E PHE* 1.3 59.3 + - - +
324E GLY 3.5 0.2 - - - -
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Residues in contact with PHE 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E HIS* 6.2 3.1 - - + -
26E VAL* 3.6 26.2 - - + -
58E LEU* 4.3 8.7 - - + -
61E LEU* 3.9 16.3 - - + +
63E CYS* 4.3 15.7 - - - -
112E SER* 3.8 24.7 - - - -
113E CYS 5.6 0.2 - - - -
114E VAL* 3.5 34.5 - - + -
284E HIS* 3.2 15.4 - - - -
289E LEU* 3.9 22.2 - - + -
291E ALA 6.1 0.2 - - - -
292E LEU* 4.3 15.3 - - + -
319E ILE* 3.2 29.3 + - + +
320E ALA 3.0 10.0 + - - +
322E SER* 1.3 81.5 - - - +
324E GLY* 1.3 54.4 + - - +
325E GLN 3.9 0.4 - - - -
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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