Contacts of the helix formed by residues 304 - 323 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B ALA* 3.5 8.9 - - - +
303B THR* 1.3 84.8 - - - +
305B GLU* 1.3 79.9 + - - +
306B GLU* 3.0 28.6 - - - +
307B GLU* 3.3 11.1 + - - +
308B ALA* 3.3 17.5 + - - +
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B THR 4.9 0.2 - - - +
304B SER* 1.3 84.7 - - - +
306B GLU* 1.3 58.4 + - - +
308B ALA* 3.3 8.6 + - - +
309B LYS* 3.0 35.6 + - - +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B SER* 3.0 24.4 - - - +
305B GLU* 1.3 78.1 + - - +
307B GLU* 1.3 83.3 + - - +
309B LYS* 3.1 7.9 + - - +
310B THR* 2.7 47.6 + - - +
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B PRO* 3.6 35.6 - - + +
262B ALA* 4.9 0.2 - - - -
301B LEU 5.2 0.2 - - - +
302B ALA* 3.9 7.8 - - + -
303B THR* 2.8 41.5 + - - -
304B SER* 3.3 20.0 + - - +
306B GLU* 1.3 97.6 + - - +
308B ALA* 1.3 64.5 + - - +
310B THR* 3.2 6.0 + - - -
311B THR* 3.1 26.7 + - - -
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA* 5.8 0.7 - - - +
262B ALA* 4.2 7.5 - - - +
297B VAL* 5.7 0.9 - - - +
299B PRO* 4.1 22.0 - - + +
302B ALA* 3.5 20.5 - - + +
304B SER 3.3 6.6 + - - +
305B GLU* 3.4 11.7 - - - +
306B GLU 3.2 0.2 - - - -
307B GLU* 1.3 81.3 - - - +
309B LYS* 1.3 62.6 + - - +
311B THR* 3.3 3.3 + - - -
312B ALA* 3.1 22.4 + - - +
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Residues in contact with LYS 309 (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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52B ALA* 6.1 2.0 - - + -
305B GLU* 3.0 19.4 + - - +
306B GLU* 3.6 10.3 - - - +
308B ALA* 1.3 73.5 - - - +
310B THR* 1.3 66.6 + - - +
312B ALA* 3.4 6.0 + - + +
313B ASN* 2.9 45.9 + - - +
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Residues in contact with THR 310 (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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258B THR 5.1 2.9 - - - +
259B LEU* 3.6 22.9 - - + +
261B PRO* 4.9 4.9 - - + -
306B GLU* 2.7 35.9 + - - +
307B GLU* 3.2 10.1 + - - -
309B LYS* 1.3 74.6 - - - +
311B THR* 1.3 57.3 + - - +
313B ASN* 3.3 8.8 + - - +
314B LEU* 2.9 27.8 + - + +
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Residues in contact with THR 311 (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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252B ILE* 3.9 24.8 - - + +
259B LEU 4.4 3.6 - - - -
260B ALA* 4.0 10.3 - - + -
261B PRO* 3.3 7.3 - - - +
262B ALA* 3.1 50.2 + - + +
297B VAL* 4.2 10.8 - - + -
307B GLU 3.1 9.8 + - - -
308B ALA 3.7 2.7 - - - -
310B THR* 1.3 75.4 - - - +
312B ALA* 1.3 66.3 + - - +
314B LEU* 3.0 8.7 + - - +
315B ALA* 2.9 22.1 + - - +
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Residues in contact with ALA 312 (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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48B ALA* 3.8 36.3 - - + +
49B ILE* 4.7 1.9 - - - +
52B ALA* 3.8 9.1 - - + +
297B VAL* 4.8 7.3 - - + +
308B ALA 3.1 14.2 + - - +
309B LYS* 3.7 9.0 - - + +
311B THR* 1.3 77.7 - - - +
313B ASN* 1.3 62.8 + - - +
315B ALA* 3.2 10.1 + - - +
316B VAL* 3.0 25.1 + - - +
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Residues in contact with ASN 313 (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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52B ALA* 3.6 23.0 - - - +
309B LYS* 2.9 41.3 + - - +
310B THR* 3.6 7.3 - - - +
312B ALA* 1.3 75.7 - - - +
314B LEU* 1.3 63.4 + - - +
316B VAL* 3.2 8.1 + - - +
317B ASP* 2.9 33.2 + - - +
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Residues in contact with LEU 314 (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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252B ILE* 4.4 2.2 - - + -
255B PHE* 3.5 49.8 - - + -
259B LEU* 3.4 34.3 - - + +
260B ALA* 3.9 7.6 - - + -
273B TYR* 3.5 36.1 - - + -
277B MET* 5.4 0.2 - - + -
310B THR* 2.9 13.9 + - + +
311B THR* 3.0 10.3 + - - +
313B ASN* 1.3 76.8 - - - +
315B ALA* 1.3 63.5 + - - +
317B ASP* 3.3 5.9 + - + +
318B VAL* 3.2 22.4 + - + +
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Residues in contact with ALA 315 (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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49B ILE* 3.9 21.3 - - + -
252B ILE* 3.9 13.0 - - + +
294B LEU* 3.7 26.5 - - + +
297B VAL* 4.3 3.4 - - + -
311B THR 2.9 13.1 + - - +
312B ALA 3.2 10.3 + - - +
314B LEU* 1.3 77.6 - - - +
316B VAL* 1.3 63.3 + - - +
318B VAL* 3.2 6.7 + - - +
319B ILE* 3.1 27.3 + - - +
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 3.6 31.4 - - + +
52B ALA* 3.6 15.0 - - + +
54B LEU* 4.0 21.5 - - + +
57B ARG* 3.3 41.5 - - + +
312B ALA 3.0 14.2 + - - +
313B ASN* 3.2 8.5 + - - +
315B ALA* 1.3 76.8 - - - +
317B ASP* 1.3 51.8 + - - +
319B ILE* 3.3 9.1 + - - +
320B ALA* 2.8 32.7 + - - +
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Residues in contact with ASP 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 2.5 38.0 + - - +
273B TYR* 2.6 30.5 + - + +
277B MET* 3.5 18.8 - - - -
313B ASN* 2.9 23.6 + - - +
314B LEU* 3.6 9.5 - - - +
315B ALA 3.2 0.2 - - - -
316B VAL* 1.3 76.0 - - - +
318B VAL* 1.3 54.2 + - - +
320B ALA* 3.8 0.3 - - - +
321B SER* 2.7 39.2 + - - -
325B GLN* 4.2 3.9 - - - +
268C VAL* 5.1 2.3 - - - +
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B PHE* 3.7 33.0 - - + -
252B ILE* 5.3 0.7 - - + -
255B PHE* 3.3 41.3 - - + -
276B GLY 5.1 0.7 - - - +
277B MET* 3.4 13.9 - - + -
280B ALA* 3.7 6.2 - - + +
292B LEU* 5.3 3.1 - - + -
294B LEU* 3.9 16.4 - - + -
314B LEU 3.2 10.4 + - - +
315B ALA* 3.4 8.5 - - - +
317B ASP* 1.3 79.5 - - - +
319B ILE* 1.3 58.5 + - + +
322B SER* 2.8 39.5 + - - +
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Residues in contact with ILE 319 (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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49B ILE* 4.3 8.3 - - + -
54B LEU* 3.8 29.6 - - + -
58B LEU* 4.5 4.9 - - + -
114B VAL* 4.1 18.2 - - + -
116B LEU* 3.8 28.7 - - + -
292B LEU* 4.2 11.2 - - + -
294B LEU* 4.1 22.2 - - + -
315B ALA 3.1 14.9 + - - +
316B VAL 3.7 4.3 - - - +
318B VAL* 1.3 73.1 - - - +
320B ALA* 1.3 64.9 + - - +
322B SER* 3.0 14.5 + - - -
323B PHE* 3.2 36.2 - - + -
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Residues in contact with ALA 320 (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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54B LEU* 5.3 0.8 - - + +
57B ARG* 4.0 21.5 - - + +
58B LEU* 4.4 8.5 - - + -
61B LEU* 3.4 15.6 - - + +
316B VAL* 2.8 21.3 + - + +
317B ASP 3.8 0.4 - - - +
319B ILE* 1.3 71.7 - - - +
321B SER* 1.3 57.9 + - - +
323B PHE 3.0 15.6 + - - -
324B GLY 3.3 1.4 + - - -
325B GLN* 3.0 44.2 + - + +
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Residues in contact with SER 321 (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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277B MET* 3.6 27.7 + - - +
280B ALA* 3.6 13.8 - - - +
281B GLU* 3.3 30.0 + - - +
284B HIS* 3.9 2.6 - - - +
317B ASP 2.7 23.2 + - - -
318B VAL 3.8 3.8 - - - -
320B ALA* 1.3 74.3 - - - +
322B SER* 1.3 59.6 + - - +
323B PHE 3.4 0.3 + - - -
324B GLY* 3.6 6.9 + - - -
325B GLN* 3.7 22.5 + - - +
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Residues in contact with SER 322 (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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248B LEU* 3.8 11.2 - - - +
280B ALA* 3.4 21.7 - - - +
283B ILE* 5.4 0.9 - - - -
284B HIS* 3.2 19.8 + - - +
289B LEU* 3.6 22.2 - - - +
292B LEU* 3.5 28.1 - - - +
318B VAL* 2.8 24.3 + - - +
319B ILE 3.0 6.9 + - - -
321B SER* 1.3 76.7 - - - +
323B PHE* 1.3 60.2 + - - +
324B GLY 3.5 0.4 - - - -
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Residues in contact with PHE 323 (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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24B HIS* 6.2 3.4 - - + -
26B VAL* 3.6 26.5 - - + -
58B LEU* 4.3 8.5 - - + -
61B LEU* 3.9 16.5 - - + +
63B CYS* 4.3 15.9 - - - -
112B SER* 3.8 24.5 - - - -
113B CYS 5.6 0.4 - - - -
114B VAL* 3.5 33.4 - - + -
284B HIS* 3.2 15.1 - + - -
289B LEU* 3.9 20.6 - - + -
291B ALA 6.1 0.2 - - - -
292B LEU* 4.3 15.0 - - + -
319B ILE* 3.2 30.9 + - + +
320B ALA 3.0 10.8 + - - +
322B SER* 1.3 81.6 - - - +
324B GLY* 1.3 55.8 + - - +
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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
------------------------------------------------------------
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