Contacts of the helix formed by residues 278 - 293 (chain B) in PDB entry 1PG3
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 THR 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LEU* 4.1 24.5 - - + -
77B LEU* 4.5 24.0 - - + +
253B MET* 4.8 10.1 - - + +
254B ASN 4.0 9.4 + - - +
255B ALA 3.1 7.3 + - - -
257B ASP* 3.0 18.5 + - - +
258B PRO 4.5 0.7 + - - -
259B LEU* 4.0 20.5 + - + +
277B THR* 1.3 79.4 - - - +
279B GLY* 1.3 67.3 + - - +
280B GLY 3.7 0.7 - - - -
281B TYR* 3.5 2.0 + - - +
282B LEU* 2.9 29.3 + - + +
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Residues in contact with GLY 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 4.3 0.3 - - - +
48B TRP* 3.9 22.7 - - - -
70B TYR* 4.2 2.5 - - - -
75B LEU* 4.3 8.3 - - - -
255B ALA* 2.9 20.4 + - - +
278B THR* 1.3 78.5 - - - +
280B GLY* 1.3 62.9 + - - +
282B LEU* 3.9 1.4 - - - +
283B VAL* 3.0 30.7 + - - +
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Residues in contact with GLY 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TRP* 4.3 2.7 + - - -
70B TYR* 3.9 15.9 - - - -
255B ALA 4.8 0.4 + - - -
277B THR* 5.1 0.2 + - - -
279B GLY* 1.3 73.2 - - - +
281B TYR* 1.3 62.3 + - - +
283B VAL* 3.8 0.2 - - - +
284B TYR* 3.0 24.1 + - - +
471B PRO* 3.1 36.2 - - - +
475B ARG* 4.0 15.1 - - - +
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Residues in contact with TYR 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 4.7 0.7 - - + -
259B LEU* 3.5 24.5 - - + -
260B PHE* 3.5 28.1 - + - -
276B HIS* 3.9 25.4 - + + +
277B THR* 3.3 22.5 + - - +
278B THR 3.5 0.8 + - - -
279B GLY 3.2 0.6 - - - -
280B GLY* 1.3 76.9 - - - +
282B LEU* 1.3 64.4 + - + +
284B TYR* 3.8 1.4 - - - +
285B ALA* 2.9 32.2 + - + +
313B HIS 3.5 5.2 - - - -
314B SER* 2.6 48.9 + - - -
318B TYR* 3.6 20.7 - + + -
419B GLY* 3.7 18.6 - - - -
471B PRO 3.5 2.8 + - - -
472B GLY* 3.9 9.2 - - - -
475B ARG* 4.9 2.4 - - - +
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Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.7 19.9 - - + +
75B LEU* 4.7 5.2 - - + -
77B LEU* 3.5 54.7 - - + +
80B ASN* 4.0 20.9 - - + +
81B CYS* 4.6 0.9 - - - -
278B THR* 2.9 21.7 + - + +
279B GLY* 4.0 0.4 - - - +
281B TYR* 1.3 73.5 - - + +
283B VAL* 1.3 66.6 + - - +
285B ALA* 4.5 3.4 - - + -
286B ALA* 3.1 23.9 + - - +
318B TYR* 4.1 29.4 - - + +
322B ALA* 4.1 7.6 - - + -
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TRP* 4.4 12.1 - - + -
42B GLN 4.1 3.6 - - - +
43B GLY* 3.9 16.8 - - - -
45B ILE* 4.4 2.1 - - + +
46B LEU* 3.3 26.4 - - + +
48B TRP* 4.0 11.7 - - + -
70B TYR* 3.6 35.7 - - + +
279B GLY 3.0 21.7 + - - +
280B GLY 3.8 3.8 - - - +
282B LEU* 1.3 77.0 - - - +
284B TYR* 1.3 58.2 + - - +
286B ALA* 3.8 1.6 - - - +
287B THR* 2.9 42.3 + - - +
471B PRO* 5.0 1.6 - - + -
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Residues in contact with TYR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TRP* 3.6 36.6 - + - -
280B GLY 3.0 18.4 + - - +
281B TYR 3.8 0.9 - - - +
283B VAL* 1.3 79.5 - - - +
285B ALA* 1.3 54.1 + - - +
287B THR* 3.8 2.8 - - - -
288B THR* 2.7 42.3 + - + +
419B GLY 5.9 0.4 - - - -
420B GLY* 3.7 30.1 - - - -
421B PHE 2.8 29.1 + - - -
422B MET* 3.8 0.6 - - - -
441B PHE* 3.5 14.3 - + - -
442B PHE 4.0 3.8 - - - -
444B VAL* 3.0 25.1 - - - +
470B TRP* 3.8 19.1 - + + -
471B PRO* 3.9 13.7 - - + -
472B GLY* 3.4 20.0 - - - +
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B TYR* 2.9 36.9 + - + +
282B LEU* 3.9 7.4 - - + +
284B TYR* 1.3 76.2 - - - +
286B ALA* 1.3 58.1 + - - +
288B THR* 3.0 18.0 + - - -
289B PHE* 3.1 19.8 + - - +
314B SER* 4.2 14.1 - - - +
315B TYR* 3.7 8.7 - - - -
319B GLY* 3.8 18.2 - - - +
419B GLY 5.0 2.4 + - - +
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Residues in contact with ALA 286 (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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45B ILE* 4.1 10.9 - - + +
46B LEU* 4.2 11.9 - - + -
84B ARG* 5.9 0.2 - - - +
282B LEU 3.1 18.4 + - - +
283B VAL 3.8 2.9 - - - +
285B ALA* 1.3 75.1 - - - +
287B THR* 1.3 63.9 + - - +
289B PHE* 4.5 0.2 - - - -
290B LYS* 3.1 25.5 + - - +
319B GLY* 4.1 9.9 - - - -
322B ALA* 4.1 22.9 - - + -
323B CYS* 3.5 13.4 - - - -
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Residues in contact with THR 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TRP* 4.4 7.2 - - + -
42B GLN* 3.1 34.5 + - + +
45B ILE* 4.1 10.2 - - - +
283B VAL* 2.9 23.3 + - - +
284B TYR* 3.3 5.8 + - - -
286B ALA* 1.3 75.3 - - - +
288B THR* 1.3 64.2 + - - +
290B LYS* 3.8 1.2 - - - +
291B TYR* 3.1 52.0 + - + -
441B PHE* 3.9 16.2 - - + -
442B PHE* 5.1 2.9 - - + -
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Residues in contact with THR 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B TYR* 2.7 37.1 + - + +
285B ALA 3.0 4.0 + - - -
287B THR* 1.3 71.7 - - - +
289B PHE* 1.3 64.8 + - - +
292B VAL* 2.8 36.7 + - - +
315B TYR* 2.6 24.9 + - - +
421B PHE* 3.6 27.6 - - + -
441B PHE* 3.5 37.5 - - + -
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Residues in contact with PHE 289 (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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285B ALA 3.1 15.8 + - - +
286B ALA 3.8 2.0 - - - +
288B THR* 1.3 81.6 + - - +
290B LYS* 1.3 65.7 + - - +
293B PHE* 3.1 52.2 + + + +
295B TYR* 3.5 35.4 - + + -
301B TYR* 3.6 33.4 - + - -
315B TYR* 3.8 10.9 - + + -
319B GLY 4.0 8.1 - - - -
320B PRO* 3.6 36.3 - - + -
323B CYS* 3.6 28.3 - - + -
325B ALA* 3.8 12.8 - - + -
353B ILE* 5.6 0.2 - - + -
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Residues in contact with LYS 290 (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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18B LEU* 3.8 26.1 - - + +
45B ILE* 4.0 26.4 - - + +
286B ALA 3.1 16.5 + - - +
287B THR 3.8 3.4 - - - +
289B PHE* 1.3 85.5 - - - +
291B TYR* 1.3 76.9 + - + +
294B ASP* 3.0 8.1 + - - -
295B TYR* 2.9 40.3 + - + +
323B CYS* 4.1 11.4 - - - -
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Residues in contact with TYR 291 (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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18B LEU* 4.1 17.0 - - + +
19B ILE* 3.8 24.5 - - + +
27B LYS* 3.7 18.0 + - - -
38B PHE* 6.0 0.4 - + - -
42B GLN* 3.6 23.7 + - - -
45B ILE* 5.9 0.2 - - - +
287B THR* 3.1 41.1 + - + +
288B THR 4.4 0.2 - - - +
290B LYS* 1.3 100.5 + - + +
292B VAL* 1.3 66.1 + - - +
294B ASP* 3.3 11.9 + - - +
426B LEU* 3.8 22.5 - - + +
427B PRO* 3.8 10.4 - - - +
441B PHE* 4.4 7.9 - + + -
442B PHE* 4.0 20.4 - + - -
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B THR 2.8 23.7 + - - +
291B TYR* 1.3 72.1 - - - +
293B PHE* 1.3 57.2 + - + +
294B ASP 3.3 0.4 - - - -
382B ILE* 4.8 0.5 - - - +
410B VAL* 3.6 20.9 - - + +
412B THR* 4.1 2.2 - - + -
421B PHE* 3.5 33.0 - - + -
424B THR* 3.6 36.3 - - + +
425B PRO 3.8 8.5 - - - +
426B LEU* 4.4 4.5 - - + -
427B PRO* 2.9 24.6 - - - +
441B PHE* 3.9 18.4 - - + -
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Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PHE* 3.1 41.9 + + + +
292B VAL* 1.3 79.3 - - - +
294B ASP* 1.3 70.8 + - - +
295B TYR* 3.0 3.1 + - + +
301B TYR* 3.5 22.2 - + + -
315B TYR* 4.1 6.3 - + - -
353B ILE* 3.6 41.6 - - + +
355B TYR* 3.6 41.5 - + + -
382B ILE* 4.2 14.2 - - + +
384B GLY* 4.9 1.8 - - - -
410B VAL* 4.0 18.4 - - + -
412B THR* 5.1 0.2 - - + -
421B PHE* 3.4 36.3 - + - -
427B PRO* 4.6 0.9 - - - -
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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