Contacts of the helix formed by residues 280 - 297 (chain A) in PDB entry 1PE7
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 ASN 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLU* 3.2 24.5 - - + +
161A SER* 5.7 0.2 - - - +
164A ILE* 3.6 7.7 - - - +
278A THR 4.6 2.9 + - - +
279A SER* 1.4 73.2 - - - +
281A PHE* 1.3 66.4 + - - +
282A SER* 3.2 10.7 + - - -
283A GLN* 2.8 51.5 + - - +
284A LEU 2.8 18.7 + - - -
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Residues in contact with PHE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU* 2.7 54.9 + - + +
163A ALA* 3.8 13.5 - - + -
164A ILE* 3.8 16.6 - - + -
217A TYR* 3.6 28.3 - + + -
220A ARG* 5.9 0.9 - - + -
233A ASN* 3.7 22.7 - - + -
236A ILE* 4.0 28.9 - - + -
237A ILE* 4.0 19.7 - - + -
280A ASN* 1.3 71.8 - - - +
282A SER* 1.3 64.5 + - - +
284A LEU* 3.0 9.6 + - - +
285A ARG 3.0 18.9 + - - -
315A VAL* 3.6 26.2 - - + +
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Residues in contact with SER 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU* 4.4 0.6 + - - -
280A ASN* 3.1 11.0 + - - -
281A PHE* 1.3 79.4 - - - +
283A GLN* 1.3 64.0 + - - +
285A ARG* 3.2 5.9 + - - +
286A ALA* 3.2 19.9 + - - +
315A VAL* 4.2 4.9 - - - -
316A LYS* 3.0 30.4 + - - +
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Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 4.6 2.4 - - + +
276A THR* 5.0 5.7 + - - +
278A THR* 3.9 5.6 + - - +
279A SER* 3.6 19.5 + - - +
280A ASN* 2.8 47.1 + - - +
282A SER* 1.3 80.8 - - - +
284A LEU* 1.3 61.1 + - - +
286A ALA* 3.3 8.7 + - + +
287A ALA* 3.0 23.2 + - - +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ILE* 4.1 23.8 - - + -
168A ILE* 5.6 1.3 - - + -
237A ILE* 3.5 46.0 - - + -
267A PHE* 4.5 18.6 - - + -
270A ALA* 5.0 4.3 - - + -
275A LEU* 4.1 32.3 - - + +
280A ASN 2.8 12.0 + - - +
281A PHE 3.3 8.1 - - - +
283A GLN* 1.3 76.0 - - - +
285A ARG* 1.3 66.8 + - - +
287A ALA* 3.1 3.3 + - + -
288A ALA* 2.9 25.8 + - + +
310A PHE* 4.0 14.6 - - + -
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Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE 3.0 12.1 + - - +
282A SER 3.4 9.4 - - - +
283A GLN 3.2 0.2 - - - -
284A LEU* 1.3 79.1 - - - +
286A ALA* 1.3 64.0 + - - +
288A ALA* 3.8 1.0 - - - +
289A VAL* 2.9 34.4 + - + +
306A VAL 5.7 0.2 - - - +
307A LYS* 3.8 36.2 + - - +
310A PHE* 3.4 32.2 - - + +
311A ASP* 2.7 41.2 + - - +
315A VAL* 2.7 36.7 + - + -
316A LYS* 3.6 25.1 + - - +
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A SER 3.2 9.5 + - - +
283A GLN* 3.6 11.4 - - + +
285A ARG* 1.3 78.4 - - - +
287A ALA* 1.3 58.4 + - - +
289A VAL* 3.8 5.3 - - - +
290A GLN* 2.9 31.4 + - - +
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ALA* 4.2 8.5 - - + -
274A TYR* 3.7 29.4 - - + +
275A LEU* 3.9 18.6 - - + -
283A GLN 3.0 16.2 + - - +
284A LEU 3.1 4.7 + - - +
286A ALA* 1.3 79.7 - - - +
288A ALA* 1.3 55.7 + - - +
290A GLN* 3.4 4.1 + - - +
291A SER* 2.8 34.9 + - - -
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ILE* 3.8 19.1 - - + +
267A PHE* 4.8 11.0 - - + -
270A ALA* 4.4 6.2 - - + +
284A LEU* 2.9 19.9 + - + +
285A ARG 3.9 2.9 - - - +
287A ALA* 1.3 73.8 - - - +
289A VAL* 1.3 61.5 + - - +
291A SER* 3.2 2.8 + - - -
292A ALA* 2.9 31.4 + - - +
306A VAL* 3.9 17.7 - - + +
310A PHE* 4.0 14.1 - - + -
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ARG* 2.9 31.4 + - + +
286A ALA* 3.8 6.3 - - - +
288A ALA* 1.3 77.8 - - - +
290A GLN* 1.3 64.1 + - - +
292A ALA* 3.9 3.2 - - - +
293A THR* 2.9 34.5 + - - +
303A VAL* 4.4 15.1 - - + +
306A VAL* 3.8 20.0 - - + -
307A LYS* 4.0 29.2 - - + +
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Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A TYR* 3.5 32.5 - - + -
286A ALA 2.9 19.1 + - - +
287A ALA* 3.8 4.5 - - - +
289A VAL* 1.3 78.6 - - - +
291A SER* 1.3 59.0 + - - +
293A THR* 3.2 15.5 + - - +
294A ASP* 2.8 55.4 + - - +
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Residues in contact with SER 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ILE* 3.6 23.1 - - - -
269A ARG* 3.7 12.0 - - - +
270A ALA* 3.3 22.2 + - - -
274A TYR* 3.4 8.1 - - - -
287A ALA 2.8 24.2 + - - -
288A ALA* 3.7 3.8 - - - -
290A GLN* 1.3 77.1 - - - +
292A ALA* 1.3 59.0 + - - +
294A ASP* 3.3 10.7 + - - +
295A LEU* 2.9 35.8 + - - +
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ILE* 3.9 26.2 - - + +
288A ALA 2.9 17.9 + - - +
289A VAL 3.9 1.6 - - - +
291A SER* 1.3 78.2 - - - +
293A THR* 1.3 55.1 + - - +
296A TYR* 2.6 47.9 + - + +
297A GLY 3.7 0.3 + - - -
302A GLU 4.4 0.9 - - - -
303A VAL* 3.8 23.5 - - + +
306A VAL* 4.2 11.9 - - + -
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Residues in contact with THR 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A VAL* 2.9 29.3 + - - +
290A GLN* 3.3 20.4 + - - +
292A ALA* 1.3 73.3 - - - +
294A ASP* 1.3 67.9 + - - +
297A GLY* 2.8 22.7 + - - +
298A SER* 4.0 25.1 - - - +
303A VAL* 3.6 17.7 - - - +
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Residues in contact with ASP 294 (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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269A ARG* 2.6 35.0 + - - +
274A TYR* 2.4 30.1 + - - -
290A GLN* 2.8 39.4 + - - +
291A SER 3.4 7.0 - - - +
293A THR* 1.3 76.8 - - - +
295A LEU* 1.3 63.6 + - + +
297A GLY 4.7 0.5 + - - -
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LYS* 3.9 37.9 - - + +
266A ILE* 4.0 7.0 - - + -
269A ARG* 4.0 24.5 - - + +
291A SER 2.9 17.8 + - - +
294A ASP* 1.3 85.8 - - + +
296A TYR* 1.3 97.5 + - + +
297A GLY 3.8 0.2 - - - -
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Residues in contact with TYR 296 (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 LYS* 3.5 41.3 - - + +
265A LYS* 4.0 19.2 - - - +
266A ILE* 4.0 14.6 - - + -
292A ALA* 2.6 25.2 + - - +
295A LEU* 1.3 103.9 - - + +
297A GLY* 1.3 60.1 + - - +
300A SER* 3.1 28.6 - - - +
302A GLU* 3.6 31.6 - - + +
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Residues in contact with GLY 297 (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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292A ALA 3.7 0.6 + - - -
293A THR* 2.8 17.9 + - - -
294A ASP 4.7 0.4 + - - -
295A LEU 3.8 0.6 - - - -
296A TYR* 1.3 78.1 - - - +
298A SER* 1.3 64.6 + - - -
299A THR* 3.1 4.3 - - - -
300A SER* 2.6 28.8 + - - -
303A VAL* 3.3 4.0 - - - +
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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
------------------------------------------------------------
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