Contacts of the helix formed by residues 315 - 329 (chain A) in PDB entry 3PMM
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 TYR 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A ASP* 4.2 23.0 + - - -
266A ILE* 3.6 27.4 - - + -
267A ALA* 3.4 26.0 - - - +
270A ALA* 4.0 18.2 - - + -
302A ILE* 3.7 13.7 - - + +
306A VAL* 3.9 13.0 - - + -
311A VAL* 3.8 15.9 - - + -
312A GLY 3.1 22.4 + - - +
314A HIS* 1.3 104.6 - + - +
316A ALA* 1.3 65.4 + - - +
317A GLY 3.1 2.7 - - - -
318A VAL* 3.1 30.6 + - + +
319A ALA 3.3 7.6 + - - -
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Residues in contact with ALA 316 (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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303A LEU* 5.5 3.2 - - + +
306A VAL* 4.0 19.4 - - + +
313A GLN* 3.0 16.8 + - - +
314A HIS 3.0 0.4 - - - -
315A TYR* 1.3 78.4 - - - +
317A GLY* 1.3 56.7 + - - +
319A ALA* 3.4 7.2 + - - +
320A GLU* 2.9 31.2 + - - +
377A LYS* 5.3 12.2 + - - +
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Residues in contact with GLY 317 (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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314A HIS 3.3 9.1 + - - -
315A TYR 3.1 1.6 - - - -
316A ALA* 1.3 76.3 - - - +
318A VAL* 1.3 64.0 - - - +
320A GLU* 3.4 7.5 + - - +
321A LYS* 3.1 28.9 + - - +
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Residues in contact with VAL 318 (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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266A ILE* 6.0 0.2 - - + -
270A ALA* 3.7 31.6 - - + +
273A GLN* 3.1 37.4 + - - +
279A TRP* 3.9 11.4 - - + -
302A ILE* 3.9 24.5 - - + -
314A HIS 4.6 1.1 + - - +
315A TYR* 3.1 22.9 + - + +
317A GLY* 1.3 77.8 - - - +
319A ALA* 1.3 61.1 + - - +
321A LYS* 3.3 3.5 + - - -
322A ALA* 3.1 18.5 + - - +
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Residues in contact with ALA 319 (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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299A ALA* 4.4 4.3 - - - +
302A ILE* 4.0 24.2 - - + +
303A LEU* 3.5 36.8 - - + +
315A TYR 3.3 4.9 + - - +
316A ALA* 3.8 7.2 - - - +
318A VAL* 1.3 76.8 - - - +
320A GLU* 1.3 61.2 + - - +
322A ALA* 3.2 8.1 + - - +
323A ILE* 2.9 34.0 + - - +
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Residues in contact with GLU 320 (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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16A GLU 5.5 2.8 - - - +
18A PHE* 3.5 5.5 - - - -
303A LEU* 5.3 0.4 - - - +
316A ALA 2.9 19.0 + - - +
317A GLY* 3.7 8.7 - - - +
318A VAL 3.3 0.2 - - - -
319A ALA* 1.3 77.3 - - - +
321A LYS* 1.3 62.9 + - + +
323A ILE* 3.4 4.3 + - - +
324A ARG* 2.8 64.4 + - - +
374A TYR* 2.6 34.7 + - - -
377A LYS* 3.3 19.9 + - - +
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Residues in contact with LYS 321 (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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273A GLN* 3.7 17.9 - - - +
274A ASP 4.1 13.0 - - - -
275A ASP* 3.0 34.2 + - - +
276A SER 4.0 2.0 - - - +
277A GLY* 3.6 11.8 - - - +
317A GLY 3.1 16.8 + - - +
318A VAL* 3.6 9.0 - - - +
320A GLU* 1.3 78.9 - - + +
322A ALA* 1.3 62.1 + - - +
324A ARG* 3.5 10.6 + - - +
325A GLY* 3.1 17.3 + - - -
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Residues in contact with ALA 322 (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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273A GLN* 3.6 0.2 - - - +
277A GLY 3.5 20.9 - - - +
279A TRP* 3.7 20.4 - - + -
295A THR* 4.0 6.2 - - + +
299A ALA* 4.0 17.0 - - + -
318A VAL 3.1 13.0 + - - +
319A ALA* 3.2 9.2 + - - +
321A LYS* 1.3 75.8 - - - +
323A ILE* 1.3 54.2 + - - +
325A GLY* 3.1 2.8 + - - -
326A ILE* 2.8 39.8 + - - +
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Residues in contact with ILE 323 (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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18A PHE* 3.9 11.4 - - + -
299A ALA* 3.9 19.3 - - + -
303A LEU* 3.9 9.6 - - + -
319A ALA 2.9 20.2 + - - +
320A GLU 3.8 4.0 - - - +
322A ALA* 1.3 72.8 - - - +
324A ARG* 1.3 66.1 + - - +
326A ILE* 3.1 4.4 + - - +
327A VAL* 2.9 23.7 + - + +
370A CYS* 3.8 36.1 - - - +
371A LEU* 4.3 12.6 - - + -
374A TYR* 3.7 50.0 - - + -
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Residues in contact with ARG 324 (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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16A GLU* 4.8 12.7 + - - +
17A ARG 5.4 0.2 - - - -
18A PHE* 3.7 54.9 - - + +
320A GLU* 2.8 46.6 + - - +
321A LYS* 3.7 11.2 - - - +
323A ILE* 1.3 75.7 - - - +
325A GLY* 1.3 62.5 + - - +
327A VAL* 3.4 1.7 + - - +
328A GLN* 3.0 32.4 + - + +
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Residues in contact with GLY 325 (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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276A SER 3.6 21.7 + - - -
278A LEU* 3.8 13.0 - - - -
321A LYS 3.1 10.7 + - - -
322A ALA 3.1 5.1 + - - -
324A ARG* 1.3 75.4 - - - +
326A ILE* 1.3 59.8 + - - +
328A GLN* 3.4 6.7 + - - +
329A ASN* 2.7 33.6 + - - -
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Residues in contact with ILE 326 (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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278A LEU* 5.3 0.7 - - + -
292A ALA* 3.4 32.1 - - + +
295A THR* 3.8 13.5 - - + +
296A ALA* 3.6 22.0 - - + +
299A ALA* 5.2 0.4 - - + -
322A ALA 2.8 23.3 + - - +
323A ILE* 3.1 9.8 + - - +
325A GLY* 1.3 70.3 - - - +
327A VAL* 1.3 61.7 + - - +
329A ASN* 2.8 20.6 + - - +
330A ILE* 3.3 28.6 + - + +
336A LEU* 4.1 13.8 - - + +
367A ALA* 4.6 4.9 - - + -
370A CYS* 4.1 21.1 - - - -
371A LEU* 4.5 7.2 - - + -
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Residues in contact with VAL 327 (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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18A PHE* 3.8 29.8 - - + -
19A ILE* 4.5 12.8 - - + -
24A LEU* 5.1 1.8 - - + -
27A LEU* 4.1 22.2 - - + +
323A ILE* 2.9 20.4 + - + +
324A ARG 4.0 3.1 - - - +
326A ILE* 1.3 74.8 - - - +
328A GLN* 1.3 62.4 + - + +
329A ASN 3.2 0.9 + - - -
330A ILE* 3.4 23.6 + - - +
371A LEU* 4.0 22.0 - - + -
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Residues in contact with GLN 328 (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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324A ARG* 3.0 24.2 + - + +
325A GLY* 3.5 9.4 - - - +
326A ILE 3.1 0.4 - - - -
327A VAL* 1.3 78.1 - - + +
329A ASN* 1.3 64.6 + - - +
330A ILE 3.5 2.5 + - - +
337A LEU* 5.5 1.7 - - - +
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Residues in contact with ASN 329 (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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278A LEU* 4.1 22.7 - - - +
292A ALA* 4.7 2.9 - - + -
325A GLY* 2.7 26.3 + - - +
326A ILE* 2.8 9.4 + - - +
328A GLN* 1.3 86.9 - - - +
330A ILE* 1.3 58.3 + - - +
331A SER 4.0 0.2 - - - -
335A GLU 3.4 0.2 - - - +
336A LEU* 3.6 8.6 - - + -
337A LEU* 2.8 59.3 + - + +
338A GLN* 3.9 21.4 + - - +
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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
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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