Contacts of the helix formed by residues 266 - 280 (chain A) in PDB entry 3PWH
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 PRO 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A SER* 5.2 2.5 - - - +
264A HIS 3.2 6.9 - - - +
265A ALA* 1.3 87.8 - - + +
267A LEU* 1.3 60.1 + - - +
268A TRP* 3.2 38.6 - - + +
269A LEU* 4.2 18.6 - - + +
270A MET* 2.8 30.0 + - - +
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Residues in contact with LEU 267 (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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265A ALA 3.8 2.9 + - - +
266A PRO* 1.3 71.3 - - - +
268A TRP* 1.3 58.2 + - - +
270A MET* 3.4 11.7 - - + +
271A TYR* 2.7 33.8 + - - +
401A ZMA 5.0 21.2 - - + +
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Residues in contact with TRP 268 (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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9A TYR* 5.6 10.4 - - + +
266A PRO* 3.2 33.3 - - + +
267A LEU* 1.3 80.0 - - - +
269A LEU* 1.3 101.4 + - + +
271A TYR* 3.3 8.6 + - - +
272A LEU* 3.1 38.1 + - + +
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Residues in contact with LEU 269 (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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252A ILE* 4.5 14.3 - - + +
265A ALA* 5.2 3.4 - - + -
266A PRO* 3.5 24.8 + - + +
268A TRP* 1.3 115.1 - - + +
270A MET* 1.3 59.4 + - - +
272A LEU* 3.6 17.2 + - + -
273A ALA* 3.0 28.1 + - + +
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Residues in contact with MET 270 (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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249A LEU* 4.0 19.1 - - - -
252A ILE* 3.4 31.2 - - + -
256A THR* 5.0 4.0 - - - +
265A ALA* 3.5 21.7 - - + +
266A PRO 2.8 20.0 + - - +
267A LEU* 3.4 15.9 - - + +
268A TRP 3.2 0.2 - - - -
269A LEU* 1.3 75.8 - - - +
271A TYR* 1.3 60.3 + - - +
273A ALA* 3.4 3.6 + - - +
274A ILE* 2.9 47.5 + - + +
401A ZMA 3.9 43.3 - - + +
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Residues in contact with TYR 271 (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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9A TYR* 2.8 71.7 + + + +
10A ILE* 4.5 0.7 - - - -
12A VAL* 4.8 2.8 - - + +
13A GLU* 3.2 19.4 + - + +
64A ILE* 6.5 1.1 - - + -
67A SER* 5.5 0.7 - - - -
267A LEU 2.7 20.4 + - - +
268A TRP* 3.5 8.7 - - - +
269A LEU 3.3 0.2 - - - -
270A MET* 1.3 71.0 - - - +
272A LEU* 1.3 57.5 + - - +
274A ILE* 3.1 6.5 + - + +
275A VAL* 2.7 60.3 + - + +
401A ZMA 3.2 45.7 - + + -
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Residues in contact with LEU 272 (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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268A TRP* 3.1 22.4 + - + +
269A LEU* 3.7 25.1 - - + +
271A TYR* 1.3 82.4 - - + +
273A ALA* 1.3 69.4 + - + +
275A VAL* 3.2 9.2 + - - +
276A LEU* 3.0 29.7 + - + +
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Residues in contact with ALA 273 (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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245A CYS 5.2 0.7 - - - +
248A PRO* 4.8 7.4 - - + +
249A LEU* 4.0 27.8 + - + +
252A ILE* 3.6 26.0 - - + -
269A LEU* 3.0 19.0 + - + +
270A MET 3.7 4.5 - - - +
272A LEU* 1.3 82.6 - - + +
274A ILE* 1.3 62.1 + - - +
276A LEU* 3.4 19.4 + - - +
277A ALA* 3.6 4.0 + - - +
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Residues in contact with ILE 274 (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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13A GLU* 5.5 0.2 - - - +
63A ALA* 5.5 1.1 - - + -
249A LEU* 3.7 30.3 - - + -
270A MET* 2.9 37.1 + - + +
271A TYR* 3.6 4.7 - - + +
273A ALA* 1.3 73.2 - - - +
275A VAL* 1.3 63.3 + - + +
277A ALA* 3.2 14.1 + - + +
278A HIS* 2.8 38.9 + - + -
401A ZMA 3.5 69.1 - - + +
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Residues in contact with VAL 275 (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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12A VAL* 4.5 11.7 - - + -
13A GLU* 3.1 24.5 - - + +
16A ILE* 4.0 22.2 - - + -
271A TYR* 2.7 56.7 + - + +
272A LEU* 3.4 8.1 - - - +
274A ILE* 1.3 71.0 - - + +
276A LEU* 1.3 61.3 + - - +
278A HIS* 2.8 21.7 + - - +
279A THR* 3.2 12.1 + - - +
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Residues in contact with LEU 276 (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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244A LEU 3.7 22.0 - - - +
245A CYS* 3.6 26.6 - - - +
248A PRO* 3.8 23.8 - - + -
272A LEU* 3.0 19.9 + - + +
273A ALA* 3.5 12.3 - - - +
274A ILE 3.3 0.2 - - - -
275A VAL* 1.3 77.0 - - - +
277A ALA* 1.3 62.1 + - - +
279A THR* 3.1 29.0 + - + +
280A ASN 3.5 4.5 + - - -
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Residues in contact with ALA 277 (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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55A VAL* 5.8 0.2 - - - +
245A CYS 3.2 18.5 + - - +
246A TRP* 3.7 44.1 - - + -
249A LEU* 4.7 8.1 - - + -
273A ALA 3.6 5.2 + - - +
274A ILE* 3.2 13.4 + - + +
275A VAL 3.1 0.8 - - - -
276A LEU* 1.3 77.8 - - - +
278A HIS* 1.3 65.9 + - + +
279A THR 3.0 1.0 + - - -
280A ASN* 3.4 17.0 + - - +
281A SER* 4.4 4.2 + - - -
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Residues in contact with HIS 278 (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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13A GLU* 3.4 28.6 + - - +
16A ILE* 3.1 21.3 - - + +
55A VAL* 4.3 16.6 - - + +
59A ALA* 4.8 3.5 + - + -
60A ILE* 3.6 30.7 + - + -
63A ALA* 3.5 27.2 - - + +
84A VAL* 4.9 13.6 - - + +
246A TRP* 6.6 0.2 - + - -
274A ILE* 2.8 44.5 + - + -
275A VAL 2.8 8.0 + - - +
277A ALA* 1.3 79.3 - - + +
279A THR* 1.3 59.5 + - - +
280A ASN 3.4 0.6 + - - -
281A SER* 3.8 14.2 + - - -
282A VAL* 4.4 0.5 - - - +
401A ZMA 5.7 0.7 - - - -
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Residues in contact with THR 279 (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 ILE* 3.5 22.3 - - + +
245A CYS* 5.4 4.0 - - - -
275A VAL* 3.2 14.4 + - - +
276A LEU* 3.2 24.0 + - + +
277A ALA 3.0 1.0 - - - -
278A HIS* 1.3 76.5 - - - +
280A ASN* 1.3 56.5 + - - +
281A SER 2.9 11.4 + - - -
282A VAL* 3.1 21.5 + - + +
283A VAL* 3.7 17.7 + - + +
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Residues in contact with ASN 280 (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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48A LEU* 6.0 1.2 - - - +
52A ASP* 3.4 13.8 - - - +
238A ILE 4.9 1.6 + - - -
241A LEU* 3.6 7.9 + - - +
242A PHE* 2.9 58.9 - - - +
245A CYS* 3.8 13.3 - - + +
246A TRP* 3.5 11.2 + - - +
276A LEU 3.5 2.6 + - - -
277A ALA 3.4 13.6 + - - +
279A THR* 1.3 77.5 - - - +
281A SER* 1.3 57.1 + - - +
282A VAL 3.2 4.8 + - - -
283A VAL* 3.8 23.4 - - - +
284A ASN* 4.1 9.5 + - - +
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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