Contacts of the helix formed by residues 273 - 284 (chain A) in PDB entry 2POD
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 ALA 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A PHE 5.0 1.4 - - - +
75A ARG* 5.2 5.2 + - - +
76A SER* 3.6 36.4 - - - +
77A ALA 4.0 0.7 - - - +
81A MSE 3.9 14.4 - - + -
271A THR 4.0 0.6 + - - -
272A LEU* 1.3 77.1 - - - +
274A THR* 1.3 75.7 + - - +
277A GLY* 3.3 14.5 + - - -
278A PHE* 4.5 0.4 - - - -
296A TRP 3.7 16.8 - - - +
297A CYS* 3.8 5.2 - - - +
75B ARG* 6.1 0.2 - - - +
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Residues in contact with THR 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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69A SER* 5.8 3.1 - - - +
74A PHE 4.2 9.0 + - - +
81A MSE 3.8 28.7 - - + -
273A ALA* 1.3 80.5 + - - +
275A ARG* 1.3 63.9 + - - +
276A TRP* 3.3 27.2 + - + +
277A GLY 3.7 2.3 + - - -
278A PHE* 3.1 22.0 + - - -
297A CYS* 2.7 30.0 + - - +
302A GLU* 3.6 21.1 - - + -
306A ILE* 3.7 10.4 - - - +
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Residues in contact with ARG 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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274A THR* 1.3 76.4 - - - +
276A TRP* 1.3 82.7 + - + +
278A PHE* 3.4 1.2 - - - +
279A ARG* 2.6 37.6 + - - +
302A GLU* 2.9 39.3 + - - +
305A LYS* 3.6 52.7 - - + +
306A ILE* 4.1 14.6 - - + +
309A MSE 4.2 20.9 - - - +
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Residues in contact with TRP 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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66A LYS* 6.2 5.2 - - + -
74A PHE 6.1 0.4 - - - +
75A ARG* 6.3 0.7 - - + -
274A THR* 3.2 25.2 + - + +
275A ARG* 1.3 115.5 - - + +
277A GLY* 1.3 65.2 + - - +
279A ARG* 4.3 8.6 - - + +
280A ASP* 3.3 29.8 + - - +
302A GLU* 4.1 9.4 - - - -
188B TYR* 6.1 0.4 - - - -
248B ARG* 5.4 12.1 - - - -
250B ASP* 3.3 49.9 + - + -
251B SER* 3.2 27.2 - - - +
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Residues in contact with GLY 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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75A ARG* 6.2 1.0 - - - +
252A LEU* 4.1 1.6 - - - +
272A LEU* 3.9 20.4 - - - +
273A ALA 3.3 22.5 + - - -
274A THR* 3.7 0.4 + - - -
276A TRP* 1.3 76.2 - - - +
278A PHE* 1.3 59.5 + - - +
280A ASP* 3.4 6.7 + - - +
281A LEU* 3.3 19.1 + - - +
75B ARG* 4.3 19.7 - - - +
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Residues in contact with PHE 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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269A SER 3.5 14.4 - - - -
272A LEU* 3.6 27.1 - - + -
273A ALA 4.6 0.9 - - - -
274A THR 3.1 28.5 + - - +
275A ARG* 3.9 3.1 - - - +
277A GLY* 1.3 76.2 - - - +
279A ARG* 1.3 57.9 + - - +
280A ASP 3.2 1.3 - - - -
281A LEU* 3.4 26.5 + - + +
282A LEU* 3.0 41.3 + - + +
290A VAL* 3.7 26.7 - - + -
291A MSE 3.1 28.5 - - - -
292A LEU* 4.0 11.7 - - + -
297A CYS* 4.7 0.9 - - + -
306A ILE* 3.6 35.0 - - + -
309A MSE 4.9 2.9 - - + -
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Residues in contact with ARG 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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275A ARG 2.6 21.3 + - - +
276A TRP* 3.8 9.4 - - + +
277A GLY 3.5 0.2 - - - -
278A PHE* 1.3 71.2 - - - +
280A ASP* 1.3 64.7 - - - +
282A LEU* 3.3 3.2 + - - +
283A GLU* 3.1 56.9 + - - +
309A MSE 4.2 19.6 - - + +
251B SER* 3.2 33.6 + - - +
253B SER* 3.5 23.8 - - - -
254B SER* 2.5 32.7 + - - +
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Residues in contact with ASP 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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75A ARG* 4.4 3.9 + - - -
252A LEU* 3.8 16.5 - - + +
276A TRP 3.3 14.1 + - - +
277A GLY 3.5 9.9 - - - +
278A PHE 3.2 0.6 - - - -
279A ARG* 1.3 79.2 - - - +
281A LEU* 1.3 62.2 + - - +
283A GLU* 3.7 16.7 + - - +
284A THR* 3.4 18.5 + - - +
75B ARG* 3.3 20.8 + - - +
250B ASP 3.7 5.2 - - - +
251B SER* 3.2 30.0 - - - -
252B LEU 4.2 4.7 + - - -
253B SER* 4.9 3.1 + - - -
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Residues in contact with LEU 281 (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 LEU* 3.7 11.2 - - + +
255A LEU* 3.7 29.4 - - + -
268A ALA* 3.4 37.7 - - + +
272A LEU* 4.0 13.0 - - + -
277A GLY 3.3 10.3 + - - +
278A PHE* 3.6 29.4 - - + +
279A ARG 3.3 0.2 - - - -
280A ASP* 1.3 78.3 - - - +
282A LEU* 1.3 63.6 + - + +
284A THR* 2.7 28.9 + - - +
285A ASN 4.1 0.5 + - - -
286A ALA 4.7 1.4 + - - -
287A ALA* 3.8 23.1 + - + +
290A VAL* 4.7 6.7 - - + -
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Residues in contact with LEU 282 (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 PHE* 3.0 25.1 + - + +
279A ARG* 3.3 4.9 + - - +
281A LEU* 1.3 80.2 - - + +
283A GLU* 1.3 61.7 + - - +
285A ASN* 3.5 13.6 + - - +
287A ALA* 5.8 0.7 - - + -
290A VAL* 4.2 14.1 - - + -
306A ILE 5.7 0.2 - - - +
309A MSE 3.7 35.0 - - + -
310A ALA* 4.3 7.6 - - + +
313A TRP* 3.5 60.1 + - + -
315A LEU* 3.6 31.6 - - + -
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Residues in contact with GLU 283 (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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279A ARG* 3.1 50.7 + - - +
280A ASP* 4.0 12.7 - - - +
281A LEU 3.2 0.8 - - - -
282A LEU* 1.3 76.6 - - + +
284A THR* 1.3 62.7 + - - +
285A ASN* 3.2 12.9 + - - +
313A TRP* 5.5 6.5 - - + +
253B SER* 3.1 27.3 + - - -
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Residues in contact with THR 284 (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 LEU* 3.3 37.9 - - + +
253A SER* 4.5 3.8 - - - +
255A LEU* 4.4 6.1 - - + +
256A LYS* 3.2 22.9 - - - +
280A ASP 3.4 17.7 - - - +
281A LEU* 2.7 18.3 + - - +
283A GLU* 1.3 77.7 - - - +
285A ASN* 1.3 64.4 + - - +
286A ALA* 3.1 24.9 + - - +
287A ALA 4.3 1.0 + - - -
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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
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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