Contacts of the helix formed by residues 281 - 290 (chain A) in PDB entry 3OP5
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 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A ARG 3.2 10.6 + - - +
278A TYR 3.1 10.4 - - - +
280A GLU* 1.3 78.3 - - + +
282A ILE* 1.3 61.9 + - - +
283A ALA* 3.7 12.5 + - - +
284A SER* 2.7 53.9 + - - +
285A LEU 3.4 2.9 + - - -
314D LYS* 4.8 9.1 + - + +
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Residues in contact with ILE 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 TYR 3.4 11.0 - - - +
279A ARG* 3.5 23.8 - - + +
280A GLU 4.0 0.6 - - - -
281A ASN* 1.3 68.4 - - - +
283A ALA* 1.3 58.5 + - - +
285A LEU* 3.0 8.4 + - + +
286A MET* 2.9 33.7 + - + +
300A ALA* 4.0 24.7 - - + +
303A MET* 3.7 47.6 - - + +
304A GLU* 3.7 36.2 + - - +
307A LYS* 3.8 10.3 - - + +
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASN* 3.3 10.9 + - - +
282A ILE* 1.3 77.9 - - - +
284A SER* 1.4 56.0 + - - +
286A MET* 3.4 9.4 + - - +
287A ASP* 3.0 38.2 + - - +
304A GLU* 5.3 1.6 + - - -
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Residues in contact with SER 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ARG 4.9 0.5 + - - -
278A TYR* 3.6 16.8 - - - -
281A ASN* 2.7 46.3 + - - +
283A ALA* 1.4 75.0 - - - +
285A LEU* 1.3 59.6 + - - +
287A ASP* 3.5 10.9 + - - +
288A LYS* 3.0 29.6 + - - +
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Residues in contact with LEU 285 (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 TYR* 5.3 4.3 - - + -
252A ILE* 3.8 24.7 - - + -
260A PRO* 3.9 12.6 - - + -
261A TRP* 4.3 9.6 - - + -
278A TYR* 3.5 50.3 - - + +
281A ASN 3.4 0.4 + - - -
282A ILE* 3.0 13.5 + - + +
284A SER* 1.3 79.2 + - - +
286A MET* 1.4 69.5 + - + +
288A LYS* 3.3 1.4 + - - +
289A CYS* 3.0 52.3 + - - -
303A MET* 3.9 18.8 - - + -
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Residues in contact with MET 286 (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* 4.2 6.5 - - + -
282A ILE* 2.9 27.1 + - + +
283A ALA* 3.6 10.3 - - - +
284A SER 3.4 0.2 - - - -
285A LEU* 1.4 101.8 - - + +
287A ASP* 1.3 56.4 + - - +
290A PHE* 2.9 58.2 + - + +
295A ALA* 4.1 20.2 - - + +
296A PRO 4.8 1.6 - - - +
299A ILE* 4.0 26.7 - - + -
300A ALA* 4.0 27.1 - - + -
303A MET* 4.5 2.5 - - + -
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Residues in contact with ASP 287 (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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283A ALA* 3.0 29.1 + - - +
284A SER* 3.7 9.4 - - - +
285A LEU 3.3 0.2 - - - -
286A MET* 1.3 78.8 - - - +
288A LYS* 1.3 57.6 + - - +
290A PHE 3.2 17.5 - - - +
292A ALA* 5.4 8.7 + - - +
293A ALA 5.7 1.2 + - - -
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Residues in contact with LYS 288 (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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260A PRO* 3.8 37.1 + - + -
278A TYR* 3.5 24.9 - - + +
284A SER 3.0 18.8 + - - +
285A LEU* 3.7 4.5 - - - +
287A ASP* 1.3 78.5 - - - +
289A CYS* 1.3 59.4 - - - +
290A PHE 4.8 0.3 - - - +
94B GLU* 4.5 8.9 + - - +
98B LYS* 5.4 6.1 - - - +
101B ARG* 4.0 21.4 - - - +
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Residues in contact with CYS 289 (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* 3.6 31.0 - - + -
256A THR* 3.3 24.4 - - + +
258A HIS 5.3 2.2 - - - -
260A PRO* 3.7 31.6 - - - -
285A LEU* 3.0 29.0 + - - +
288A LYS* 1.3 76.2 - - - +
290A PHE* 1.3 72.2 - - + +
291A PRO* 4.6 1.6 - - - +
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Residues in contact with PHE 290 (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* 4.4 15.7 - - + -
255A LEU* 4.1 25.1 - - + -
256A THR* 3.5 26.7 - - + -
286A MET* 2.9 41.1 + - - +
287A ASP* 3.2 19.9 - - - +
288A LYS 5.2 0.4 - - - -
289A CYS* 1.3 89.8 - - + +
291A PRO* 1.4 74.9 - - + +
292A ALA 3.6 0.7 + - - -
294A ASN 4.7 3.4 - - - -
295A ALA* 3.7 30.1 - - + +
296A PRO* 3.5 27.6 - - + -
299A ILE* 4.6 2.9 - - + -
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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
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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