Contacts of the helix formed by residues 278 - 284 (chain A) in PDB entry 3AS2
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 SER 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A GLY 2.7 19.7 + - - -
275A GLY 4.2 3.5 + - - -
276A THR 3.4 2.8 - - - -
277A LEU* 1.3 76.3 - - - +
279A ASP* 1.3 66.5 + - - +
280A PRO* 3.3 4.0 - - - -
281A PHE* 3.0 29.7 + - - +
282A TYR* 3.8 8.3 - - - -
313A ASP 3.1 8.7 + - - -
314A TRP* 3.5 3.0 - - - -
315A GLU 2.8 42.9 + - - -
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Residues in contact with ASP 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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198A PRO* 3.1 21.2 - - - +
199A ASN* 4.1 3.1 - - - +
200A GLU* 3.0 14.6 + - - +
201A SER* 2.8 51.8 + - - -
276A THR 4.4 1.5 - - - +
277A LEU 3.5 0.6 - - - -
278A SER* 1.3 76.6 + - - +
280A PRO* 1.4 65.7 - - + +
281A PHE 3.1 1.4 + - - -
282A TYR* 3.1 27.8 + - - +
283A ASP* 4.5 2.8 + - - +
322A ALA* 5.3 0.5 - - - +
323A ALA* 3.5 18.4 + - - +
326A LYS* 4.4 16.4 + - - +
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Residues in contact with PRO 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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195A ILE* 3.4 50.9 - - + +
196A CYS 4.3 2.5 - - - +
198A PRO* 3.2 24.9 - - + +
199A ASN* 3.4 12.3 - - - +
223A TYR* 3.6 18.1 - - + -
277A LEU 3.7 7.2 - - - +
278A SER 3.4 4.0 - - - -
279A ASP* 1.4 89.6 - - - +
281A PHE* 1.3 61.9 + - - +
283A ASP* 3.0 18.2 + - - +
284A PHE* 3.5 12.3 - - + -
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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
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195A ILE* 3.7 24.0 - - + -
272A ILE* 3.7 22.7 - - + -
273A GLY* 3.9 10.3 - - - -
278A SER* 3.0 25.6 + - - +
280A PRO* 1.3 77.9 - - - +
282A TYR* 1.3 57.2 + - - +
283A ASP 3.0 0.2 - - - -
284A PHE* 2.9 57.3 + + - +
293A PHE* 4.4 6.1 - + - -
312A ILE* 3.8 25.1 - - + -
313A ASP 3.8 7.6 - - - -
314A TRP* 3.4 65.3 - + + -
339A LEU* 4.4 3.4 - - + -
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Residues in contact with TYR 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 SER* 3.8 16.6 - - - -
279A ASP* 3.2 24.9 - - - +
280A PRO 3.1 1.4 - - - -
281A PHE* 1.3 78.0 - - - +
283A ASP* 1.3 62.0 + - - +
284A PHE 3.3 1.5 + - - -
285A VAL* 4.1 17.6 + - - +
314A TRP* 3.5 14.8 - + - -
315A GLU 3.4 6.6 + - - -
316A PHE 3.2 40.3 + - - -
319A GLY* 4.0 8.2 - - - -
321A GLY* 4.6 4.9 + - - -
323A ALA* 3.9 23.8 + - + +
326A LYS* 3.7 28.4 + - + -
327A GLY* 3.7 23.8 - - - +
332A ASP* 3.6 21.7 - - - +
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Residues in contact with ASP 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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198A PRO* 3.3 20.6 - - - +
223A TYR* 2.6 35.0 + - + +
279A ASP 4.8 2.1 - - - +
280A PRO* 3.0 12.2 + - - +
282A TYR* 1.3 81.5 - - - +
284A PHE* 1.3 63.1 + - - +
285A VAL* 3.1 7.2 - - - +
286A ASP* 3.2 17.7 + - - +
289A ASN* 3.0 24.3 + - - +
326A LYS* 5.1 7.2 + - - -
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Residues in contact with PHE 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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195A ILE* 4.2 5.6 - - + -
223A TYR* 3.9 17.3 - + + -
280A PRO 3.5 21.5 - - - -
281A PHE* 2.9 41.3 + + - +
283A ASP* 1.3 77.6 - - - +
285A VAL* 1.3 61.5 + - - +
286A ASP 3.1 2.6 + - - -
289A ASN* 4.4 10.3 - - + -
290A ARG* 2.9 49.0 + - + +
293A PHE* 3.4 54.7 - + + -
314A TRP* 4.9 4.7 - + + -
335A ALA* 3.7 11.6 - - + +
339A LEU* 3.8 21.3 - - + -
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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