Contacts of the helix formed by residues 273 - 281 (chain A) in PDB entry 3NTY
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 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A SER* 3.0 7.6 + - - +
272A TYR* 1.3 77.9 - - - +
274A GLU* 1.3 65.8 + - - +
275A GLN* 3.0 20.6 - - - +
276A ARG* 2.9 75.5 + - - +
277A ILE* 2.9 24.2 + - - +
351A NAP 3.9 1.3 - - - +
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Residues in contact with GLU 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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36A GLU* 5.3 1.2 - - - +
40A LEU* 3.7 41.9 - - + +
272A TYR 4.0 2.6 + - - -
273A ASN* 1.3 72.9 - - - +
275A GLN* 1.3 78.0 + - + +
277A ILE* 3.5 5.1 + - - +
278A ARG* 3.1 44.4 + - + +
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Residues in contact with GLN 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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273A ASN* 3.0 13.1 - - - +
274A GLU* 1.3 92.8 + - + +
276A ARG* 1.3 64.6 + - + +
278A ARG* 3.4 14.3 + - - +
279A GLN* 3.1 24.1 + - - +
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Residues in contact with ARG 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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271A SER* 3.3 13.2 - - - +
273A ASN* 2.9 41.3 + - - +
275A GLN* 1.3 75.0 - - + +
277A ILE* 1.3 67.9 + - - +
279A GLN* 3.2 12.2 + - - +
280A ASN* 2.9 31.3 + - - -
351A NAP 2.7 87.8 + - + +
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Residues in contact with ILE 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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21A PHE* 4.3 3.8 - - + -
37A ALA* 3.7 26.9 - - - +
40A LEU* 3.8 23.1 - - + +
41A ALA* 3.7 31.2 - - + +
44A ALA* 4.0 6.3 - - + -
46A PHE* 3.9 12.0 - - + -
271A SER* 3.3 34.5 + - - +
272A TYR 4.1 1.3 - - - -
273A ASN 2.9 28.3 + - - +
274A GLU* 3.7 5.2 - - - +
276A ARG* 1.3 79.6 - - - +
278A ARG* 1.3 63.3 + - + +
280A ASN* 3.3 12.4 + - - +
281A VAL* 3.8 9.5 + - - +
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Residues in contact with ARG 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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40A LEU* 5.8 1.1 + - + +
43A GLU* 5.4 4.9 + - - +
44A ALA* 4.1 30.5 - - + +
274A GLU* 3.1 40.9 + - + +
275A GLN* 3.9 15.7 - - - +
276A ARG 3.3 0.2 - - - -
277A ILE* 1.3 73.8 - - + +
279A GLN* 1.3 64.9 + - - +
281A VAL* 3.2 18.1 - - - +
282A GLN* 3.9 10.3 + - - +
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Residues in contact with GLN 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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251A THR* 2.8 38.9 + - + +
253A ALA* 4.4 0.6 - - - +
254A LEU* 3.5 20.3 - - + +
275A GLN 3.1 17.1 + - - +
276A ARG* 3.4 12.3 - - - +
278A ARG* 1.3 77.1 - - - +
280A ASN* 1.3 61.5 + - - +
282A GLN* 2.9 41.4 + - - +
351A NAP 2.5 33.7 + - - -
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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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19A LEU* 3.9 5.6 - - - +
46A PHE* 4.1 14.9 - - + -
219A LEU* 4.3 1.0 - - - +
253A ALA* 4.4 3.6 - - - +
254A LEU* 3.8 8.4 - - - +
257A LEU* 4.0 23.1 - - + +
269A ALA* 4.0 15.3 + - + +
270A LYS 4.8 0.2 + - - -
271A SER* 4.3 6.1 - - - -
276A ARG 2.9 21.8 + - - +
277A ILE* 3.3 7.0 + - - +
279A GLN* 1.3 76.3 + - - +
281A VAL* 1.3 60.0 + - - +
282A GLN 3.1 1.4 + - - -
283A VAL* 3.5 18.9 + - - +
351A NAP 3.0 48.0 + - - -
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Residues in contact with VAL 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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19A LEU* 3.9 12.8 - - + -
44A ALA* 3.6 31.0 - - + +
45A GLY* 4.4 3.4 - - - -
46A PHE* 3.4 41.1 - - + +
277A ILE 3.8 2.8 + - - +
278A ARG* 3.2 23.1 - - - +
280A ASN* 1.3 71.5 - - - +
282A GLN* 1.3 61.8 + - + +
283A VAL* 3.1 7.8 + - - -
284A PHE* 3.9 19.5 + - + +
285A GLU* 5.1 1.1 - - - +
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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