Contacts of the helix formed by residues 271 - 276 (chain A) in PDB entry 3DBL
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 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A TRP* 3.3 59.0 - - + +
218A ILE* 4.2 2.2 - - + -
267A GLU* 2.8 32.4 + - - +
268A ALA 4.0 5.6 - - - +
270A LYS* 1.3 79.4 - - - +
272A VAL* 1.3 53.4 + - - +
273A ASN 3.1 1.1 - - - -
274A THR* 3.0 19.2 + - + +
275A ALA* 2.5 40.9 + - + +
131I GLU* 5.7 0.9 - - - +
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE* 4.3 8.1 - - + -
240A LYS* 4.0 18.4 - - + +
243A PHE* 3.9 22.9 - - + -
244A ARG* 3.8 26.0 - - + +
247A ILE* 3.9 23.3 - - + -
268A ALA 3.5 11.4 + - - +
269A ILE 2.8 20.3 + - - +
270A LYS 2.6 6.1 + - - -
271A ASN* 1.3 72.3 - - - +
273A ASN* 1.3 63.0 + - - +
274A THR 2.9 1.2 + - - -
275A ALA* 3.7 5.9 + - - +
276A LEU* 3.8 27.1 + - + +
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Residues in contact with ASN 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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237A TYR* 5.8 1.0 - - - -
240A LYS* 3.8 22.7 + - - +
244A ARG* 3.6 18.9 - - - +
270A LYS 3.0 13.8 + - - +
272A VAL* 1.3 80.5 - - - +
274A THR* 1.3 57.8 + - - +
128I GLU* 3.4 50.9 + - - +
129I ARG* 5.2 3.1 + - - -
131I GLU* 3.1 27.5 + - - -
132I GLU* 3.7 20.7 - - - +
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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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180A LEU* 3.6 24.6 - - - +
183A LEU* 6.5 0.4 - - + -
271A ASN* 3.0 28.5 + - + +
272A VAL 3.0 0.4 - - - -
273A ASN* 1.3 90.9 - - - +
275A ALA* 1.3 62.8 + - + +
276A LEU 3.1 11.3 + - - -
277A ASN 3.6 8.8 + - - +
278A THR* 3.6 16.0 - - + +
131I GLU* 4.3 24.4 + - - +
132I GLU* 4.4 5.1 + - - +
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Residues in contact with ALA 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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183A LEU* 4.9 9.8 - - + +
185A LEU* 3.8 31.4 - - + +
186A ASP* 5.0 0.7 - - - +
214A TRP* 4.7 4.9 - - - +
218A ILE* 3.8 24.5 - - + -
271A ASN* 2.5 27.9 + - + +
272A VAL* 4.7 1.3 - - - -
274A THR* 1.3 74.7 - - + +
276A LEU* 1.3 63.2 + - + +
277A ASN 3.6 0.2 - - - -
278A THR* 4.3 15.6 + - - +
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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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185A LEU* 5.5 1.6 - - + -
186A ASP* 3.7 13.4 - - - +
218A ILE* 4.8 7.6 - - + -
222A LEU* 3.7 29.4 - - + -
233A ILE* 3.6 27.8 - - + +
234A PRO* 3.1 48.5 - - + +
240A LYS* 4.3 17.3 - - + +
243A PHE* 4.6 7.4 - - + -
272A VAL* 3.8 27.1 + - + +
274A THR 3.1 2.8 + - - -
275A ALA* 1.3 85.5 - - - +
277A ASN* 1.3 61.5 + - + +
278A THR 4.0 0.4 - - - -
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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