Contacts of the helix formed by residues 267 - 275 (chain C) in PDB entry 3A0B
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 267 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C TRP* 5.0 0.2 - - - -
265C ILE* 3.3 10.3 + - - +
266C TRP* 1.3 79.1 - - - +
268C GLY* 1.3 60.6 + - - +
269C GLU* 3.6 13.3 + - - +
270C ALA* 3.7 17.4 + - - -
271C TYR* 2.6 36.3 + - - -
448C ALA* 4.4 14.4 - - - +
451C ALA* 4.6 12.7 - - - +
452C ALA* 5.8 1.3 - - - -
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Residues in contact with GLY 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C TRP* 3.2 47.4 + - - +
267C SER* 1.3 75.2 + - - +
269C GLU* 1.3 61.0 + - - +
271C TYR* 3.1 18.8 + - - +
1033C CLA 2.8 23.7 - - - +
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Residues in contact with GLU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C TRP* 5.2 0.6 - - - -
267C SER* 3.6 8.0 + - - +
268C GLY* 1.3 71.7 - - - +
270C ALA* 1.3 57.0 - - - +
272C LEU* 2.6 39.6 + - + +
273C SER 3.4 1.6 + - - -
444C HIS* 3.5 27.7 + - + +
447C ARG* 2.6 58.6 + - - +
448C ALA* 3.6 12.9 - - + +
451C ALA* 5.1 4.5 - - - +
1032C CLA 4.7 9.7 - - + +
1033C CLA 3.6 12.1 - - - +
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Residues in contact with ALA 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C ILE* 3.7 16.2 - - + +
267C SER* 3.7 12.9 - - - +
268C GLY 3.3 0.2 - - - -
269C GLU* 1.3 77.6 - - - +
271C TYR* 1.3 55.9 + - - +
273C SER* 2.5 39.2 + - - -
274C TYR* 2.7 29.4 - - + +
444C HIS* 5.4 0.2 - - - -
445C ALA* 5.6 0.7 - - - -
448C ALA* 3.5 25.3 - - + +
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Residues in contact with TYR 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C TRP* 3.5 45.2 + + + +
154C LYS* 5.7 0.2 - - - -
157C MET* 4.0 9.2 - - + +
265C ILE 4.5 1.3 - - - -
266C TRP* 2.9 54.8 + - - +
267C SER 2.6 20.6 + - - -
268C GLY* 3.1 8.8 + - - +
270C ALA* 1.3 78.7 - - - +
272C LEU* 1.3 60.2 + - - +
274C TYR* 3.6 7.8 - + - +
275C SER* 3.1 20.3 + - - +
1031C CLA 3.2 55.9 - + + +
1033C CLA 3.0 24.4 - - + +
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C GLY 3.5 1.0 + - - -
269C GLU* 2.6 25.2 + - + +
271C TYR* 1.3 74.3 - - - +
273C SER* 1.3 56.3 + - - +
275C SER* 3.8 1.7 - - - -
276C LEU* 2.8 33.2 + - + +
444C HIS* 3.6 24.0 - - + +
1032C CLA 3.4 66.0 - - + -
1033C CLA 3.4 48.5 - - + +
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Residues in contact with SER 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C GLU 3.4 0.8 + - - -
270C ALA* 2.5 26.5 + - - -
272C LEU* 1.3 73.4 - - - +
274C TYR* 1.3 67.1 + - - +
276C LEU* 2.4 37.7 + - - +
277C GLY* 3.0 8.9 + - - +
441C HIS* 4.0 12.8 + - - +
444C HIS* 3.9 7.8 - - - +
445C ALA* 3.4 44.9 - - - +
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Residues in contact with TYR 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C PHE* 2.8 26.1 - + - -
265C ILE* 2.3 46.1 + - - +
270C ALA* 2.7 45.5 + - + -
271C TYR* 3.6 12.3 - + - +
273C SER* 1.3 84.2 + - - +
275C SER* 1.3 60.3 + - - +
276C LEU 3.5 0.2 + - - -
277C GLY 4.6 0.5 + - - -
278C ALA* 4.4 4.2 + - - +
441C HIS* 5.8 1.8 - - - -
445C ALA* 5.6 0.4 - - + -
1029C CLA 3.5 35.0 + + + +
1031C CLA 3.0 79.4 - - + +
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Residues in contact with SER 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C TYR* 3.1 13.8 + - - +
272C LEU 3.8 0.9 - - - -
273C SER 3.1 0.4 - - - -
274C TYR* 1.3 76.3 - - - +
276C LEU* 1.3 62.6 + - - +
278C ALA* 3.7 10.4 - - - +
279C LEU* 4.0 4.7 - - - +
1031C CLA 2.9 49.5 + - - +
1033C CLA 3.1 49.5 + - - +
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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