Contacts of the helix formed by residues 271 - 279 (chain C) in PDB entry 5TWV
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 ALA 271 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C ASP 4.3 0.6 + - - -
270C LEU* 1.3 74.8 - - - +
272C PRO* 1.3 70.0 - - + +
273C SER 3.7 0.4 - - - -
274C ASP* 3.8 27.8 - - + +
275C LEU* 3.0 33.5 + - - +
311C TRP* 4.8 3.4 - - - -
343C LEU 5.4 1.3 - - - +
345C THR* 4.3 9.2 - - + +
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Residues in contact with PRO 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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271C ALA* 1.3 90.0 - - + +
273C SER* 1.3 60.8 + - - +
274C ASP* 5.8 0.2 - - - +
275C LEU 4.2 0.7 + - - -
276C HIS* 3.1 31.7 + - - -
311C TRP* 3.4 48.8 - - + +
343C LEU* 3.6 52.5 - - + +
344C CYS 4.0 11.0 - - - +
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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
----------------------------------------------------------
272C PRO* 1.3 81.2 - - - +
274C ASP* 1.3 73.4 + - - +
275C LEU 3.5 0.2 - - - -
276C HIS* 4.3 9.4 + - - +
277C HIS* 4.7 8.0 + - - +
278C HIS* 5.2 0.9 + - - -
343C LEU* 5.1 13.5 - - - +
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Residues in contact with ASP 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C ALA* 3.7 23.5 + - + +
272C PRO 3.4 0.2 - - - -
273C SER* 1.3 90.7 + - - +
275C LEU* 1.3 60.1 + - - +
276C HIS 3.5 0.2 - - - -
278C HIS* 3.0 54.0 + - + +
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Residues in contact with LEU 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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270C LEU* 4.0 20.4 - - + -
271C ALA 3.0 24.0 + - - +
272C PRO 4.9 1.1 - - - +
274C ASP* 1.3 77.9 - - - +
276C HIS* 1.3 69.2 + - + +
277C HIS 3.4 0.6 + - - -
279C GLN* 3.4 45.4 + - - +
306C ALA* 4.2 3.8 - - - +
311C TRP* 6.3 1.8 - - + -
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Residues in contact with HIS 276 (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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189C ILE* 5.7 1.3 - - + -
272C PRO 3.1 24.2 + - - +
273C SER* 4.9 5.6 - - - +
274C ASP 3.5 1.2 - - - -
275C LEU* 1.3 83.5 - - + +
277C HIS* 1.3 58.4 + - + +
279C GLN 4.1 0.3 - - - +
306C ALA* 3.1 42.7 + - - +
307C ASP* 4.0 7.7 + - - +
309C ILE* 3.3 40.8 + - + +
310C LEU* 5.3 0.2 - - - -
311C TRP* 3.6 31.9 + + + +
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Residues in contact with HIS 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C SER 4.7 6.0 + - - +
274C ASP 4.0 1.8 + - - -
276C HIS* 1.3 79.2 - - + +
278C HIS* 1.3 78.8 + - + +
279C GLN 3.3 7.0 + - - +
280C ASP* 4.4 8.8 - - - +
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Residues in contact with HIS 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C SER 5.2 0.8 + - - -
274C ASP* 3.0 44.8 + - + +
277C HIS* 1.3 88.6 + - + +
279C GLN* 1.3 62.5 + - + +
280C ASP* 3.9 8.0 + - - +
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Residues in contact with GLN 279 (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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221C ARG* 3.8 24.6 - - - +
270C LEU* 3.4 41.6 - - - +
275C LEU* 3.4 27.2 + - - +
276C HIS 4.1 0.2 - - - +
277C HIS 3.3 4.5 - - - +
278C HIS* 1.3 83.6 - - + +
280C ASP* 1.3 64.9 + - - +
281C LEU* 3.6 32.1 - - + +
306C ALA* 3.2 21.9 - - + +
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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