Contacts of the helix formed by residues 275 - 285 (chain C) in PDB entry 5E1T
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 275 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274C THR* 1.3 80.6 - - - +
276C VAL* 1.3 62.8 + - - +
277C THR* 4.9 0.3 + - - -
278C ARG* 3.2 33.6 - - + +
279C ARG* 3.2 21.7 + - - +
404C ASP* 2.8 30.5 + - - +
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Residues in contact with VAL 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C ILE* 3.8 17.3 - - + +
274C THR 4.4 1.6 - - - -
275C ASN* 1.3 73.5 - - - +
277C THR* 1.3 77.5 + - - +
279C ARG* 3.1 4.8 + - - +
280C CYS* 2.9 31.5 + - - +
311C LEU* 5.0 4.8 - - + +
393C LEU* 6.3 1.3 - - + -
394C GLN* 4.0 11.2 - - - +
401C VAL* 3.5 30.1 - - + -
404C ASP* 3.1 32.5 + - - +
405C THR* 3.8 11.2 - - - +
406C MET* 3.8 24.2 - - + +
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Residues in contact with THR 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C VAL* 1.3 74.1 - - - +
278C ARG* 1.3 67.0 + - - +
280C CYS* 3.3 6.8 + - - +
281C HIS* 3.0 33.9 + - - +
394C GLN* 3.1 33.0 - - - +
404C ASP* 3.1 24.1 + - - +
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Residues in contact with ARG 278 (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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275C ASN* 3.2 41.4 + - + +
276C VAL 3.2 0.2 - - - -
277C THR* 1.3 81.7 + - - +
279C ARG* 1.3 80.5 + - + +
281C HIS* 3.1 6.2 + - - +
282C GLU* 2.7 70.6 + - - +
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Residues in contact with ARG 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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273C ILE* 5.7 3.1 - - + -
274C THR 5.3 2.5 - - - +
275C ASN 3.2 13.3 + - - +
276C VAL* 3.1 6.1 + - - +
278C ARG* 1.3 100.5 - - + +
280C CYS* 1.3 61.5 + - - +
282C GLU* 4.7 7.8 + - - +
283C SER* 2.9 26.9 + - - +
289C VAL* 3.3 41.0 - - - +
290C SER* 3.7 11.3 + - - +
291C LEU* 3.4 40.7 - - + +
311C LEU* 3.4 27.0 - - + +
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Residues in contact with CYS 280 (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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276C VAL* 2.9 23.4 + - - +
277C THR* 3.7 7.0 - - - +
279C ARG* 1.3 75.2 - - - +
281C HIS* 1.3 69.3 + - - +
283C SER* 2.4 28.9 + - - +
284C ALA* 3.0 8.0 + - - +
311C LEU* 4.1 30.7 - - - -
390C LEU* 4.7 12.8 - - + -
393C LEU* 4.9 11.9 - - - -
394C GLN* 5.7 4.9 - - - -
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Residues in contact with HIS 281 (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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277C THR* 3.0 21.8 + - - +
278C ARG* 3.5 5.4 - - - +
280C CYS* 1.3 79.0 - - - +
282C GLU* 1.3 70.0 + - - +
284C ALA* 3.6 7.5 + - - +
285C CYS* 3.2 20.4 + - - +
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Residues in contact with GLU 282 (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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278C ARG* 2.7 57.6 + - - +
279C ARG* 3.8 11.8 + - - +
281C HIS* 1.3 84.4 - - - +
283C SER* 1.3 64.0 + - - +
284C ALA 3.3 0.7 - - - -
285C CYS* 3.4 30.3 + - + +
289C VAL* 3.9 12.3 - - - +
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Residues in contact with SER 283 (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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279C ARG* 2.9 19.3 + - - +
280C CYS* 2.4 28.3 + - - +
282C GLU* 1.3 78.0 - - - +
284C ALA* 1.3 60.3 + - - +
285C CYS 3.5 4.2 + - - +
289C VAL* 4.0 23.0 + - - +
311C LEU* 4.1 9.7 + - - -
312C ASN* 3.2 42.5 + - - +
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Residues in contact with ALA 284 (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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280C CYS 3.0 9.6 + - - +
281C HIS* 3.6 6.9 + - - +
283C SER* 1.3 78.1 + - - +
285C CYS* 1.3 66.5 + - - +
312C ASN* 3.1 18.8 - - - +
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Residues in contact with CYS 285 (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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281C HIS 3.2 8.8 + - - +
282C GLU* 3.4 40.3 - - + +
283C SER 3.2 6.8 - - - +
284C ALA* 1.3 82.7 - - - +
289C VAL* 6.0 0.3 - - - +
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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