Contacts of the helix formed by residues 273 - 280 (chain A) in PDB entry 5E0F
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 LYS 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A VAL* 3.7 13.2 - - - +
271A GLY 3.6 9.0 - - - +
272A GLU* 1.3 83.0 - - - +
274A MET* 1.3 65.8 + - - +
275A SER* 3.9 4.0 - - - +
276A TYR* 3.0 59.7 + - + +
277A LEU 4.2 0.5 + - - -
413A GLY 3.7 19.9 + - - -
414A SER* 3.3 26.0 - - - +
415A ASN* 3.3 13.9 - - - +
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Residues in contact with MET 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A VAL* 3.9 14.1 - - + +
266A ILE* 3.9 25.6 - - + -
273A LYS* 1.3 71.7 - - - +
275A SER* 1.3 62.0 + - - +
277A LEU* 2.9 41.2 + - + +
323A MET* 4.6 1.1 - - - +
327A PHE* 4.0 9.2 - - + -
409A TRP* 3.8 1.4 - - - -
414A SER 3.5 0.2 + - - -
415A ASN* 2.9 26.5 + - - +
417A VAL* 3.7 26.4 - - + +
429A PHE* 3.7 47.3 - - + -
431A ASN* 4.0 22.2 - - + +
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Residues in contact with SER 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 LYS* 3.9 4.5 - - - -
274A MET* 1.3 76.6 - - - +
276A TYR* 1.3 75.9 + - - +
277A LEU 3.1 1.1 + - - -
278A LYS* 3.5 15.4 + - - +
409A TRP* 3.7 5.9 - - - -
411A ASP* 3.6 31.8 - - - +
413A GLY* 3.5 13.8 + - - -
414A SER 3.0 26.5 + - - -
417A VAL* 3.8 10.0 - - - +
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Residues in contact with TYR 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 GLY 3.6 22.6 + - - -
272A GLU* 3.5 20.4 - - - -
273A LYS* 3.0 53.6 + - - +
275A SER* 1.3 79.5 - - - +
277A LEU* 1.3 56.6 + - - +
278A LYS* 3.1 7.1 + - - +
279A ASN* 3.1 23.0 - - - +
284A TRP* 3.3 21.3 + - + -
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Residues in contact with LEU 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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262A LEU* 4.3 11.7 - - + -
265A VAL* 4.0 28.9 - - + -
273A LYS 4.6 0.2 - - - +
274A MET* 2.9 37.7 + - + +
276A TYR* 1.3 75.6 - - - +
278A LYS* 1.3 64.7 + - - +
279A ASN 3.2 1.8 - - - -
280A TRP* 3.0 56.2 + - + +
284A TRP* 4.1 9.4 - - + -
327A PHE* 3.7 36.0 - - + -
331A HIS* 4.8 1.9 + - - -
406A PHE* 4.9 0.7 - - - -
409A TRP* 3.9 8.1 - - + -
417A VAL* 5.7 0.2 - - + -
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Residues in contact with LYS 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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275A SER 3.5 9.4 + - - +
276A TYR 3.1 2.5 - - - +
277A LEU* 1.3 78.5 - - - +
279A ASN* 1.3 58.6 + - + +
280A TRP 3.7 1.2 + - - +
331A HIS* 5.3 0.9 + - - -
406A PHE* 3.5 23.3 - - + -
409A TRP* 3.5 55.0 - - + +
411A ASP* 4.4 8.1 + - - +
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Residues in contact with ASN 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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276A TYR 3.1 8.0 - - - +
278A LYS* 1.3 76.2 - - + +
280A TRP* 1.3 66.7 + - - +
281A GLY 3.4 1.0 + - - -
283A GLY* 3.6 32.3 + - - -
284A TRP* 2.8 29.1 + - - -
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Residues in contact with TRP 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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258A TYR* 3.0 73.0 + + - -
261A LYS* 4.1 2.2 - - + -
262A LEU* 3.8 22.4 - - + -
277A LEU* 3.0 42.5 + - + +
278A LYS 3.4 1.2 + - - -
279A ASN* 1.3 78.7 + - - +
281A GLY* 1.3 60.5 + - - +
284A TRP* 3.6 37.9 - + - -
286A PHE* 3.6 22.0 - + - -
327A PHE* 3.5 22.7 - + + -
331A HIS* 3.5 44.9 + + + +
333A TYR* 4.7 1.6 - - + -
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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