Contacts of the helix formed by residues 274 - 285 (chain A) in PDB entry 5IVK
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 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A GLU* 2.9 19.5 + - + +
273A ASP* 1.3 75.4 + - - +
275A ASP* 1.3 70.3 + - - +
276A LYS* 3.1 14.0 + - - +
277A ASP* 3.1 34.9 + - - +
278A VAL* 2.9 25.4 + - - +
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Residues in contact with ASP 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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175A LEU* 4.0 24.7 - - + +
176A ASN* 3.3 16.1 + - - +
177A SER* 3.0 34.5 + - - -
180A LEU* 3.7 18.7 - - + +
257A GLN 4.8 4.7 - - - +
273A ASP* 4.8 6.8 - - - +
274A ASN* 1.3 74.2 - - - +
276A LYS* 1.3 58.0 + - - +
278A VAL* 3.3 6.7 + - - +
279A LEU* 2.8 31.9 + - - +
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Residues in contact with LYS 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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177A SER* 5.7 0.2 - - - -
180A LEU* 3.9 28.9 - - + +
274A ASN* 3.2 11.8 + - - +
275A ASP* 1.3 79.8 - - - +
277A ASP* 1.3 66.3 + - - +
279A LEU* 3.2 5.0 + - + -
280A GLU* 2.9 55.7 + - - +
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Residues in contact with ASP 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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269A TYR* 3.3 26.0 + - + +
272A GLU* 5.3 6.9 + - - +
274A ASN* 3.1 23.5 + - + +
276A LYS* 1.3 85.7 + - - +
278A VAL* 1.3 60.2 + - - +
280A GLU* 2.9 41.6 - - - +
281A PHE* 3.2 8.5 + - - +
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Residues in contact with VAL 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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175A LEU* 5.0 4.0 - - + -
260A ALA* 3.7 26.0 - - + +
261A PHE* 3.9 24.9 - - + +
264A ALA* 4.1 4.5 - - + -
269A TYR* 4.0 25.4 - - + -
272A GLU 4.1 2.9 - - - +
273A ASP* 5.5 0.2 - - - +
274A ASN 2.9 22.0 + - - +
275A ASP* 3.7 5.8 - - - +
277A ASP* 1.3 74.9 - - - +
279A LEU* 1.3 66.3 + - - +
281A PHE* 3.2 6.6 + - - +
282A LEU* 3.0 40.7 + - + +
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Residues in contact with LEU 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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73A PHE* 3.7 31.4 - - + -
74A LYS* 4.1 8.1 - - - +
173A LEU* 4.4 5.2 - - + -
175A LEU* 3.8 17.7 - - + +
180A LEU* 3.9 34.1 - - + -
182A VAL* 4.0 17.9 - - + -
275A ASP 2.8 17.3 + - - +
276A LYS* 3.8 5.6 - - + +
278A VAL* 1.3 75.9 - - - +
280A GLU* 1.3 66.7 + - - +
282A LEU* 3.0 3.7 + - - +
283A MET* 2.8 40.4 + - + +
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Residues in contact with GLU 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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269A TYR* 5.9 1.3 - - - -
276A LYS* 2.9 34.2 + - - +
277A ASP* 2.9 45.5 - - - +
278A VAL 3.3 0.2 - - - -
279A LEU* 1.3 76.8 - - - +
281A PHE* 1.3 68.7 + - + +
283A MET* 3.6 8.8 + - - +
284A LYS* 3.2 28.7 - - + +
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Residues in contact with PHE 281 (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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264A ALA* 3.6 34.5 - - + -
267A ALA* 3.8 26.5 - - + -
268A GLY 4.3 2.9 - - - -
269A TYR* 3.5 46.9 - + + -
277A ASP 3.2 9.8 + - - +
278A VAL 3.6 6.3 - - - +
279A LEU 3.1 0.4 - - - -
280A GLU* 1.3 85.2 - - + +
282A LEU* 1.3 68.8 + - + +
284A LYS* 3.3 17.1 + - + +
285A ALA* 3.5 15.9 + - + +
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Residues in contact with LEU 282 (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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72A ARG* 2.9 22.0 + - - -
73A PHE* 3.9 18.5 - - + -
173A LEU* 4.0 28.5 - - + -
260A ALA* 3.9 12.1 - - + +
263A LEU* 4.2 9.2 - - + -
264A ALA* 4.1 21.3 - - - +
278A VAL* 3.0 39.1 + - + +
279A LEU* 3.0 4.2 + - - +
281A PHE* 1.3 83.1 - - + +
283A MET* 1.3 58.4 + - - +
285A ALA* 3.4 9.3 + - - +
290A LEU* 3.9 30.9 - - + +
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Residues in contact with MET 283 (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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69A GLY* 3.2 28.4 - - - +
70A GLU* 3.6 41.7 - - - +
72A ARG* 3.5 37.5 + - - +
73A PHE* 3.6 15.9 - - - -
74A LYS* 5.3 5.2 - - - -
279A LEU* 2.8 37.3 + - + +
280A GLU* 3.8 8.3 - - - +
281A PHE 3.2 0.2 - - - -
282A LEU* 1.3 78.5 - - - +
284A LYS* 1.3 58.6 + - + +
285A ALA 3.4 0.4 - - - -
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Residues in contact with LYS 284 (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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280A GLU* 3.2 23.6 - - + +
281A PHE* 3.3 8.2 + - + +
282A LEU 3.3 0.4 - - - -
283A MET* 1.3 78.1 - - + +
285A ALA* 1.3 65.2 + - - +
286A LYS* 3.6 4.3 + - - +
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Residues in contact with ALA 285 (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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72A ARG* 2.9 27.5 + - - -
267A ALA* 6.1 0.7 - - + -
281A PHE* 3.5 15.6 + - + +
282A LEU* 3.4 14.3 + - - +
283A MET 3.4 2.2 - - - -
284A LYS* 1.3 79.1 - - - +
286A LYS* 1.3 61.4 + - - +
287A PRO* 3.9 0.2 - - - +
289A ASP* 5.7 1.8 - - + -
290A LEU* 3.8 32.8 - - + -
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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