Contacts of the helix formed by residues 279 - 287 (chain A) in PDB entry 1LVK
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 HIS 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A GLU* 3.4 18.6 - - + -
224A ALA* 3.5 7.4 + - - +
227A ASN* 3.2 23.5 + - + +
228A ALA* 3.7 15.7 + - - -
229A LYS 3.9 0.6 + - - -
234A ASN 3.5 22.4 - - - -
235A ASN* 2.9 25.6 + - + -
276A ARG* 3.4 24.0 + - - +
277A ASN 3.4 1.8 + - - -
278A TYR* 1.3 71.1 - - - +
280A ILE* 1.3 63.4 + - - +
282A TYR* 2.9 16.2 + - - +
283A GLN* 3.0 32.3 + - + +
315A ILE* 3.8 12.5 - - + +
320A ASP* 4.5 0.8 - - - +
999A MNT 5.4 3.2 - + - -
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Residues in contact with ILE 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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224A ALA* 2.9 26.9 + - + +
225A PHE* 3.7 36.6 - - + -
278A TYR* 3.2 0.9 + - + -
279A HIS* 1.3 75.1 - - - +
281A PHE* 1.3 87.0 + - + +
283A GLN* 3.6 20.4 - - + +
284A LEU* 3.0 24.0 + - + +
324A PHE* 5.1 3.1 - - + -
327A THR* 4.9 3.6 - - + -
345A PHE* 4.7 14.8 - - + -
348A ILE* 4.0 17.3 - - + +
426A TYR* 3.1 29.2 - - + +
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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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268A VAL* 4.1 17.7 - - + -
277A ASN* 3.4 30.3 - - - -
278A TYR* 3.1 22.8 + + + +
279A HIS 3.0 1.4 + - - -
280A ILE* 1.3 84.2 - - + +
282A TYR* 1.3 64.2 + - + +
284A LEU* 3.7 1.7 - - - +
285A LEU* 3.3 27.6 + - - +
306A TYR* 6.2 0.2 - + - -
307A LEU* 3.6 24.2 - - + -
348A ILE* 3.7 35.9 - - + -
351A ILE* 4.2 9.2 - - + -
352A LEU* 3.7 28.6 - - + +
426A TYR* 3.7 33.7 - + - -
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Residues in contact with TYR 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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271A GLN* 5.0 1.4 + - - -
276A ARG* 3.3 41.0 - - + +
277A ASN* 2.8 50.0 + - + +
278A TYR 3.3 14.6 - - - -
279A HIS 2.9 6.2 + - - +
281A PHE* 1.3 78.2 - - - +
283A GLN* 1.3 63.1 + - - +
285A LEU* 4.0 4.6 - - - +
286A ALA* 3.1 28.2 + - - +
301A PRO* 4.7 7.2 - - + -
307A LEU* 3.6 36.3 + - + +
310A SER* 5.3 0.5 + - - -
312A CYS 4.1 4.7 + - - -
313A VAL* 3.5 38.8 - - + +
320A ASP* 3.6 11.3 - - + +
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Residues in contact with GLN 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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224A ALA* 4.0 10.0 - - - +
279A HIS* 3.0 35.1 + - - +
280A ILE* 3.8 7.5 - - - +
282A TYR* 1.3 75.4 - - - +
284A LEU* 1.3 60.4 + - - +
287A GLY 2.8 26.5 + - - -
320A ASP* 3.8 24.0 - - - +
323A GLU* 3.5 24.6 - - + +
324A PHE* 3.1 28.4 - - + +
327A THR* 2.9 39.0 + - - +
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Residues in contact with LEU 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 ILE* 3.0 18.2 + - + +
281A PHE 3.7 3.6 - - - +
283A GLN* 1.3 78.2 - - - +
285A LEU* 1.3 61.4 + - + +
286A ALA 3.1 0.2 - - - -
288A ALA* 2.7 47.2 + - + +
292A GLU* 5.6 1.8 - - - +
296A LEU* 4.8 3.8 - - + -
298A LEU* 4.3 21.5 - - + -
324A PHE* 3.6 28.2 - - + -
345A PHE* 3.7 32.1 - - + +
348A ILE* 3.4 28.5 - - + -
349A ALA* 4.2 7.9 - - + +
352A LEU* 5.3 2.2 - - + -
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Residues in contact with LEU 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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281A PHE 3.3 16.5 + - - +
282A TYR* 4.2 4.7 - - - +
284A LEU* 1.3 81.7 - - + +
286A ALA* 1.3 56.7 + - - +
288A ALA* 4.6 2.9 - - - -
293A LYS* 4.6 12.3 - - - +
298A LEU* 3.9 34.5 - - + -
299A ALA 3.4 27.9 - - - +
300A GLY* 5.9 0.2 - - - -
301A PRO* 3.5 35.1 - - + +
304A PHE* 3.7 17.5 - - + -
307A LEU* 3.8 12.3 - - + -
352A LEU* 4.4 9.0 - - + -
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Residues in contact with ALA 286 (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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282A TYR 3.1 17.5 + - - +
284A LEU 3.1 0.6 - - - -
285A LEU* 1.3 77.3 - - - +
287A GLY* 1.3 62.9 - - - +
288A ALA 3.6 4.4 - - - +
293A LYS* 5.2 3.5 + - - -
320A ASP* 4.1 4.7 - - + -
321A GLU* 2.9 43.0 - - - +
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Residues in contact with GLY 287 (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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283A GLN 2.8 9.8 + - - -
286A ALA* 1.3 77.5 - - - +
288A ALA* 1.4 63.4 + - - +
289A THR* 3.5 2.1 + - - +
321A GLU* 4.0 7.1 - - - +
324A PHE* 3.2 24.2 - - - -
325A LYS* 3.0 24.6 + - - -
328A ARG* 3.3 8.5 + - - -
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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