Contacts of the helix formed by residues 279 - 287 (chain B) in PDB entry 1LL9
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 279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264B ASP* 5.0 3.3 + - - +
278B VAL* 1.3 77.9 - - - +
280B PRO* 1.3 71.9 - - - +
281B ASP* 3.0 30.5 + - - +
282B SER* 2.9 33.3 + - - -
283B ILE 3.5 3.5 + - - -
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Residues in contact with PRO 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B VAL 3.2 8.0 - - - +
279B ASN* 1.3 87.8 - - - +
281B ASP* 1.3 66.3 + - - +
282B SER 3.1 0.7 + - - -
283B ILE* 3.2 11.0 + - + +
284B ILE* 2.9 37.7 + - + +
354B TRP* 3.2 52.5 - - + +
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Residues in contact with ASP 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B ASN* 3.0 14.3 + - - +
280B PRO* 1.3 80.0 - - - +
282B SER* 1.3 57.7 + - - +
284B ILE* 4.5 8.0 - - - +
285B ASN* 2.9 50.5 + - - +
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B ASP* 2.4 39.5 + - - -
274B LEU* 3.9 7.5 - - - +
279B ASN* 2.9 27.2 + - - -
281B ASP* 1.3 78.9 - - - +
283B ILE* 1.3 57.5 + - - -
285B ASN* 5.3 0.4 - - - -
286B GLY* 2.9 25.5 + - - -
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B LEU* 3.5 41.5 - - + -
278B VAL* 3.9 18.8 - - + -
279B ASN 3.5 1.8 + - - +
280B PRO* 3.3 13.5 - - + +
282B SER* 1.3 74.6 - - - +
284B ILE* 1.3 68.3 + - + +
286B GLY* 3.9 1.2 - - - -
287B SER* 3.1 24.4 + - - -
312B TRP* 3.7 36.3 - - + -
314B HIS* 4.1 15.1 - - + -
350B VAL* 3.7 22.1 - - + +
354B TRP* 4.4 12.6 - - + -
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B PRO* 2.9 35.3 + - + +
281B ASP* 4.2 6.7 - - - +
283B ILE* 1.3 75.2 - - + +
285B ASN* 1.3 72.4 - - - +
287B SER* 2.8 22.0 + - - -
347B PRO* 3.8 34.9 - - + +
350B VAL* 3.9 20.4 - - + +
351B ASP* 3.8 33.0 - - + +
354B TRP* 4.8 7.6 - - + -
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Residues in contact with ASN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B ASP* 2.9 38.2 + - - +
282B SER* 4.8 0.4 - - - +
284B ILE* 1.3 84.9 - - - +
286B GLY* 1.3 61.5 + - - +
288B ASP* 3.1 23.4 + - - +
291B ILE* 3.6 18.4 - - + +
347B PRO* 5.6 1.7 - - - +
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Residues in contact with GLY 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B SER 2.9 23.2 + - - -
283B ILE* 3.9 1.6 - - - -
284B ILE 3.2 0.2 - - - -
285B ASN* 1.3 79.2 - - - +
287B SER* 1.3 57.4 + - - +
288B ASP 3.6 1.0 + - - -
291B ILE* 4.0 17.9 - - - +
292B ALA* 3.6 23.6 + - - +
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Residues in contact with SER 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B ILE 3.1 15.1 + - - -
284B ILE 2.8 18.0 + - - -
285B ASN 3.1 0.2 - - - -
286B GLY* 1.3 74.6 - - - +
288B ASP* 1.3 64.7 + - - +
289B ASN* 3.3 2.1 + - - -
292B ALA* 4.0 8.1 - - - +
314B HIS* 5.9 3.4 - - - -
316B THR* 4.6 8.9 + - - -
346B ASN* 3.2 30.0 + - - +
347B PRO* 3.4 19.9 - - - +
350B VAL* 3.7 17.8 - - - +
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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