Contacts of the helix formed by residues 241 - 253 (chain A) in PDB entry 1LIK
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 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A GLU* 3.4 16.3 + - - +
242A VAL* 1.3 61.1 + - - +
243A ALA* 3.3 2.4 - - - +
244A LEU* 3.2 15.2 + - - +
245A SER* 2.9 25.8 + - - -
277A MET* 3.0 21.3 - - - +
279A ARG* 3.2 36.1 - - - +
285A ILE* 3.5 12.6 - - + -
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Residues in contact with VAL 242 (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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241A LYS* 1.3 75.1 - - - +
243A ALA* 1.3 57.3 + - - +
245A SER* 3.4 6.9 + - - -
246A VAL* 2.9 29.5 + - - +
285A ILE* 4.1 20.3 - - + +
297A VAL* 5.3 8.5 - - + -
299A GLU* 5.5 6.3 - - - +
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Residues in contact with ALA 243 (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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237A VAL 5.4 1.6 - - - +
241A LYS 3.3 1.0 - - - +
242A VAL* 1.3 73.7 - - - +
244A LEU* 1.3 58.0 + - - +
246A VAL* 3.1 5.0 + - - +
247A ALA* 2.6 37.8 + - - +
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Residues in contact with LEU 244 (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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227A PHE* 4.8 19.0 - - + +
228A ALA* 5.5 2.5 - - - +
231A ALA* 4.8 3.7 - - + +
236A LEU* 4.6 1.9 - - - +
237A VAL 4.3 15.6 + - - +
241A LYS 3.2 19.2 + - - +
243A ALA* 1.3 77.7 - - - +
245A SER* 1.3 57.5 + - - +
247A ALA* 3.1 8.9 - - - +
248A ASN* 2.9 29.3 + - - +
277A MET* 3.9 12.6 - - + -
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Residues in contact with SER 245 (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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227A PHE* 4.9 5.4 - - - -
241A LYS 2.9 16.7 + - - -
242A VAL* 3.6 9.4 - - - -
244A LEU* 1.3 79.4 - - - +
246A VAL* 1.3 61.7 + - - +
247A ALA 3.2 0.7 + - - -
248A ASN* 3.4 7.3 + - - +
249A LYS* 3.4 4.2 + - - +
275A VAL* 3.3 33.9 - - - +
277A MET* 3.9 19.0 - - - +
285A ILE* 4.3 16.8 - - - -
287A ALA* 4.8 5.8 - - - -
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Residues in contact with VAL 246 (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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242A VAL 2.9 17.5 + - - +
243A ALA* 3.9 4.3 - - - +
245A SER* 1.3 72.9 - - - +
247A ALA* 1.3 68.9 + - - +
249A LYS* 3.4 15.9 + - - +
250A GLU* 4.0 3.1 + - - +
287A ALA* 4.7 12.9 - - + +
295A VAL* 5.8 8.1 - - + -
297A VAL* 6.0 2.5 - - + -
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Residues in contact with ALA 247 (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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236A LEU* 3.1 44.1 - - + +
237A VAL 5.0 0.4 - - - +
243A ALA 2.6 22.8 + - - +
244A LEU* 3.1 11.0 - - - +
246A VAL* 1.3 74.6 - - - +
248A ASN* 1.3 65.3 + - - +
250A GLU* 2.9 22.9 + - - +
251A HIS 4.1 1.0 + - - -
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Residues in contact with ASN 248 (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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220A LEU* 4.5 10.4 - - + +
227A PHE* 4.2 16.8 - - + -
230A LEU* 4.0 24.2 - - + -
236A LEU* 4.0 8.2 - - - +
244A LEU 2.9 11.7 + - - +
245A SER 3.4 8.5 + - - +
247A ALA* 1.3 76.5 - - - +
249A LYS* 1.3 61.7 + - - +
250A GLU 3.0 1.6 + - - -
251A HIS* 3.0 24.9 + - + +
252A ALA* 3.6 4.5 + - - +
275A VAL* 4.5 4.6 - - + +
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Residues in contact with LYS 249 (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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245A SER 3.4 5.9 + - - +
246A VAL* 3.4 12.7 + - - +
247A ALA 2.9 2.4 + - - -
248A ASN* 1.3 77.5 - - - +
250A GLU* 1.3 61.5 + - - +
252A ALA* 3.5 7.6 + - + +
253A VAL* 3.1 23.4 + - - +
273A LYS* 5.5 8.6 - - + +
275A VAL* 3.8 24.4 - - + +
287A ALA* 5.0 9.0 - - + +
288A GLU 6.4 0.2 - - - -
289A GLN* 6.0 6.7 - - + +
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Residues in contact with GLU 250 (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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215A LEU* 4.7 1.6 - - - +
236A LEU* 6.1 2.7 - - + -
246A VAL 4.0 3.4 + - - +
247A ALA* 2.9 13.5 + - - +
249A LYS* 1.3 72.7 - - - +
251A HIS* 1.3 62.3 + - - +
252A ALA 3.0 2.5 - - - -
253A VAL* 2.8 30.7 + - - +
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Residues in contact with HIS 251 (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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211A GLN* 4.8 4.4 - - + +
214A LEU* 4.0 28.8 - - + +
215A LEU* 2.8 31.1 + - - +
220A LEU* 6.0 0.4 - - + -
230A LEU* 6.0 2.2 - - + -
234A HIS* 6.0 5.8 - - + +
236A LEU* 6.1 5.0 - - + +
247A ALA 4.1 1.0 + - - -
248A ASN* 3.0 18.3 + - + +
250A GLU* 1.3 78.7 - - - +
252A ALA* 1.3 56.0 + - + +
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Residues in contact with ALA 252 (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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214A LEU* 3.6 23.8 - - + +
215A LEU* 3.8 8.8 - - - +
217A THR* 4.2 6.3 - - - +
220A LEU* 6.1 4.3 - - + -
248A ASN 3.6 4.7 + - - +
249A LYS* 3.5 12.3 + - + +
250A GLU 3.0 0.6 - - - -
251A HIS* 1.3 80.9 - - + +
253A VAL* 1.3 66.4 + - - +
273A LYS* 3.0 42.5 + - + -
275A VAL* 5.5 6.3 - - + -
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Residues in contact with VAL 253 (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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215A LEU* 4.5 11.0 - - - +
249A LYS 3.1 17.9 + - - +
250A GLU* 2.8 18.8 + - - +
252A ALA* 1.3 83.5 - - - +
273A LYS* 5.0 9.3 - - + +
289A GLN* 4.3 25.1 - - - +
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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