Contacts of the helix formed by residues 199 - 206 (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 ALA 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ALA* 4.6 10.5 - - + +
169A TYR* 4.0 15.5 - - + +
197A LEU 2.4 26.8 + - - +
198A SER* 1.3 74.1 - - - +
200A PRO* 1.3 78.1 - - + +
201A PHE* 4.0 24.7 - - + -
202A CYS* 3.0 13.2 + - - -
203A VAL* 3.3 6.4 + - - +
225A GLU* 5.1 0.4 - - - -
226A GLU* 3.8 9.2 - - - -
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Residues in contact with PRO 200 (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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43A ASP* 6.1 0.9 - - - +
44A ALA* 5.8 3.8 - - + +
199A ALA* 1.3 86.4 - - + +
201A PHE* 1.3 51.2 + - - +
203A VAL* 3.0 13.3 - - + +
204A GLU* 2.7 39.6 + - + +
225A GLU* 3.7 29.4 - - + +
226A GLU* 3.8 10.3 - - + -
229A HIS* 4.1 32.5 - - + +
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Residues in contact with PHE 201 (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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44A ALA 3.6 26.0 - - - +
45A THR* 4.2 13.9 - - - -
46A LEU* 3.8 33.2 - - + -
169A TYR* 4.0 26.0 - + - -
172A THR* 4.3 11.0 - - - -
199A ALA* 3.2 9.5 - - + -
200A PRO* 1.3 76.9 - - - +
202A CYS* 1.3 79.4 + - - +
204A GLU* 4.2 6.5 - - - -
205A LEU* 2.7 59.7 + - + +
206A TYR* 4.4 2.7 - - - -
699A ADN 4.7 2.9 - - - -
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Residues in contact with CYS 202 (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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168A ALA* 3.7 17.0 - - + +
169A TYR* 3.8 34.8 - - - -
197A LEU 3.6 9.2 - - - +
198A SER* 3.8 12.6 - - - -
199A ALA* 3.0 12.6 + - - +
201A PHE* 1.3 99.5 - - - +
203A VAL* 1.3 60.7 - - - +
204A GLU 3.1 0.3 + - - -
205A LEU 3.1 0.7 + - - -
206A TYR* 2.7 46.3 + - + +
210A MET* 4.6 2.5 - - - -
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Residues in contact with VAL 203 (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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197A LEU* 4.2 28.5 - - + +
199A ALA 3.3 17.3 - - - +
200A PRO* 3.0 9.6 - - + +
202A CYS* 1.3 76.3 - - - +
204A GLU* 1.3 64.4 + - + +
207A LYS* 4.1 9.7 + - - -
210A MET* 3.5 26.5 - - + +
226A GLU* 4.1 13.7 - - + +
229A HIS* 3.6 13.0 - - + +
230A LEU* 3.4 35.9 - - + +
233A VAL* 4.5 10.5 - - + +
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Residues in contact with GLU 204 (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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200A PRO 2.7 23.3 + - - +
201A PHE* 3.8 7.0 - - - +
202A CYS 3.0 0.2 - - - -
203A VAL* 1.3 79.1 - - - +
205A LEU* 1.3 64.8 + - + +
207A LYS* 3.4 20.3 - - - +
229A HIS* 3.0 39.2 - - + +
232A LYS* 3.2 24.5 + - - +
233A VAL* 3.1 24.1 - - - +
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Residues in contact with LEU 205 (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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46A LEU* 6.1 1.1 - - + -
201A PHE* 2.7 54.0 + - + +
204A GLU* 1.3 78.3 - - + +
206A TYR* 1.3 86.7 + - + +
207A LYS* 2.8 32.4 + - - +
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Residues in contact with TYR 206 (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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46A LEU* 5.2 0.9 - - - +
168A ALA 4.1 6.5 - - - -
171A LEU* 3.0 54.5 - - + -
172A THR* 2.8 45.2 + - - +
175A PRO* 6.2 2.5 - - + -
201A PHE* 4.4 5.6 - + - -
202A CYS* 2.7 31.1 + - + +
203A VAL 4.5 0.7 - - - -
205A LEU* 1.3 102.9 - - + +
207A LYS* 1.3 56.3 + - - +
208A ASP 3.7 1.1 - - - -
209A ALA* 4.1 9.6 - - + +
210A MET* 2.6 39.5 + - + +
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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