Contacts of the strand formed by residues 215 - 220 (chain A) in PDB entry 1O6K
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 LEU 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A SER 4.6 1.1 - - - +
204A LEU* 3.6 48.1 + - + +
205A GLN* 3.9 11.0 - - + -
208A ARG* 5.6 3.8 + - - +
213A THR 4.0 1.0 + - - -
214A ALA* 1.3 76.0 - - - +
216A LYS* 1.3 61.1 + - - +
217A TYR 3.4 21.8 - - - +
218A ALA* 3.8 17.3 - - + -
227A PHE* 4.0 18.8 - - + -
228A VAL 3.6 17.0 - - - +
229A MET* 4.1 3.8 - - + -
475A TYR* 3.7 30.8 + - + -
477A ALA* 3.7 14.0 - - - +
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Residues in contact with LYS 216 (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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171A GLU* 5.1 1.1 - - - -
176A ARG* 4.7 12.0 - - - +
178A TYR* 3.8 41.8 + - + +
214A ALA 4.0 1.4 + - - +
215A LEU* 1.3 74.1 - - - +
217A TYR* 1.3 101.6 + - + +
228A VAL* 2.8 17.9 + - + +
229A MET* 5.4 1.1 - - - -
475A TYR* 4.0 2.1 - - - -
476A SER* 3.6 0.7 - - - -
477A ALA* 3.0 50.7 + - + +
479A ILE 4.8 15.0 + - - -
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Residues in contact with TYR 217 (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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147A VAL* 3.6 35.4 - - + -
152A PHE* 3.8 23.6 - + - -
171A GLU* 2.7 38.3 + - - -
174A THR* 5.7 0.9 - - - +
178A TYR* 5.1 0.2 - + - -
215A LEU* 3.4 10.9 - - - +
216A LYS* 1.3 116.7 - - + +
218A ALA* 1.3 59.6 + - - +
219A PHE* 4.2 2.9 - - + -
228A VAL* 2.8 46.4 + - + -
475A TYR* 3.4 6.7 - - - +
476A SER* 3.9 18.6 - - - -
477A ALA 5.0 1.8 - - - -
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Residues in contact with ALA 218 (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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147A VAL* 5.7 0.5 - - - +
201A SER* 4.3 10.5 - - - +
205A GLN* 4.9 0.4 - - - +
215A LEU* 3.8 19.7 - - + -
217A TYR* 1.3 75.9 - - - +
219A PHE* 1.3 61.1 + - - +
226A CYS 3.4 7.4 - - - +
227A PHE* 4.4 4.9 - - + +
473A PHE* 4.3 15.3 - - + -
474A ASP* 3.2 8.6 - - - +
475A TYR* 2.8 43.7 + - + +
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Residues in contact with PHE 219 (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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147A VAL* 3.5 39.5 - - + +
148A THR* 3.7 28.7 - - - -
149A MET* 3.8 12.3 - - - -
152A PHE* 3.9 10.1 - + - -
180A MET* 4.0 13.0 - - + -
217A TYR* 4.5 2.0 - - + -
218A ALA* 1.3 76.6 - - - +
220A GLN* 1.3 74.6 + - - +
221A THR* 4.5 6.1 - - + -
226A CYS* 2.9 61.4 + - + +
228A VAL* 3.7 29.2 - - + -
473A PHE* 3.9 9.6 - - - -
474A ASP* 4.6 12.1 - - - +
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Residues in contact with GLN 220 (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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146A LYS* 6.1 0.5 - - - -
147A VAL 5.4 1.0 - - - +
185A LYS* 3.0 22.0 + - - +
219A PHE* 1.3 84.0 - - - +
221A THR* 1.3 68.6 + - - +
224A ARG 3.5 13.0 - - - +
225A LEU* 3.9 10.5 - - + -
226A CYS* 5.6 0.4 - - - -
469A HIS* 3.5 21.1 + - + +
470A PHE* 2.9 50.3 + - - +
473A PHE* 3.5 10.6 - - + +
474A ASP* 3.3 27.2 + - - +
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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