Contacts of the strand formed by residues 219 - 223 (chain A) in PDB entry 1K86
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 PHE 219 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A THR 3.9 6.3 - - - -
166A PHE* 3.6 23.8 - - + -
167A ARG* 3.7 13.7 - - - -
168A GLY 4.6 0.7 - - - -
179A LYS* 3.4 24.0 - - + -
181A PHE* 3.6 35.7 - + - -
214A PRO* 3.6 26.5 - - + -
216A GLU* 3.4 36.1 - - + +
217A ALA 3.2 22.5 + - - -
218A ASP* 1.3 80.1 - - - +
220A LEU* 1.3 62.4 + - - +
221A PHE* 4.0 14.6 - + + -
292A VAL 4.3 0.2 - - - +
293A SER* 4.0 0.2 - - - -
294A MET* 2.9 31.2 + - + +
295A LEU* 3.7 2.4 + - - -
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Residues in contact with LEU 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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179A LYS 3.0 7.5 + - - +
180A LEU* 4.3 17.5 - - + -
181A PHE* 2.9 28.6 + - - +
182A PHE* 5.4 4.0 - - + -
219A PHE* 1.3 77.1 - - - +
221A PHE* 1.3 79.4 + - - +
222A ALA* 4.4 3.4 - - + +
258A ILE* 4.3 12.1 - - + -
259A MET* 4.1 17.7 - - - -
262A LEU* 3.9 20.6 - - + -
291A VAL* 4.4 1.3 - - + -
292A VAL 3.3 10.3 - - - +
293A SER* 3.9 13.5 - - - -
295A LEU* 3.4 36.6 - - + -
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Residues in contact with PHE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 4.6 2.9 - - + -
163A THR* 3.7 19.5 - - + -
181A PHE* 3.3 22.4 - + + +
183A ILE* 4.1 7.9 - - + -
212A LYS 4.4 0.9 - - - -
213A ILE* 2.8 31.0 - - + -
214A PRO* 2.9 31.0 - - + -
219A PHE* 4.0 16.2 - + + -
220A LEU* 1.3 80.1 - - - +
222A ALA* 1.3 60.8 + - - +
223A TYR* 3.5 35.0 - - + -
290A CYS 4.3 0.4 - - - -
291A VAL* 3.3 8.3 - - - +
292A VAL* 2.7 50.0 + - + +
294A MET* 3.9 13.0 - - + -
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Residues in contact with ALA 222 (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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181A PHE 3.0 6.6 + - - +
182A PHE* 3.6 25.9 - - + -
183A ILE 2.8 28.3 + - - +
220A LEU* 4.7 1.6 - - + -
221A PHE* 1.3 75.3 - - - +
223A TYR* 1.3 61.9 + - - +
224A SER 4.0 0.2 + - - -
241A PHE* 4.2 15.8 - - + -
262A LEU* 4.4 22.0 - - + -
290A CYS 3.4 6.1 - - - -
291A VAL* 4.5 2.7 - - + +
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Residues in contact with TYR 223 (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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148A ASN* 6.4 0.2 - - - -
159A ILE* 4.1 16.3 - - + +
183A ILE* 3.3 35.4 - - + +
185A ALA* 6.4 0.9 - - + -
212A LYS 3.4 20.9 + - - -
213A ILE* 3.9 7.1 - - - +
221A PHE* 3.5 30.8 - - + -
222A ALA* 1.3 74.3 - - - +
224A SER* 1.3 62.5 + - - +
225A THR 4.0 4.4 - - - +
226A VAL* 4.6 11.4 - - - +
227A PRO* 5.6 7.9 - - + -
241A PHE* 4.6 1.8 - - - -
289A PRO* 3.2 6.1 - - - +
290A CYS* 2.8 54.1 + - + +
292A VAL* 4.0 19.5 - - + -
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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
------------------------------------------------------------
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