Contacts of the strand formed by residues 218 - 223 (chain A) in PDB entry 3KJO
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 ILE 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A LEU* 3.9 31.9 - - + -
164A LEU* 4.1 2.9 - - + -
181A LEU 3.7 0.5 - - - +
182A LYS* 3.4 6.2 - - - +
183A VAL* 3.0 52.9 + - + +
189A THR* 3.8 29.4 - - + +
193A SER* 3.5 18.2 - - - +
195A ARG* 3.8 0.7 - - - +
215A ASN 5.1 2.5 - - - +
216A LEU 4.8 0.7 - - - +
217A THR* 1.3 79.0 - - - +
219A ASP* 1.3 64.8 + - - +
220A ILE* 3.8 18.6 - - + -
263A PHE* 3.9 20.6 - - + -
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Residues in contact with ASP 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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180A LEU* 3.7 20.1 - - + +
181A LEU 3.8 3.1 - - - -
182A LYS* 2.7 35.0 + - - +
193A SER* 3.0 7.3 + - - -
194A TRP* 2.8 49.4 + - + +
195A ARG* 2.8 17.3 + - - +
196A VAL* 2.9 29.5 + - + +
218A ILE* 1.3 72.9 - - - +
220A ILE* 1.3 60.6 + - - +
263A PHE* 3.6 10.6 - - - +
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Residues in contact with ILE 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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164A LEU* 4.1 1.1 - - + -
179A PHE 3.6 0.7 - - - +
180A LEU* 3.5 6.1 - - - +
181A LEU* 2.8 45.4 + - + +
183A VAL* 3.6 24.9 - - + -
218A ILE* 3.8 15.0 - - + -
219A ASP* 1.3 77.4 - - - +
221A LEU* 1.3 70.9 + - - +
222A VAL* 3.9 13.4 + - + -
241A ILE* 3.4 31.9 - - + -
244A LEU* 3.6 36.6 - - + -
263A PHE* 3.7 10.5 - - + +
265A LEU* 4.7 1.8 - - + +
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Residues in contact with LEU 221 (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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174A VAL* 3.9 24.9 - - + -
178A SER* 3.9 17.5 - - - +
179A PHE 3.6 13.2 - - - +
180A LEU* 4.2 4.0 - - - +
194A TRP* 3.7 28.2 - - + -
196A VAL* 3.9 24.5 - - + -
219A ASP 4.1 0.6 - - - -
220A ILE* 1.3 74.3 - - - +
222A VAL* 1.3 62.0 + - - +
223A TYR* 3.2 38.0 - - + +
263A PHE 3.1 7.0 + - - +
264A HIS* 3.5 1.4 - - - -
265A LEU 2.9 23.0 + - - -
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Residues in contact with VAL 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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178A SER* 3.1 6.4 - - - -
179A PHE* 2.9 57.4 + - + +
181A LEU* 4.1 23.3 - - + -
220A ILE* 4.2 8.1 - - + +
221A LEU* 1.3 77.3 - - - +
223A TYR* 1.3 61.5 + - - +
226A HIS* 3.8 23.6 - - + +
227A VAL* 4.0 1.0 - - - +
230A ALA* 3.8 16.2 - - + -
241A ILE* 6.0 0.2 - - + -
265A LEU* 3.6 29.2 - - + -
275A ILE* 4.5 2.9 - - + -
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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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177A ALA* 3.5 8.1 - - + +
178A SER* 3.7 15.0 - - - -
194A TRP* 4.2 0.2 - - - -
221A LEU* 3.2 46.2 - - + +
222A VAL* 1.3 74.7 - - - +
224A ASP* 1.3 72.8 + - - +
225A ASN 3.2 1.2 + - - -
226A HIS* 3.0 24.2 + - - -
227A VAL* 4.1 2.5 - - - -
264A HIS* 2.7 38.9 + - + -
265A LEU 3.2 18.2 + - - -
267A GLY* 4.0 2.6 - - - +
12B G 3.4 75.8 - + + +
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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