Contacts of the strand formed by residues 223 - 229 (chain C) in PDB entry 2K03
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 VAL 223 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B TYR* 3.3 32.4 - - + +
108B THR 4.8 0.2 + - - -
218C VAL* 4.9 0.2 - - + -
219C ALA 3.5 16.8 - - - +
220C ARG 3.2 19.1 - - - +
221C ALA 3.9 5.7 - - - +
222C ASN* 1.3 83.3 - - - +
224C LYS* 1.3 60.2 + - - +
225C HIS 4.0 13.0 - - - +
226C LEU* 4.7 8.1 - - + -
240C ALA* 3.5 31.4 - - + -
241C ARG 3.5 4.9 - - - -
242C LEU* 4.0 9.9 - - + +
243C LYS* 4.2 5.2 - - - +
251C ILE* 4.8 2.7 - - + -
257C TRP* 4.1 14.8 - - + -
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Residues in contact with LYS 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 3.8 11.7 - - + +
107B TYR* 3.3 22.9 - - - +
108B THR 4.5 13.9 - - - +
110B ASP* 2.7 29.4 + - + +
111B ASN* 3.3 32.0 - - + +
112B TYR* 5.8 1.1 - - + +
223C VAL* 1.3 76.1 - - - +
225C HIS* 1.3 71.1 + - - +
241C ARG* 2.7 37.8 + - + +
242C LEU 2.9 26.7 + - - +
243C LYS* 3.7 13.5 - - + +
244C ASN 2.9 18.0 + - - +
245C ASN* 4.5 6.1 + - - -
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Residues in contact with HIS 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS* 3.6 25.6 - - + +
28A ILE 3.3 14.6 - - - +
29A LEU* 3.3 23.4 - - + +
107B TYR* 5.1 4.9 - - - -
111B ASN* 2.9 29.2 + - - -
112B TYR* 4.7 5.3 - + - +
223C VAL* 3.5 5.9 - - - +
224C LYS* 1.3 86.6 - - - +
226C LEU* 1.3 84.7 + - - +
227C LYS* 4.0 17.2 - - + +
239C VAL 5.0 0.9 - - - -
240C ALA* 3.4 26.9 - - - +
241C ARG* 3.6 16.2 + - + +
261C TYR* 5.4 1.6 - - - -
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Residues in contact with LEU 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU 3.9 0.2 - - - +
27A LYS* 3.2 3.3 - - - -
28A ILE* 2.7 50.0 + - + +
223C VAL* 4.7 5.2 - - + -
225C HIS* 1.3 87.8 - - - +
227C LYS* 1.3 59.7 + - - +
228C ILE* 4.1 2.9 - - + -
238C ILE* 3.7 28.3 - - + -
239C VAL 3.9 1.3 - - - -
240C ALA* 4.3 11.2 - - + -
251C ILE* 4.8 0.7 - - + -
257C TRP* 4.2 13.0 - - + -
258C ILE* 3.8 25.4 - - + -
261C TYR* 3.5 48.2 + - + +
262C LEU* 5.2 1.6 - - + -
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Residues in contact with LYS 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A HIS* 3.6 32.1 - - + +
26A LEU 3.2 4.9 - - - +
27A LYS* 4.3 3.1 - - + +
225C HIS* 4.3 17.3 - - + +
226C LEU* 1.3 73.5 - - - +
228C ILE* 1.3 58.9 + - - +
229C LEU* 3.5 14.1 - - + -
238C ILE* 4.1 0.2 - - - +
239C VAL* 2.6 57.1 + - - +
240C ALA 6.4 0.2 - - - -
241C ARG* 6.2 5.2 - - - +
248C GLN* 2.8 31.1 + - - +
312D TYR* 2.9 30.3 + - + -
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Residues in contact with ILE 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A HIS* 3.2 7.1 - - - +
26A LEU* 2.7 45.0 + - + +
28A ILE* 3.6 31.6 - - + -
61A TYR* 3.6 23.1 + - + -
62A LEU* 4.9 4.5 - - + -
65A CYS* 5.4 1.8 - - + -
226C LEU* 4.8 1.3 - - + -
227C LYS* 1.3 78.6 - - - +
229C LEU* 1.3 64.9 + - - +
236C CYS* 3.5 31.0 - - - -
237C GLN 3.5 7.0 - - - +
238C ILE* 3.7 30.1 - - + -
262C LEU* 4.5 9.9 - - + -
307D TYR* 3.4 2.6 + - - -
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Residues in contact with LEU 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS 3.9 9.2 - - - +
25A HIS* 3.3 25.1 - - + -
210C PRO* 4.3 9.8 - - + +
227C LYS* 3.5 33.4 - - + +
228C ILE* 1.3 72.1 - - - +
230C ASN* 1.3 65.1 + - - +
231C THR* 3.9 4.3 - - + +
237C GLN* 2.9 40.8 + - - +
239C VAL* 4.9 2.2 - - + -
307D TYR* 3.1 4.0 - - + +
309D SER* 4.8 12.6 - - - +
312D TYR* 3.3 58.3 - - + +
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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