Contacts of the strand formed by residues 233 - 239 (chain A) in PDB entry 3K3T
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 ARG 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A ARG* 3.2 5.5 - - - +
222A THR* 2.7 53.6 + - - +
223A VAL 5.1 3.6 - - - -
231A LYS* 3.2 53.3 - - - +
232A VAL* 1.3 83.2 - - - +
234A VAL* 1.3 66.7 + - - +
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Residues in contact with VAL 234 (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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219A GLU* 3.9 42.0 - - + +
220A ALA 3.8 4.9 - - - +
221A ARG* 4.5 24.9 - - + +
232A VAL 5.9 0.2 - - - +
233A ARG* 1.3 77.1 - - - +
235A GLU* 1.3 62.4 + - - +
236A ARG* 4.4 1.5 + - + +
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Residues in contact with GLU 235 (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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208A LYS* 3.7 35.8 + - + +
219A GLU* 3.4 5.2 - - - +
220A ALA 3.0 32.4 + - - +
222A THR* 3.9 19.7 + - + +
233A ARG 3.9 1.0 + - - -
234A VAL* 1.3 74.8 - - - +
236A ARG* 1.3 70.7 + - - +
237A PHE* 3.5 34.7 - - + -
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Residues in contact with ARG 236 (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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208A LYS* 3.5 10.6 - - - +
209A ALA* 2.9 35.3 + - - +
210A GLY 5.8 1.8 + - - -
213A TRP 5.9 1.0 + - - -
217A VAL* 3.8 40.9 - - + +
218A VAL 3.9 2.5 - - - -
219A GLU* 4.2 24.2 + - + +
234A VAL* 5.8 1.1 - - + +
235A GLU* 1.3 80.8 + - - +
237A PHE* 1.3 62.2 + - - +
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Residues in contact with PHE 237 (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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193A ILE* 3.7 20.0 - - + -
203A ASN* 3.8 7.6 - - - +
206A ASN* 3.5 30.5 - - + -
207A ILE 3.6 9.6 - - - -
208A LYS* 4.1 10.5 - - + -
209A ALA* 3.6 5.2 - - - +
217A VAL* 3.4 7.4 - - - +
218A VAL* 2.8 45.3 + - + +
220A ALA* 3.7 32.1 - - + -
222A THR* 4.1 13.7 - - + -
235A GLU* 3.5 43.7 - - + -
236A ARG* 1.3 73.4 - - - +
238A ARG* 1.3 61.0 + - - +
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Residues in contact with ARG 238 (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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203A ASN* 2.8 25.1 + - - +
207A ILE* 3.0 27.8 + - - +
208A LYS 3.1 26.4 + - - +
209A ALA* 3.9 2.2 - - - -
210A GLY 5.2 1.0 - - - +
212A ASN* 3.8 24.2 + - - +
213A TRP* 3.5 41.3 - - + +
216A LYS 3.8 4.7 - - - -
218A VAL* 3.6 7.1 - - - +
237A PHE* 1.3 75.7 - - - +
239A ALA* 1.3 58.8 + - - +
240A TYR* 3.4 16.2 - - + +
249A ASP* 2.7 47.0 + - - -
253A LEU* 5.0 18.3 - - - +
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Residues in contact with ALA 239 (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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195A ASN* 4.1 13.9 - - - +
201A SER* 3.7 14.8 - - - -
213A TRP* 3.7 12.0 - - - -
216A LYS* 3.0 44.8 + - + +
217A VAL 4.3 0.9 - - - +
218A VAL* 4.0 17.3 - - + -
238A ARG* 1.3 76.6 - - - +
240A TYR* 1.3 65.1 + - - +
245A GLN* 4.8 0.7 - - - +
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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