Contacts of the strand formed by residues 229 - 234 (chain A) in PDB entry 6EBT
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 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLN 3.4 12.2 + - - +
228A ILE* 1.3 72.3 - - - +
230A LYS* 1.3 62.9 + - - +
241A PRO* 3.7 25.4 - - + -
242A LEU 4.0 3.6 - - - +
243A THR* 4.3 5.2 - - + +
445A ILE* 3.2 18.4 - - - +
446A ASN* 5.6 0.2 - - - -
449A MET* 3.7 24.6 - - + +
503A PRO* 3.9 7.2 - - + -
504A LYS* 3.6 39.9 - - + +
507A LEU* 3.8 23.8 - - + -
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Residues in contact with LYS 230 (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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228A ILE* 4.7 0.9 - - + +
229A ILE* 1.3 75.8 - - - +
231A ILE* 1.3 69.9 + - - +
233A ARG* 5.1 1.8 - - - +
241A PRO* 3.1 7.3 - - - +
242A LEU* 3.0 50.6 + - - +
244A LEU* 3.4 31.2 - - + +
247A GLU* 3.0 42.6 + - - -
345A LEU* 5.2 0.2 - - - -
355A GLU* 2.8 34.5 + - - +
445A ILE* 3.8 18.4 - - + -
449A MET* 3.9 10.8 - - - -
404B GLU* 4.0 4.9 + - - -
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Residues in contact with ILE 231 (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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230A LYS* 1.3 84.1 + - - +
232A GLY* 1.3 70.8 + - - +
233A ARG* 3.9 22.3 + - + +
238A ASP* 4.1 17.3 - - + +
239A ALA 3.2 28.0 - - - +
241A PRO* 4.4 3.1 - - + -
355A GLU* 4.2 3.0 + - - +
448A LEU* 4.3 11.0 - - + +
449A MET* 3.4 27.4 - - + -
452A SER* 3.5 33.2 - - - +
454A MET* 4.5 0.9 - - + -
455A LEU* 4.4 14.8 - - + -
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Residues in contact with GLY 232 (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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230A LYS* 3.7 3.4 + - - -
231A ILE* 1.3 81.5 - - - +
233A ARG* 1.3 59.3 + - - +
239A ALA* 2.8 31.3 + - - -
240A VAL 3.1 23.2 + - - -
241A PRO* 4.1 0.4 - - - +
242A LEU* 4.5 6.9 - - - +
279B VAL* 4.6 1.6 - - - -
404B GLU* 3.3 17.9 - - - -
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Residues in contact with ARG 233 (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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230A LYS* 5.1 3.0 - - - +
231A ILE* 3.9 14.1 + - + +
232A GLY* 1.3 78.3 - - - +
234A THR* 1.3 62.3 + - - +
236A THR* 4.3 17.5 - - - +
237A GLN 3.3 10.8 - - - +
238A ASP* 5.1 6.9 + - - +
239A ALA* 4.2 0.2 - - - +
247A GLU* 5.4 0.4 + - - -
345A LEU* 3.7 15.0 - - - +
353A LEU* 3.8 37.9 + - - +
355A GLU* 2.6 37.3 + - - +
448A LEU* 5.4 7.3 - - - +
402B HIS 4.0 3.3 - - - +
403B PHE* 3.8 35.9 - - + +
404B GLU* 2.8 38.8 + - - +
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Residues in contact with THR 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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233A ARG* 1.3 76.5 - - - +
235A HIS* 1.3 80.8 + - - +
236A THR 3.0 3.1 - - - -
237A GLN* 2.9 24.9 + - - +
238A ASP 4.9 1.0 + - - -
239A ALA* 3.7 13.2 - - + +
188B ASN* 3.9 12.2 + - - +
278B ALA* 3.5 25.1 - - + +
279B VAL* 3.8 17.7 - - + -
404B GLU* 4.1 7.9 - - + -
405B LEU* 4.2 12.6 - - + -
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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