Contacts of the strand formed by residues 284 - 289 (chain B) in PDB entry 4KPE
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 284 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B ILE* 4.9 4.5 - - + +
275B VAL* 4.4 23.6 - - + -
276B ARG* 3.3 48.3 - - + +
281B VAL* 4.6 8.6 + - + +
283B GLY* 1.3 78.2 - - - +
285B ALA* 1.3 61.0 + - - +
286B GLU 4.1 5.2 - - - +
287B VAL* 4.2 6.7 - - + -
300B ILE* 4.1 23.8 - - + -
301B GLU 4.1 1.8 - - - +
302B LEU* 3.9 5.8 - - + -
303B LYS* 3.5 14.3 - - - +
311B VAL* 3.7 33.2 - - + -
315B LEU* 4.4 10.8 - - + -
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ARG* 3.4 14.5 + - - -
283B GLY 3.6 2.6 + - - -
284B ILE* 1.3 72.8 - - - +
286B GLU* 1.3 60.9 + - + +
301B GLU* 2.7 35.9 + - + +
302B LEU 3.5 19.1 - - - +
303B LYS* 4.0 13.7 - - + +
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Residues in contact with GLU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B ARG* 4.0 7.8 - - - +
284B ILE* 3.8 1.9 - - - +
285B ALA* 1.3 84.3 - - + +
287B VAL* 1.3 75.2 + - - +
288B ARG* 3.3 40.2 + - + +
299B ALA 4.1 0.9 - - - +
300B ILE* 3.9 0.5 - - - -
301B GLU* 3.1 35.7 + - + +
420C GLN* 5.4 3.8 - - - +
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B VAL* 3.8 28.5 - - + +
272B ILE* 3.7 31.4 - - + -
273B ASP* 3.9 34.7 + - + +
276B ARG* 4.5 0.2 - - - +
284B ILE* 4.2 10.1 - - + -
286B GLU* 1.3 82.8 - - - +
288B ARG* 1.3 69.9 + - - +
298B ILE* 4.4 10.8 - - + -
299B ALA 3.9 7.4 - - - +
300B ILE* 4.2 13.7 - - + -
420C GLN* 5.1 0.9 + - - -
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Residues in contact with ARG 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B GLN* 3.2 21.8 + - - +
286B GLU* 3.3 36.9 + - + +
287B VAL* 1.3 81.6 - - - +
289B ASP* 1.3 61.4 + - - +
290B GLU* 2.1 48.3 + - + +
297B ARG* 5.0 0.4 - - - +
298B ILE* 3.6 2.6 - - - -
299B ALA* 3.0 41.8 + - - +
301B GLU* 2.5 37.2 + - - +
420C GLN* 4.0 24.0 - - + +
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Residues in contact with ASP 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ASP* 4.2 4.3 - - - +
265B LYS* 2.9 34.7 - - - +
266B ALA* 5.4 1.2 - - - -
269B VAL* 4.1 26.8 - - + +
288B ARG* 1.3 69.7 - - - +
290B GLU* 1.3 58.1 + - - +
291B SER* 2.7 27.4 + - - -
297B ARG 3.3 4.1 - - - +
298B ILE* 4.3 5.3 - - - +
420C GLN* 3.5 14.7 + - - +
447C ARG* 3.0 47.6 + - - +
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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