Contacts of the strand formed by residues 269 - 273 (chain B) in PDB entry 4PIM
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 LEU 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B ARG* 4.3 25.4 - - + +
26B LEU* 4.5 7.2 - - + -
27B THR* 3.8 29.2 - - + -
262B VAL 3.8 0.5 - - - +
263B ARG* 3.4 4.4 - - - +
264B VAL* 2.8 41.6 + - + +
267B LEU* 3.9 34.5 - - + +
268B ASP* 1.3 77.5 - - - +
270B GLU* 1.3 71.6 + - - +
271B VAL* 3.8 20.4 + - + -
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Residues in contact with GLU 270 (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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261B HIS* 2.6 43.1 + - + +
262B VAL 3.5 1.8 - - - -
263B ARG* 3.1 47.2 + - - +
268B ASP 5.4 1.1 - - - +
269B LEU* 1.3 79.2 - - - +
271B VAL* 1.3 66.3 + - - +
272B ASP* 5.2 1.3 - - - +
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Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.7 31.0 - - + +
27B THR* 5.3 1.3 - - + -
31B LYS* 3.3 31.9 - - + -
260B GLN 4.0 0.2 - - - +
261B HIS* 3.5 5.8 + - - -
262B VAL* 2.7 47.6 + - + +
264B VAL* 5.0 2.0 - - + -
269B LEU* 3.8 29.6 - - + -
270B GLU* 1.3 81.2 - - - +
272B ASP* 1.3 67.0 + - - +
273B PHE* 4.1 11.0 - - + -
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Residues in contact with ASP 272 (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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31B LYS* 3.0 24.6 + - - -
260B GLN 3.5 3.5 - - - +
261B HIS* 2.8 38.5 + - - +
270B GLU 5.2 1.2 - - - +
271B VAL* 1.3 76.2 + - - +
273B PHE* 1.3 65.5 + - - +
277B GLU* 3.8 1.7 - - - +
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Residues in contact with PHE 273 (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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26B LEU* 4.5 3.1 - - + -
31B LYS* 3.3 30.1 - - + -
232B PHE* 3.6 34.1 - + - -
237B PHE* 3.9 23.3 - + - -
254B LEU 5.9 0.2 - - - -
256B ALA* 3.9 19.3 - - + -
259B ALA* 3.3 5.5 - - - +
260B GLN* 2.9 37.8 + - + +
262B VAL* 3.8 19.3 - - + -
271B VAL* 4.1 13.0 - - + -
272B ASP* 1.3 78.3 - - - +
274B ALA* 1.3 60.5 - - - +
277B GLU* 3.4 17.3 - - + +
279B MSE 4.1 25.8 - - + -
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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