Contacts of the strand formed by residues 278 - 285 (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 GLU 278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B GLN* 3.0 20.8 + - - +
31B LYS* 4.8 2.1 + - - +
240B VAL* 4.5 0.7 - - - +
242B LYS* 2.7 31.5 + - - -
253B TRP* 3.7 28.0 - - + -
254B LEU 3.4 5.2 - - - +
255B ARG* 2.7 49.6 + - + +
273B PHE* 6.0 0.2 - - - -
276B GLY 3.6 13.9 - - - +
277B GLU* 1.3 83.9 - - - +
279B MSE 1.3 61.6 + - - +
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Residues in contact with MSE 279 (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* 3.6 31.2 - - - -
31B LYS* 3.3 26.5 - - + +
32B SER* 3.7 7.2 - - - +
33B LEU* 4.1 14.6 - - + +
221B LEU* 3.8 29.2 - - + -
232B PHE* 4.7 1.6 - - + -
237B PHE* 4.7 4.5 - - + -
253B TRP* 3.2 6.9 - - - -
254B LEU* 2.8 52.0 + - + +
273B PHE* 4.1 25.8 - - + -
277B GLU 4.3 0.2 + - - -
278B GLU* 1.3 74.4 - - - +
280B LEU* 1.3 65.7 - - - +
281B THR* 3.5 4.1 + - + +
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Residues in contact with LEU 280 (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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30B GLN* 4.7 5.6 - - + +
31B LYS 3.0 13.1 + - - +
32B SER* 3.1 13.4 - - - -
33B LEU 2.9 25.8 + - - +
249B ARG* 6.3 0.4 - - - +
251B GLU* 4.1 10.5 - - + +
252B MSE 3.5 16.2 - - - +
253B TRP* 3.5 40.3 - - + -
279B MSE 1.3 71.9 - - - +
281B THR* 1.3 58.8 + - - +
282B GLU 3.6 17.9 - - - +
283B VAL* 4.1 18.4 - - + -
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Residues in contact with THR 281 (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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33B LEU* 3.3 25.0 - - + +
35B PRO* 3.5 16.4 - - - +
38B PHE* 3.6 14.1 - - - -
217B ASN* 2.7 34.3 + - - +
220B VAL* 4.4 10.3 - - + -
252B MSE 2.9 16.5 + - - +
254B LEU* 3.9 21.1 - - + -
279B MSE 3.5 15.5 + - + +
280B LEU* 1.3 78.1 - - - +
282B GLU* 1.3 63.7 + - - +
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Residues in contact with GLU 282 (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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35B PRO* 3.8 19.7 - - + +
38B PHE* 3.6 25.5 - - + -
39B TYR* 4.6 9.5 + - - -
166B ASN* 3.6 18.0 + - - +
206B TYR* 4.2 9.2 - - - -
216B PHE* 4.7 4.3 - - - -
250B ILE* 6.4 0.2 - - - -
251B GLU* 3.5 2.8 - - - -
252B MSE 2.9 55.6 + - + +
280B LEU* 3.6 7.5 - - - +
281B THR* 1.3 84.3 + - - +
283B VAL* 1.3 76.0 + - - +
284B SER* 4.7 2.4 - - - -
401B ACT 4.1 13.2 - - - +
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Residues in contact with VAL 283 (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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35B PRO* 5.4 1.0 - - - +
165B GLY 4.1 7.2 - - - +
166B ASN* 2.8 52.1 + - - +
168B THR* 3.9 23.1 - - + -
249B ARG* 4.1 26.2 - - - +
250B ILE 3.2 8.3 - - - +
251B GLU* 4.2 9.4 - - + +
280B LEU* 4.1 22.0 - - + -
282B GLU* 1.3 81.3 - - - +
284B SER* 1.3 54.8 + - - +
285B CYS* 4.4 5.8 - - - -
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Residues in contact with SER 284 (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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162B SER* 5.7 0.7 + - - -
165B GLY* 3.6 5.3 - - - -
166B ASN* 4.2 1.8 - - - +
206B TYR* 2.9 27.7 + - - -
249B ARG* 3.4 2.7 - - - -
250B ILE* 2.8 38.8 + - - -
282B GLU* 4.7 2.9 - - - -
283B VAL* 1.3 72.7 - - - +
285B CYS* 1.3 65.5 + - - +
286B LYS* 3.1 16.5 + - - -
401B ACT 2.8 26.5 + - - -
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Residues in contact with CYS 285 (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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165B GLY* 2.8 29.4 + - - +
167B LEU 3.7 6.1 - - - -
168B THR* 4.4 6.3 - - - -
169B PRO* 4.8 2.7 - - - -
172B ARG* 3.6 29.2 - - - +
194B ASP* 4.5 1.7 - - - +
247B GLU 5.3 3.6 - - - +
248B GLU 4.6 1.1 - - - +
249B ARG* 3.6 32.5 - - + -
283B VAL* 4.4 7.2 - - - -
284B SER* 1.3 73.2 + - - +
286B LYS* 1.3 69.5 + - - +
287B PHE* 3.5 19.2 - - + -
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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