Contacts of the strand formed by residues 1345 - 1349 (chain B) in PDB entry 1CJY
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 ASP1345 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1332B LEU* 3.4 3.6 - - - -
1333B HIS* 2.8 51.2 + - + +
1335B LYS* 3.9 10.7 + - - -
1343B PHE 4.1 4.6 - - - +
1344B ALA* 1.3 76.9 - - - +
1346B TRP* 1.3 63.5 + - - +
1356B MET* 4.0 20.6 - - + -
1358B LYS* 3.5 24.9 + - + +
1359B TYR* 3.1 38.2 + - + -
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Residues in contact with TRP1346 (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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1227B LEU* 4.0 14.4 - - + -
1330B THR* 3.1 35.9 - - + +
1331B CYS 3.6 3.1 - - - -
1332B LEU* 3.4 24.6 - - + +
1341B LEU 5.6 0.6 + - - -
1342B MET 5.9 0.8 + - - -
1344B ALA 3.8 11.5 + - - -
1345B ASP* 1.3 74.3 - - - +
1347B VAL* 1.3 61.0 + - - +
1348B GLU* 4.0 1.3 + - - +
1355B GLY 4.1 0.2 - - - +
1356B MET* 4.0 20.1 - - - +
1357B ALA 4.8 1.7 + - - -
1358B LYS* 5.7 1.8 + - - +
1550B SER* 3.4 31.2 - - - -
1553B THR* 4.6 5.2 + - - +
1554B PHE* 3.6 42.5 - + - -
1556B LEU 4.2 0.4 - - - -
1557B PRO* 4.2 3.4 - - + -
1559B PRO* 3.6 35.7 - - + -
1560B LEU* 5.3 0.7 - - + -
1596B TRP* 3.9 26.9 - + + +
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Residues in contact with VAL1347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1330B THR* 2.7 36.3 + - - -
1331B CYS* 2.7 31.9 + - - +
1332B LEU 4.2 0.2 - - - -
1333B HIS* 3.9 27.6 - - + +
1346B TRP* 1.3 75.9 - - - +
1348B GLU* 1.3 60.3 + - - +
1349B PHE* 3.5 21.9 - - + -
1354B ILE* 3.9 16.2 - - + -
1355B GLY* 3.6 12.6 - - - +
1356B MET* 4.4 9.9 - - + -
1368B PHE* 5.2 4.7 - - + -
1492B PHE* 5.7 7.0 - - + -
1547B VAL* 4.6 5.6 - - + -
1560B LEU* 5.0 0.2 - - - -
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Residues in contact with GLU1348 (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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1154B GLU* 4.8 0.2 - - - +
1328B LEU* 5.1 2.0 - - + -
1329B PHE 3.6 4.3 - - - -
1346B TRP 4.0 1.5 + - - +
1347B VAL* 1.3 73.4 - - - +
1349B PHE* 1.3 67.8 + - - +
1350B SER* 5.3 2.6 - - - -
1353B GLU* 4.4 6.9 - - - +
1354B ILE* 3.1 10.0 - - - +
1355B GLY 2.8 36.9 + - - +
1357B ALA* 4.0 11.7 - - + +
1362B PHE* 4.0 12.7 - - + -
1560B LEU* 3.6 21.5 - - + +
1563B ARG* 3.1 28.2 + - - +
1566B ARG* 2.7 39.1 + - - +
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Residues in contact with PHE1349 (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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1312B LEU* 4.2 7.2 - - + -
1328B LEU* 3.3 7.4 - - - +
1329B PHE* 2.7 58.8 + - + +
1330B THR* 3.9 1.1 - - - -
1331B CYS* 3.5 34.3 - - - -
1347B VAL* 3.5 22.2 - - + -
1348B GLU* 1.3 79.8 - - - +
1350B SER* 1.3 61.2 + - - +
1353B GLU 3.6 3.1 - - - -
1354B ILE* 3.6 32.8 - - + -
1368B PHE* 4.2 15.3 - + - -
1389B LEU* 4.2 18.8 - - + -
1392B VAL* 5.3 2.9 - - + -
1393B TRP* 3.5 33.9 - + + -
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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