Contacts of the helix formed by residues 1395 - 1400 (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 SER1395 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1292B THR* 3.8 9.9 - - - -
1295B PHE* 4.9 0.2 - - - -
1391B GLY 3.0 11.3 + - - -
1392B VAL* 2.8 14.1 + - - -
1394B GLY* 1.3 72.5 - - - +
1396B ALA* 1.3 63.6 + - - +
1397B PHE 3.0 2.0 - - - -
1398B SER* 2.9 32.5 + - - +
1399B ILE* 3.1 13.8 + - - +
1486B ALA* 4.4 9.4 - - - -
1487B GLY 4.5 1.6 - - - -
1547B VAL 4.2 0.2 + - - -
1548B VAL* 3.4 9.0 - - - +
1549B ASP* 2.8 29.4 + - - -
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Residues in contact with ALA1396 (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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1394B GLY 3.0 1.4 + - - -
1395B SER* 1.3 76.6 - - - +
1397B PHE* 1.3 66.7 + - + +
1399B ILE* 3.3 9.0 + - - +
1400B LEU* 3.1 28.5 + - + +
1417B MET* 4.7 15.7 - - - -
1421B LEU* 4.8 7.2 - - + -
1549B ASP* 3.1 25.9 + - - +
1551B GLY 6.0 0.4 - - - -
1552B LEU* 3.8 21.5 - - + -
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Residues in contact with PHE1397 (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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1198B GLY* 3.4 30.5 - - - -
1228B SER* 4.1 12.1 - - - -
1232B TRP* 3.6 19.5 - + - -
1295B PHE* 3.4 22.4 - + + -
1394B GLY* 3.1 14.5 + - - +
1395B SER 3.0 0.4 - - - -
1396B ALA* 1.3 81.8 - - + +
1398B SER* 1.3 58.3 + - - +
1400B LEU 3.6 1.4 - - - +
1401B PHE* 3.1 32.9 + - - -
1404B VAL* 3.7 8.7 - - + +
1417B MET* 3.1 34.3 - - + -
1549B ASP* 4.9 1.1 - - - -
1680B THR* 3.6 20.4 - - + -
1681B PHE* 4.8 1.1 - + - -
1683B PHE* 3.3 31.6 - + + -
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Residues in contact with SER1398 (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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1291B PHE* 3.8 23.9 - - - -
1292B THR* 2.9 12.8 + - - -
1295B PHE* 4.0 19.4 - - - -
1394B GLY 4.3 0.2 + - - -
1395B SER* 2.9 18.5 + - - +
1397B PHE* 1.3 76.6 - - - +
1399B ILE* 1.3 65.3 + - - +
1401B PHE* 3.5 14.1 + - - +
1466B HIS* 5.9 0.2 - - - -
1485B ARG* 2.7 42.2 + - - +
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Residues in contact with ILE1399 (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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1395B SER 3.1 14.5 + - - +
1396B ALA* 3.3 11.4 + - - +
1398B SER* 1.3 80.6 - - - +
1400B LEU* 1.3 72.9 + - + +
1401B PHE 3.4 0.2 - - - -
1402B ASN* 3.3 12.8 - - - +
1424B ILE* 6.5 1.3 - - + -
1428B HIS* 4.8 15.0 - - + +
1429B ILE* 3.6 37.7 - - + -
1485B ARG* 3.5 21.8 - - + +
1486B ALA* 4.3 20.4 - - + +
1548B VAL* 5.2 2.7 - - + -
1552B LEU* 4.4 14.8 - - + -
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Residues in contact with LEU1400 (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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1396B ALA* 3.1 13.3 + - + +
1397B PHE 3.6 4.0 - - - +
1399B ILE* 1.3 94.3 - - + +
1401B PHE* 1.3 62.5 + - - -
1402B ASN* 3.1 6.5 - - - -
1403B ARG* 3.1 14.5 + - + +
1404B VAL* 3.0 14.4 + - + +
1417B MET* 3.8 29.4 - - - +
1420B GLU* 4.2 31.4 - - + +
1421B LEU* 4.7 5.2 - - + +
1424B ILE* 5.3 6.1 - - + -
1681B PHE* 4.0 19.1 - - + -
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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