Contacts of the strand formed by residues 1361 - 1369 (chain B) in PDB entry 5FO9
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 PHE1361 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1358B CYS* 3.2 32.9 + - + +
1359B ASN 3.5 2.4 + - - -
1360B LYS* 1.3 98.0 - - + +
1362B ASP* 1.3 69.8 + - - +
1363B LEU* 4.1 4.8 + - + +
1390B THR* 4.4 15.7 - - - +
1391B ARG 3.7 7.2 - - - -
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Residues in contact with ASP1362 (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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1358B CYS 5.3 1.4 - - - +
1360B LYS 5.6 0.8 - - - -
1361B PHE* 1.3 77.0 - - - +
1363B LEU* 1.3 59.5 + - - +
1364B LYS* 5.7 3.4 - - + -
1389B CYS 4.4 0.2 - - - -
1390B THR* 3.1 11.5 + - - -
1391B ARG* 2.4 82.4 + - + +
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Residues in contact with LEU1363 (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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1358B CYS* 5.7 7.4 - - - +
1361B PHE* 4.1 7.0 + - + +
1362B ASP* 1.3 74.9 - - - +
1364B LYS* 1.3 66.1 + - - +
1365B VAL* 4.2 17.6 + - + +
1388B ILE* 3.7 25.4 - - + -
1389B CYS 3.3 14.8 - - - +
1390B THR* 4.0 12.8 - - - +
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Residues in contact with LYS1364 (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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1362B ASP* 5.7 2.7 - - + -
1363B LEU* 1.3 78.1 - - - +
1365B VAL* 1.3 62.8 + - - +
1366B THR* 4.2 4.0 - - - +
1387B GLU 3.5 3.5 - - - +
1388B ILE* 3.6 1.7 - - - +
1389B CYS* 2.9 57.5 + - + +
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Residues in contact with VAL1365 (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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1363B LEU* 4.2 25.3 + - + +
1364B LYS* 1.3 76.0 - - - +
1366B THR* 1.3 67.6 + - - +
1367B ILE* 5.1 3.1 - - + +
1386B LEU* 3.8 24.5 - - + -
1387B GLU 3.4 4.7 - - - +
1388B ILE* 5.0 11.0 - - + -
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Residues in contact with THR1366 (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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1364B LYS* 4.2 4.9 + - - +
1365B VAL* 1.3 78.4 + - - +
1367B ILE* 1.3 61.0 + - - +
1368B LYS* 3.6 39.7 - - + +
1385B ILE 3.3 3.8 - - - +
1386B LEU* 4.3 1.8 - - - -
1387B GLU* 2.9 59.4 + - - +
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Residues in contact with ILE1367 (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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1365B VAL* 4.3 3.1 - - + +
1366B THR* 1.3 73.6 - - - +
1368B LYS* 1.3 65.1 + - - +
1369B PRO* 4.5 0.7 - - - +
1384B MET* 3.6 41.4 - - + +
1385B ILE 3.3 24.0 - - - +
1386B LEU* 3.6 25.8 - - + +
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Residues in contact with LYS1368 (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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1366B THR* 3.6 26.7 + - + +
1367B ILE* 1.3 79.9 + - - +
1369B PRO* 1.3 74.6 - - + +
1370B ALA 3.4 0.2 + - - -
1384B MET* 3.8 4.3 - - - -
1385B ILE* 2.8 39.2 + - + +
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Residues in contact with PRO1369 (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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1367B ILE 4.5 0.7 - - - +
1368B LYS* 1.3 90.4 - - + +
1370B ALA* 1.3 64.0 + - - +
1371B PRO* 3.9 3.6 - - - +
1382B ASN* 5.5 2.0 - - - +
1383B THR 3.9 7.9 - - - +
1384B MET* 3.6 22.6 - - + -
1385B ILE* 5.6 0.4 - - - +
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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