Contacts of the strand formed by residues 1345 - 1352 (chain F) in PDB entry 5YWB
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 ILE1345 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1343F GLY 3.5 12.1 - - - +
1344F LYS* 1.3 82.0 - - - +
1346F GLN* 1.3 67.4 + - - +
1347F ILE* 5.8 3.8 - - + -
1368F LEU* 3.5 0.7 - - - +
1369F ILE* 2.9 68.4 + - + +
1392F PHE* 3.5 31.6 - - + -
1403F ILE* 6.3 0.7 - - + -
1404F ILE 3.4 7.4 - - - +
1405F ILE* 3.6 33.9 - - + -
1502F ILE* 4.9 15.5 - - + -
1532F THR* 5.2 1.8 - - + -
1534F VAL* 5.1 4.9 - - + -
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Residues in contact with GLN1346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1344F LYS* 4.1 21.1 + - + +
1345F ILE* 1.3 79.2 - - - +
1347F ILE* 1.3 64.6 + - - +
1348F GLN* 4.1 4.2 + - + -
1367F ALA 3.4 11.4 - - - +
1368F LEU* 4.3 11.1 - - + +
1402F ARG 3.9 1.2 - - - +
1403F ILE* 3.8 1.3 - - - +
1404F ILE* 2.9 76.6 + - + +
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Residues in contact with ILE1347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1345F ILE* 5.6 3.6 - - + -
1346F GLN* 1.3 77.3 - - - +
1348F GLN* 1.3 59.9 + - - +
1350F LEU* 3.6 38.6 - - + -
1365F VAL* 4.3 6.3 - - + -
1366F ASN* 3.2 6.1 - - - +
1367F ALA* 2.9 41.7 + - + +
1369F ILE* 6.6 0.2 - - + -
1388F PHE* 3.6 36.3 - - + -
1392F PHE* 4.0 22.4 - - + -
1402F ARG 3.3 13.0 - - - +
1403F ILE* 3.6 21.1 - - + -
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Residues in contact with GLN1348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1346F GLN* 5.3 3.6 + - + +
1347F ILE* 1.3 72.8 - - - +
1349F ASN* 1.3 71.6 + - + +
1350F LEU 3.4 2.4 + - - -
1365F VAL 4.0 0.2 - - - -
1366F ASN* 4.3 14.1 - - - +
1401F GLY* 3.6 0.2 - - - -
1402F ARG* 2.9 67.4 + - + +
1404F ILE* 3.9 21.6 - - + +
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Residues in contact with ASN1349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1348F GLN* 1.3 75.0 - - + +
1350F LEU* 1.3 57.9 + - - +
1351F SER* 5.3 0.3 - - - -
1364F HIS* 4.1 31.5 + - - -
1365F VAL 2.8 16.3 + - - +
1366F ASN* 4.4 8.2 - - - +
1400F GLU* 2.8 14.7 - - - +
1401F GLY* 3.1 9.1 - - - -
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Residues in contact with LEU1350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1347F ILE* 3.6 39.5 - - + -
1348F GLN 4.2 0.9 - - - +
1349F ASN* 1.3 73.3 - - - +
1351F SER* 1.3 77.3 + - - +
1362F LEU* 4.3 18.8 - - + -
1364F HIS 3.5 5.9 + - - -
1365F VAL* 2.8 50.7 + - + +
1388F PHE* 5.4 4.0 - - + +
1391F ALA* 4.7 13.7 - - + -
1399F PHE* 4.2 13.5 - - + -
1400F GLU 3.1 11.7 - - - +
1401F GLY* 4.6 4.3 - - - -
1403F ILE* 4.5 20.0 - - + -
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Residues in contact with SER1351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1349F ASN 5.3 0.4 - - - -
1350F LEU* 1.3 86.1 - - - +
1352F VAL* 1.3 72.0 + - - +
1353F ARG* 4.8 6.8 + - - +
1360F PRO* 4.3 8.1 - - - +
1362F LEU* 2.7 28.8 + - - -
1363F LYS* 4.5 8.0 - - - +
1364F HIS 5.0 1.3 - - - -
1399F PHE* 3.3 4.5 - - - +
1400F GLU* 2.7 41.0 + - - -
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Residues in contact with VAL1352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1350F LEU* 5.5 0.2 - - + -
1351F SER* 1.3 81.6 + - - +
1353F ARG* 1.3 67.8 + - - +
1354F TYR* 5.6 0.9 - - + -
1360F PRO* 3.7 1.0 - - - +
1361F VAL* 2.9 42.5 + - + -
1362F LEU* 3.4 36.9 + - + +
1387F SER* 4.4 8.7 - - - +
1391F ALA* 3.9 18.8 - - + -
1396F VAL* 3.5 34.5 - - + -
1398F MET 4.0 5.4 - - - -
1399F PHE* 4.1 7.0 - - + +
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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