Contacts of the strand formed by residues 1374 - 1378 (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 LYS1374 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1372F GLY 4.6 6.7 + - - -
1373F GLN* 1.3 80.6 - - - +
1375F ILE* 1.3 68.0 + - - +
1376F GLY 4.3 0.3 + - - -
1525F MET* 4.3 35.7 - - + -
1528F PHE 2.5 29.3 + - - +
1529F ALA* 2.9 26.2 + - - +
1531F ARG 3.0 15.9 + - - +
1533F VAL* 3.6 14.5 - - + +
1535F THR* 6.6 0.2 - - + -
1546F ALA* 4.9 12.3 - - + -
1547F ASP* 4.1 12.1 + - - +
1548F LEU 4.0 12.0 + - - -
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Residues in contact with ILE1375 (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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1369F ILE* 3.6 42.4 - - + -
1373F GLN* 3.5 17.9 - - - +
1374F LYS* 1.3 83.6 - - - +
1376F GLY* 1.3 63.7 + - - +
1532F THR* 4.1 3.6 - - + -
1533F VAL 2.7 15.1 + - - +
1534F VAL* 3.2 13.1 - - + -
1535F THR* 2.9 28.8 + - - +
1546F ALA* 4.7 2.5 - - - -
1548F LEU* 3.5 32.1 - - + +
1550F MET* 3.8 29.6 - - + -
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Residues in contact with GLY1376 (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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1375F ILE* 1.3 72.9 - - - +
1377F ILE* 1.3 66.9 + - - +
1535F THR* 3.8 11.2 - - - -
1543F ILE* 5.0 4.7 - - - -
1546F ALA* 4.1 8.3 - - - +
1548F LEU 2.9 10.7 + - - +
1549F VAL* 3.1 20.4 - - - -
1550F MET* 2.9 25.8 + - - +
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Residues in contact with ILE1377 (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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1376F GLY* 1.3 79.7 - - - +
1378F CYS* 1.3 71.5 + - - +
1385F LYS* 5.0 1.3 - - + -
1388F PHE* 4.0 25.4 - - + -
1534F VAL* 3.6 24.7 - - + -
1535F THR 3.0 9.7 + - - +
1536F ILE* 3.5 37.3 - - + +
1537F ALA 4.3 1.0 + - - +
1543F ILE* 3.3 18.4 - - - +
1550F MET* 3.2 40.2 - - + +
1552F LEU* 4.2 21.5 - - + -
1557F ILE* 5.3 1.6 - - + -
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Residues in contact with CYS1378 (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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1377F ILE* 1.3 79.1 - - - +
1379F GLY* 1.3 59.8 + - - +
1385F LYS* 6.0 3.1 - - - -
1536F ILE* 5.3 2.0 - - - -
1537F ALA 5.6 2.5 - - - +
1543F ILE* 4.1 28.7 - - + -
1549F VAL* 5.0 4.7 - - - -
1550F MET 2.9 18.4 + - - -
1551F VAL* 3.8 17.9 - - + -
1552F LEU* 2.9 29.9 + - - +
1570F LYS* 5.6 4.0 - - - -
1574F PHE 6.2 0.2 - - - -
1575F ALA* 6.4 1.3 - - - -
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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