Contacts of the strand formed by residues 1548 - 1552 (chain H) 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 LEU1548 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1368H LEU* 4.4 18.8 - - + +
1370H SER* 5.1 7.9 - - - +
1373H GLN* 3.3 36.6 - - - +
1374H LYS 4.0 3.0 + - - -
1375H ILE* 3.5 28.1 - - + +
1376H GLY 2.9 24.3 + - - +
1547H ASP* 1.3 80.8 - - + +
1549H VAL* 1.3 60.3 + - - +
1550H MET* 5.6 0.4 - - - -
1559H GLU* 5.5 10.1 - - + +
1560H PHE 3.7 3.8 - - - +
1561H ASP* 3.2 37.9 - - + +
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Residues in contact with VAL1549 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1376H GLY* 3.1 13.9 - - - +
1378H CYS* 5.0 5.4 - - - -
1543H ILE* 3.5 38.6 - - + +
1546H ALA* 3.7 19.3 - - + +
1547H ASP 4.3 2.7 - - - +
1548H LEU* 1.3 76.8 - - - +
1550H MET* 1.3 60.4 + - - +
1551H VAL 4.3 0.6 + - - -
1558H LEU 4.1 0.5 - - - +
1559H GLU* 4.5 0.9 - - - -
1560H PHE* 2.9 39.1 + - + +
1566H LEU* 3.8 34.5 - - + -
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Residues in contact with MET1550 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1367H ALA* 4.0 13.0 - - + -
1369H ILE* 4.4 12.8 - - + -
1375H ILE* 3.8 22.9 - - + -
1376H GLY 2.9 9.3 + - - +
1377H ILE* 3.2 36.3 - - + +
1378H CYS* 2.9 26.9 + - - -
1388H PHE* 4.5 13.2 - - + -
1534H VAL* 5.1 0.2 - - + -
1548H LEU 5.3 0.7 - - - +
1549H VAL* 1.3 73.8 - - - +
1551H VAL* 1.3 59.4 + - - +
1557H ILE* 3.8 22.9 - - + -
1558H LEU 3.1 12.3 - - - +
1559H GLU* 3.6 35.7 - - + +
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Residues in contact with VAL1551 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1378H CYS* 3.6 22.2 - - - +
1379H GLY* 5.0 2.5 - - - -
1549H VAL 4.4 0.4 + - - +
1550H MET* 1.3 71.0 - - - +
1552H LEU* 1.3 75.0 + - - +
1553H LYS* 3.7 10.4 + - + +
1557H ILE* 3.2 4.0 - - - -
1558H LEU* 2.9 44.7 + - + +
1560H PHE* 4.8 4.0 - - + -
1570H LYS* 4.0 27.6 - - - +
1574H PHE* 5.2 14.8 - - + +
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Residues in contact with LEU1552 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1362H LEU* 4.1 20.0 - - + -
1377H ILE* 4.2 13.9 - - + -
1378H CYS 2.9 14.1 + - - +
1379H GLY* 4.0 6.9 - - - -
1380H ARG 4.8 0.9 + - - -
1383H SER* 3.2 25.8 + - - +
1384H GLY* 3.5 9.4 - - - +
1385H LYS* 3.4 40.4 - - + +
1388H PHE* 5.0 6.3 - - + -
1550H MET 3.9 0.6 + - - -
1551H VAL* 1.3 83.7 - - - +
1553H LYS* 1.3 60.6 + - - +
1555H GLY 4.8 1.1 - - - +
1556H ALA 3.2 14.8 - - - +
1557H ILE* 3.6 30.0 - - + +
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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