Contacts of the strand formed by residues 1548 - 1553 (chain F) in PDB entry 6BAA
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1373F GLN* 4.7 11.2 - - + -
1374F LYS 2.5 17.0 + - - +
1375F ILE* 3.3 16.3 - - + -
1376F GLY 2.7 28.5 + - - -
1546F ALA* 3.2 11.1 - - - +
1547F ASP* 1.3 76.2 - - - +
1549F VAL* 1.3 57.1 + - - +
1560F PHE* 4.4 10.8 - - + -
1562F LYS* 3.3 23.3 - - + +
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Residues in contact with VAL1549 (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* 3.3 4.9 - - - +
1378F CYS* 6.2 2.9 - - + -
1543F ILE* 5.3 12.3 - - + +
1546F ALA* 5.4 0.9 - - + -
1548F LEU* 1.3 74.5 - - - +
1550F MET* 1.3 60.7 + - - +
1551F VAL* 4.1 1.0 + - + +
1560F PHE* 3.6 8.6 - - - -
1561F ASP* 2.9 44.8 + - + +
1562F LYS* 3.9 1.3 + - - +
1564F GLU* 6.0 4.0 - - - -
1566F LEU* 5.3 15.7 - - + +
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Residues in contact with MET1550 (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* 5.9 1.5 - - + +
1376F GLY 2.4 27.6 + - - +
1377F ILE* 3.3 14.0 - - + -
1378F CYS* 2.5 36.7 + - - +
1549F VAL* 1.3 68.4 - - - +
1551F VAL* 1.3 58.2 + - - +
1552F LEU* 4.3 7.1 - - + +
1557F ILE* 5.7 3.6 - - + -
1559F GLU 4.9 0.2 - - - +
1560F PHE* 3.6 26.2 - - + -
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Residues in contact with VAL1551 (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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1378F CYS* 3.2 5.6 - - - -
1379F GLY* 5.2 0.4 - - - -
1549F VAL* 4.1 1.9 - - + +
1550F MET* 1.3 71.0 - - - +
1552F LEU* 1.3 60.5 + - - +
1557F ILE* 3.3 4.7 - - - -
1558F LEU* 2.9 24.9 + - + -
1559F GLU* 2.8 42.0 + - + +
1569F GLN* 5.9 2.9 - - + -
1571F ASP* 4.6 18.8 - - + -
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Residues in contact with LEU1552 (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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1362F LEU* 6.6 0.2 - - + -
1365F VAL* 5.9 3.6 - - + -
1377F ILE* 3.9 19.1 - - + -
1378F CYS 2.6 23.0 + - - +
1379F GLY* 3.3 21.9 - - - +
1380F ARG* 3.5 13.6 + - + +
1384F GLY* 4.0 10.5 - - - -
1385F LYS* 3.6 37.7 - - + +
1388F PHE* 6.1 3.1 - - + -
1550F MET* 4.3 8.1 - - + +
1551F VAL* 1.3 74.9 - - - +
1553F LYS* 1.3 62.7 + - - +
1555F GLY 5.4 0.4 - - - -
1556F ALA* 3.3 5.2 - - - +
1557F ILE* 3.8 30.3 - - + +
1558F LEU* 4.9 0.4 - - - -
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Residues in contact with LYS1553 (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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1380F ARG* 5.2 1.8 - - - +
1552F LEU* 1.3 76.0 - - - +
1554F ARG* 1.3 65.5 + - + +
1555F GLY 3.2 1.8 - - - -
1556F ALA* 2.5 33.5 + - - +
1558F LEU* 3.7 23.9 - - + +
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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