Contacts of the helix formed by residues 1543 - 1551 (chain C) in PDB entry 3B13
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 PHE1543 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1502C MET* 4.1 19.1 - - + -
1534C ILE 6.1 0.4 - - - -
1542C GLY* 1.3 67.0 - - - -
1544C ALA* 1.3 70.4 + - + +
1545C LYS 2.9 2.5 - - - -
1546C TYR* 2.9 39.0 + - + +
1547C GLU* 3.0 36.5 + - - +
1573C ILE* 3.5 41.5 - - + -
1576C GLN* 3.7 25.6 - - + -
1577C ILE* 5.6 1.6 - - + -
1609C LEU* 3.9 21.8 - - + -
1613C VAL* 3.8 20.9 - - + -
36D VAL* 3.6 3.4 - - - +
37D PHE* 4.0 5.2 - + - -
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Residues in contact with ALA1544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1541C GLY 3.8 13.9 - - - +
1542C GLY 2.9 0.8 + - - -
1543C PHE* 1.3 83.3 - - + +
1545C LYS* 1.3 55.9 + - - +
1547C GLU* 3.3 20.8 + - - +
1548C LYS* 2.9 51.5 + - - +
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Residues in contact with LYS1545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1456C GLU* 3.1 31.7 + - - +
1457C ASN* 2.8 47.9 + - - +
1458C GLU* 5.1 0.4 - - - +
1459C PHE* 3.8 25.1 - - + -
1540C MET 4.1 17.9 - - - +
1541C GLY* 4.4 10.3 - - - +
1542C GLY 3.1 13.9 + - - +
1543C PHE 2.9 0.6 - - - -
1544C ALA* 1.3 76.4 - - - +
1546C TYR* 1.3 66.6 + - - +
1548C LYS* 3.2 22.9 + - - +
1549C ALA* 2.9 10.3 + - - +
36D VAL* 4.5 2.2 - - + -
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Residues in contact with TYR1546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1459C PHE* 4.2 22.0 - + + -
1494C PRO 5.4 0.4 - - - -
1497C ASN* 5.5 2.5 + - - -
1498C ALA* 3.4 34.6 - - + -
1501C THR* 3.4 28.9 + - - +
1502C MET* 3.9 31.2 - - + -
1543C PHE* 2.9 26.4 + - + +
1545C LYS* 1.3 78.8 - - - +
1547C GLU* 1.3 56.7 + - + +
1549C ALA 3.1 0.7 + - - -
1550C PHE* 2.9 47.8 + + + +
1551C PHE* 4.2 2.7 + - - -
1569C LEU* 4.0 18.8 - - + -
1573C ILE* 5.5 1.6 - - + -
35D THR* 5.1 0.5 - - - -
36D VAL* 3.4 29.6 + - + +
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Residues in contact with GLU1547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1543C PHE* 3.0 41.9 + - + +
1544C ALA* 3.4 18.3 - - - +
1546C TYR* 1.3 76.3 - - - +
1548C LYS* 1.3 62.9 + - + +
1549C ALA 3.1 0.9 + - - -
1551C PHE* 3.2 43.3 + - + +
1552C THR* 4.2 0.9 + - - +
1573C ILE* 4.6 1.6 - - + -
1616C GLU* 5.5 0.7 - - - +
1617C TYR* 3.1 36.4 + - + +
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Residues in contact with LYS1548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1457C ASN* 4.0 9.6 + - + +
1541C GLY 5.8 0.2 + - - -
1544C ALA* 2.9 37.7 + - - +
1545C LYS* 3.2 26.3 + - - +
1547C GLU* 1.3 76.8 - - + +
1549C ALA* 1.3 59.6 + - - +
1552C THR* 3.5 20.5 - - - +
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Residues in contact with ALA1549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1457C ASN* 3.6 12.1 - - - +
1459C PHE 5.2 0.7 - - - -
1460C ALA* 3.8 24.0 - - + +
1545C LYS 2.9 16.2 + - - +
1546C TYR 3.6 2.5 - - - +
1547C GLU 3.0 0.2 - - - -
1548C LYS* 1.3 82.2 - - - +
1550C PHE* 1.3 83.5 + - + +
1551C PHE 3.6 0.2 - - - -
1552C THR* 3.8 12.2 + - - +
1555C TYR* 3.9 10.9 - - - +
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Residues in contact with PHE1550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1459C PHE 4.0 9.0 - - - -
1460C ALA* 4.6 4.7 - - + -
1494C PRO* 3.7 33.0 - - + -
1495C LEU* 3.7 26.7 - - + -
1498C ALA* 3.7 22.7 - - + -
1546C TYR* 2.9 37.7 + + - +
1549C ALA* 1.3 89.1 - - + +
1551C PHE* 1.3 67.4 + - + +
1552C THR 3.5 3.4 - - - +
1555C TYR* 3.3 50.2 - + + +
1556C VAL* 4.1 3.6 - - - +
1566C LEU* 3.6 23.1 - - + +
1569C LEU* 3.9 8.3 - - + -
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Residues in contact with PHE1551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1546C TYR 5.3 0.2 - - - -
1547C GLU* 3.2 32.3 + - + +
1550C PHE* 1.3 82.9 - - + +
1552C THR* 1.3 64.3 + - - +
1553C GLU* 3.7 1.4 + - - -
1556C VAL* 4.8 4.7 - - + +
1566C LEU* 3.4 33.2 - - + -
1569C LEU* 3.8 27.8 - - + -
1570C LYS* 3.5 39.3 - - + +
1573C ILE* 4.1 11.4 - - + -
1617C TYR* 3.4 31.0 - + - -
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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