Contacts of the helix formed by residues 1548 - 1564 (chain C) in PDB entry 3DQV
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 PRO1548 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1546C SER 4.1 3.6 - - - +
1547C LEU* 1.3 89.6 - - + +
1549C THR* 1.3 67.9 + - - +
1550C GLU* 2.9 15.7 + - + +
1551C LEU* 3.0 27.4 + - + -
1552C GLU* 3.2 6.3 + - - -
1597C THR* 6.2 1.1 - - + -
1600C LEU* 4.2 18.6 - - + -
1601C ALA* 5.5 3.6 - - - -
1604C PHE* 3.2 46.2 - - + -
24R VAL* 5.0 0.2 - - + -
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Residues in contact with THR1549 (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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1547C LEU 3.7 2.0 + - - -
1548C PRO* 1.3 70.2 - - - +
1550C GLU* 1.3 72.4 + - - +
1552C GLU* 3.2 9.5 + - + -
1553C ASP* 2.9 48.2 + - - +
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Residues in contact with GLU1550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1520C ALA* 4.4 26.4 - - - +
1521C LEU* 5.0 7.8 - - + +
1548C PRO* 2.9 18.1 + - + +
1549C THR* 1.3 89.2 + - - +
1551C LEU* 1.3 62.1 + - + +
1553C ASP* 3.6 4.8 + - - +
1554C LEU* 3.5 16.8 + - - +
1604C PHE* 4.3 8.7 - - + -
24R VAL* 3.8 30.1 + - + -
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Residues in contact with LEU1551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1521C LEU* 5.7 2.9 - - + -
1547C LEU* 4.3 14.1 - - + -
1548C PRO* 3.0 17.4 + - + +
1550C GLU* 1.3 76.5 - - - +
1552C GLU* 1.3 66.6 + - - +
1554C LEU* 3.0 22.9 + - + +
1555C ILE* 3.2 19.4 + - + +
1597C THR* 5.0 6.3 - - + -
1600C LEU* 3.4 32.8 - - + -
24R VAL* 5.1 7.2 - - + -
27R TRP* 3.1 60.6 - - + +
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Residues in contact with GLU1552 (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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1547C LEU* 4.3 28.2 + - + +
1548C PRO 3.2 9.8 + - - +
1549C THR* 3.2 14.1 + - + +
1551C LEU* 1.3 79.5 - - - +
1553C ASP* 1.3 61.8 + - - +
1555C ILE* 3.6 11.9 + - + +
1556C PRO* 2.8 27.5 - - - +
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Residues in contact with ASP1553 (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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1520C ALA* 5.1 11.8 - - + +
1549C THR* 2.9 42.0 + - - +
1550C GLU* 4.0 5.1 - - - +
1552C GLU* 1.3 79.7 - - - +
1554C LEU* 1.3 61.3 + - - +
1556C PRO* 3.5 15.2 - - - +
1557C GLU* 3.9 11.1 - - - +
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Residues in contact with LEU1554 (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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1510C PHE* 4.4 6.7 - - + -
1520C ALA* 4.6 11.2 - - + +
1521C LEU* 5.9 1.6 - - + -
1526C VAL* 3.6 43.5 - - + -
1550C GLU 3.5 9.9 + - - +
1551C LEU* 3.0 16.6 + - + +
1553C ASP* 1.3 78.8 - - - +
1555C ILE* 1.3 66.8 + - + +
1557C GLU* 3.0 25.7 + - - +
1558C VAL* 2.9 40.0 + - + +
1573C TRP* 6.2 0.4 - - + -
27R TRP* 4.6 17.7 - - + -
29R ALA* 5.1 6.1 - - + -
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Residues in contact with ILE1555 (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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1547C LEU* 3.3 33.9 - - + -
1551C LEU* 3.4 14.1 - - + +
1552C GLU* 3.8 6.5 - - + +
1554C LEU* 1.3 77.4 - - + +
1556C PRO* 1.3 65.5 - - + +
1558C VAL 3.2 0.5 + - - -
1559C GLU* 2.8 33.9 + - - +
1573C TRP* 3.0 63.6 - - + +
1575C HIS* 4.7 5.6 - - + -
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Residues in contact with PRO1556 (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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1552C GLU 2.8 28.5 - - - +
1553C ASP* 3.5 13.5 - - - +
1554C LEU 3.5 0.4 - - - -
1555C ILE* 1.3 84.9 - - + +
1557C GLU* 1.3 56.9 + - - +
1559C GLU* 2.9 15.2 + - + +
1560C GLU* 2.8 41.6 + - - +
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Residues in contact with GLU1557 (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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1510C PHE* 4.3 14.2 - - + -
1513C MSE 6.2 2.5 - - + -
1514C HIS* 4.1 26.7 + - - -
1520C ALA* 4.4 12.7 - - - +
1553C ASP 3.9 10.1 - - - +
1554C LEU* 3.0 27.0 + - + +
1556C PRO* 1.3 80.1 - - - +
1558C VAL* 1.3 60.9 + - - +
1560C GLU* 3.8 8.4 + - - +
1561C PHE* 3.4 18.4 + - - +
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Residues in contact with VAL1558 (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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1510C PHE* 3.9 6.3 - - + -
1528C ILE* 3.3 41.5 - - + -
1530C ILE* 5.1 2.5 - - + -
1554C LEU* 2.9 42.8 + - + +
1555C ILE 3.6 5.2 - - - +
1557C GLU* 1.3 74.0 - - - +
1559C GLU* 1.3 66.2 + - - +
1560C GLU 3.1 0.2 - - - -
1561C PHE* 3.0 19.8 + - + +
1562C TYR* 3.1 13.2 + - - +
1571C LEU* 4.3 7.6 - - + +
1573C TRP* 3.8 25.6 - - + -
29R ALA* 6.1 0.7 - - + -
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Residues in contact with GLU1559 (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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1555C ILE* 2.8 18.4 + - - +
1556C PRO* 3.1 17.9 - - + +
1558C VAL* 1.3 78.6 - - - +
1560C GLU* 1.3 55.9 + - - +
1562C TYR* 3.7 4.3 + - - +
1563C LYS* 2.8 46.5 + - - +
1570C LYS* 4.5 11.0 - - + +
1571C LEU* 3.3 43.3 + - + +
1573C TRP* 3.7 21.1 + - + -
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Residues in contact with GLU1560 (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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1556C PRO* 2.8 22.8 + - - +
1557C GLU* 4.2 7.5 - - - +
1559C GLU* 1.3 74.5 - - - +
1561C PHE* 1.3 65.1 + - - +
1563C LYS* 3.0 41.9 + - + +
1564C LYS* 3.6 10.9 + - - +
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Residues in contact with PHE1561 (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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1506C LEU* 3.9 31.2 - - + -
1509C ALA* 4.5 5.6 - - + -
1510C PHE* 3.3 62.1 - + + -
1513C MSE 3.8 32.1 - - + -
1528C ILE* 4.6 7.9 - - + -
1530C ILE* 5.8 1.8 - - + -
1557C GLU 3.4 13.3 + - - +
1558C VAL* 3.0 11.8 + - + +
1560C GLU* 1.3 80.3 - - - +
1562C TYR* 1.3 59.6 + + + +
1563C LYS 3.4 0.3 + - - -
1564C LYS* 4.0 17.2 - - - +
1565C ASN* 2.7 45.9 + - - -
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Residues in contact with TYR1562 (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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1506C LEU* 3.6 18.2 - - + -
1530C ILE* 3.3 35.3 - - + +
1558C VAL 3.1 4.9 + - - +
1559C GLU 4.0 3.4 - - - +
1560C GLU 3.3 0.2 - - - -
1561C PHE* 1.3 81.7 - + + +
1563C LYS* 1.3 63.7 + - - +
1564C LYS 3.5 0.2 - - - -
1565C ASN* 3.1 20.5 + - + +
1566C HIS* 3.1 40.0 + + - +
1569C ARG* 3.2 33.5 + - + -
1570C LYS 5.5 0.2 - - - -
1571C LEU* 3.4 40.8 - - + -
33R TRP* 2.7 34.6 - + - -
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Residues in contact with LYS1563 (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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1559C GLU* 2.8 47.5 + - - +
1560C GLU* 3.0 34.2 + - + +
1562C TYR* 1.3 73.8 - - - +
1564C LYS* 1.3 55.7 + - - +
1565C ASN 2.9 10.1 + - - -
1566C HIS 5.2 2.2 - - - -
1567C SER* 3.7 24.7 + - - +
1569C ARG 5.7 6.4 + - - +
1570C LYS* 6.0 4.2 - - - +
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Residues in contact with LYS1564 (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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1513C MSE 3.8 34.2 - - - +
1560C GLU 4.1 7.9 - - - +
1561C PHE* 4.0 17.7 - - - +
1562C TYR 3.5 0.2 - - - -
1563C LYS* 1.3 74.8 - - - +
1565C ASN* 1.3 60.4 + - - +
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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