Contacts of the helix formed by residues 1626 - 1641 (chain A) in PDB entry 5V7W
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 ASP1626 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1622A LEU* 4.2 13.7 - - + +
1623A LEU* 2.7 28.6 + - + +
1625A SER* 1.3 78.2 + - - +
1627A PRO* 1.4 91.6 - - - +
1628A GLU* 2.9 28.7 + - - +
1629A TYR* 3.0 9.0 + - + +
1630A ASN* 3.0 23.7 + - - -
1650A ARG* 5.4 0.2 + - - -
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Residues in contact with PRO1627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1625A SER 3.7 7.4 - - - +
1626A ASP* 1.4 91.6 - - - +
1628A GLU* 1.3 50.7 + - - +
1630A ASN* 3.2 15.6 + - + +
1631A THR* 2.7 38.9 + - - +
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Residues in contact with GLU1628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1622A LEU* 3.7 8.2 - - + +
1626A ASP* 2.9 18.7 + - - +
1627A PRO* 1.3 74.9 - - - +
1629A TYR* 1.3 64.9 + - - +
1631A THR* 3.5 7.4 + - - -
1632A VAL* 3.2 28.1 + - - +
1650A ARG* 2.5 41.3 + - - -
1794A GLU* 5.1 0.3 - - - +
1795A TYR* 2.5 40.7 + - + +
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Residues in contact with TYR1629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1622A LEU* 3.6 36.3 - - + +
1623A LEU 3.2 18.2 - - - +
1624A PRO* 3.6 42.5 - - + +
1626A ASP* 3.0 5.7 + - - +
1628A GLU* 1.3 75.8 - - - +
1630A ASN* 1.3 63.7 + - - +
1632A VAL* 3.3 3.4 + - - +
1633A ALA* 2.8 45.7 + - + -
1645A ILE* 3.2 30.4 + - + +
1646A GLU 5.5 0.3 + - - -
1647A LYS* 4.8 3.5 - - - -
1648A ILE* 3.6 38.0 - - + +
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Residues in contact with ASN1630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1624A PRO 3.1 22.3 + - - +
1625A SER* 4.5 4.4 + - - +
1626A ASP 3.0 17.0 + - - -
1627A PRO* 3.2 17.9 + - + +
1629A TYR* 1.3 79.3 - - - +
1631A THR* 1.3 54.7 + - - +
1633A ALA* 3.7 3.4 - - - +
1634A SER* 2.5 42.9 + - - +
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Residues in contact with THR1631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1627A PRO* 2.7 22.7 + - - +
1628A GLU* 3.7 9.0 - - - -
1630A ASN* 1.3 78.9 - - - +
1632A VAL* 1.3 65.2 + - + +
1634A SER* 3.5 6.8 + - - -
1635A LYS* 3.5 17.8 + - - +
1740A TYR* 5.6 2.8 - - + -
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Residues in contact with VAL1632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1628A GLU* 3.2 15.2 + - + +
1629A TYR* 3.3 6.4 + - - +
1631A THR* 1.3 78.0 - - + +
1633A ALA* 1.3 62.8 + - - +
1635A LYS* 3.3 5.0 + - - +
1636A PHE* 3.1 20.3 + - - +
1648A ILE* 4.2 18.6 - - + -
1681A PHE* 5.4 0.5 - - - -
1740A TYR* 3.8 28.2 - - + -
1795A TYR* 3.7 41.7 - - + +
1797A ILE* 3.8 24.9 - - + +
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Residues in contact with ALA1633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1629A TYR* 2.8 43.2 + - + +
1630A ASN* 3.7 4.7 - - - +
1632A VAL* 1.3 73.3 - - - +
1634A SER* 1.3 53.3 + - - +
1636A PHE* 3.1 9.1 + - - +
1637A ASN* 2.7 50.9 + - - +
1645A ILE* 4.3 8.5 - - + -
1648A ILE* 4.2 5.5 - - + +
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Residues in contact with SER1634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1630A ASN* 2.5 30.7 + - - +
1631A THR* 3.6 7.5 - - - -
1632A VAL 3.3 0.2 - - - -
1633A ALA* 1.3 72.7 - - - +
1635A LYS* 1.3 63.5 + - - +
1637A ASN* 3.3 7.6 + - - +
1638A GLN* 3.1 24.2 + - - +
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Residues in contact with LYS1635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1631A THR 3.5 7.5 + - - +
1632A VAL 3.3 7.3 + - - +
1633A ALA 3.3 0.4 - - - -
1634A SER* 1.3 79.8 - - - +
1636A PHE* 1.3 63.1 + - - +
1638A GLN* 3.3 53.5 + - - +
1639A THR* 4.5 0.7 + - - +
1679A GLN 5.2 6.2 + - - -
1681A PHE* 3.7 19.5 - - + -
1717A VAL* 4.2 25.5 + - - +
1718A ASN* 5.3 3.1 + - - +
1719A ALA* 4.8 1.6 + - - +
1740A TYR* 3.4 28.6 + - + +
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Residues in contact with PHE1636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1632A VAL 3.1 12.7 + - - +
1633A ALA* 3.1 11.0 + - - +
1635A LYS* 1.3 79.8 - - - +
1637A ASN* 1.3 68.6 + - - +
1638A GLN 3.0 5.4 + - - -
1639A THR 3.3 2.8 + - - -
1640A CYS* 3.1 55.4 + - + +
1643A PHE* 4.3 5.8 - - + -
1645A ILE* 3.7 24.7 - - + -
1681A PHE* 4.1 11.2 - + + -
1719A ALA* 3.8 20.6 - - + +
1723A ALA* 5.8 0.2 - - + -
1738A VAL* 4.8 7.2 - - + -
1797A ILE* 3.8 33.2 - - + -
1799A PHE* 3.9 40.4 - + - -
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Residues in contact with ASN1637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1633A ALA* 2.7 35.1 + - - +
1634A SER* 3.3 7.0 + - - +
1636A PHE* 1.3 84.5 - - - +
1638A GLN* 1.3 63.0 + - - +
1639A THR 3.1 2.8 + - - -
1640A CYS 3.6 9.9 - - - +
1641A SER* 3.4 38.0 + - - +
1643A PHE 4.7 3.1 - - - +
1645A ILE* 4.1 8.2 - - - +
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Residues in contact with GLN1638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1634A SER 3.1 15.7 + - - +
1635A LYS* 3.3 49.4 + - - +
1636A PHE 3.0 1.2 + - - -
1637A ASN* 1.3 78.0 - - - +
1639A THR* 1.3 68.6 + - + +
1718A ASN* 4.8 6.9 - - - +
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Residues in contact with THR1639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1635A LYS 5.2 0.6 + - - +
1636A PHE 3.3 1.0 + - - -
1638A GLN* 1.3 88.7 - - + +
1640A CYS* 1.3 60.0 + - - +
1641A SER* 3.8 2.5 - - - -
1642A HIS* 3.2 18.5 - - - -
1718A ASN* 3.8 32.1 - - + +
1719A ALA* 3.3 11.7 + - - +
1720A ASN* 2.8 52.0 + - - +
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Residues in contact with CYS1640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1636A PHE* 3.1 33.7 + - + +
1637A ASN* 3.6 10.7 - - - +
1639A THR* 1.3 79.1 - - - +
1641A SER* 1.3 60.7 + - - +
1642A HIS* 3.0 11.9 - - - -
1643A PHE* 3.1 34.8 + - + +
1719A ALA* 3.7 12.3 - - - -
1720A ASN* 3.4 39.7 - - - -
1723A ALA* 4.0 6.7 - - - -
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Residues in contact with SER1641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1637A ASN* 3.4 36.3 + - - -
1639A THR 3.8 1.3 - - - -
1640A CYS* 1.3 76.0 - - - +
1642A HIS* 1.3 60.7 + - - +
1643A PHE 3.3 8.4 + - - +
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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