Contacts of the helix formed by residues 1626 - 1641 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1622B LEU* 4.6 9.7 - - + +
1623B LEU* 2.7 35.2 + - + +
1624B PRO 3.9 1.6 - - - +
1625B SER* 1.3 72.5 + - - +
1627B PRO* 1.3 79.0 - - - +
1628B GLU* 3.0 49.8 + - - +
1629B TYR* 2.9 23.2 + - - +
1630B ASN* 3.8 1.4 + - - +
1650B ARG* 4.9 1.6 + - - -
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Residues in contact with PRO1627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1625B SER 3.5 8.0 - - - +
1626B ASP* 1.3 91.0 - - - +
1628B GLU* 1.3 65.6 + - + +
1630B ASN* 2.9 21.1 + - + +
1631B THR* 3.2 13.1 + - - +
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Residues in contact with GLU1628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1622B LEU* 4.1 11.7 - - + -
1626B ASP* 3.0 20.5 + - - +
1627B PRO* 1.3 79.9 - - + +
1629B TYR* 1.3 62.1 + - - +
1631B THR* 3.1 11.3 + - - -
1632B VAL* 3.0 27.7 + - - +
1650B ARG* 2.7 37.9 + - - -
1795B TYR* 2.7 30.4 + - - +
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Residues in contact with TYR1629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1622B LEU* 3.8 32.5 - - + +
1623B LEU 3.7 11.4 - - - +
1624B PRO* 3.7 43.4 - - + +
1626B ASP* 2.9 14.6 + - - +
1628B GLU* 1.3 78.1 - - - +
1630B ASN* 1.3 54.5 + - - +
1632B VAL 3.4 0.3 + - - -
1633B ALA* 2.8 47.5 + - + +
1645B ILE* 3.7 24.2 + - + +
1646B GLU 5.1 1.6 + - - -
1647B LYS* 5.0 4.3 - - - -
1648B ILE* 3.8 36.8 - - + +
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Residues in contact with ASN1630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1624B PRO 5.2 1.3 + - - +
1626B ASP 3.8 1.5 + - - +
1627B PRO* 2.9 13.4 + - + +
1629B TYR* 1.3 81.9 - - + +
1631B THR* 1.3 55.1 + - - +
1633B ALA* 4.2 5.5 - - - +
1634B SER* 2.7 52.9 + - - -
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Residues in contact with THR1631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1627B PRO 3.2 14.7 + - - -
1628B GLU* 3.1 12.8 + - - -
1630B ASN* 1.3 80.2 + - - +
1632B VAL* 1.3 62.7 + - - +
1634B SER* 3.9 4.9 - - - -
1635B LYS* 3.3 21.7 + - - +
1740B TYR* 5.1 3.7 + - + -
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Residues in contact with VAL1632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1628B GLU 3.0 15.7 + - - +
1629B TYR 3.9 2.9 - - - +
1631B THR* 1.3 75.1 - - - +
1633B ALA* 1.3 60.6 + - - +
1635B LYS* 3.3 2.4 + - - +
1636B PHE* 2.9 28.8 + - - +
1648B ILE* 4.2 16.8 - - + -
1681B PHE* 5.4 0.2 - - - -
1740B TYR* 3.9 27.3 - - + -
1795B TYR* 3.8 40.4 - - + -
1797B ILE* 3.7 31.9 - - + -
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Residues in contact with ALA1633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1629B TYR* 2.8 38.5 + - + +
1630B ASN* 3.8 6.7 - - - +
1632B VAL* 1.3 71.9 - - - +
1634B SER* 1.3 59.2 + - - +
1636B PHE* 3.6 5.2 + - - +
1637B ASN* 2.8 42.0 + - - +
1645B ILE* 4.3 20.0 - - + -
1648B ILE* 4.2 2.8 - - + +
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Residues in contact with SER1634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1630B ASN* 2.7 44.6 + - - -
1631B THR* 3.9 5.6 - - - -
1633B ALA* 1.3 72.6 - - - +
1635B LYS* 1.3 65.9 + - - +
1637B ASN* 3.2 12.9 + - - +
1638B GLN* 3.3 17.1 + - - +
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Residues in contact with LYS1635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1631B THR 3.3 12.8 + - - +
1632B VAL 3.3 6.5 + - - +
1634B SER* 1.3 78.2 - - - +
1636B PHE* 1.3 64.4 + - - +
1638B GLN* 3.0 49.9 + - - +
1639B THR* 4.5 0.5 + - - -
1679B GLN 4.7 6.9 + - - -
1681B PHE* 3.5 22.0 - - + -
1717B VAL* 4.1 27.5 + - - +
1718B ASN* 5.2 2.9 + - - -
1719B ALA* 5.4 0.2 - - - +
1740B TYR* 3.3 31.2 - - + +
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Residues in contact with PHE1636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1632B VAL 2.9 17.7 + - - +
1633B ALA* 3.8 5.2 - - - +
1635B LYS* 1.3 75.7 - - - +
1637B ASN* 1.3 68.9 + - - +
1638B GLN 3.2 0.9 + - - -
1639B THR 3.5 1.9 + - - -
1640B CYS* 3.1 64.2 + - + +
1643B PHE* 4.3 5.8 - - + -
1645B ILE* 3.8 26.7 - - + -
1681B PHE* 3.9 13.1 - + + -
1719B ALA* 3.8 21.7 - - + +
1723B ALA* 5.6 0.2 - - + -
1738B VAL* 5.0 5.4 - - + -
1797B ILE* 3.6 29.4 - - + -
1799B PHE* 4.0 45.5 - + + -
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Residues in contact with ASN1637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1633B ALA* 2.8 33.7 + - - +
1634B SER* 3.8 7.3 - - - +
1635B LYS 3.1 0.6 + - - -
1636B PHE* 1.3 77.4 - - - +
1638B GLN* 1.3 65.1 + - - +
1639B THR 3.1 3.6 + - - -
1640B CYS 3.7 4.7 - - - +
1641B SER* 3.3 46.5 + - - +
1643B PHE 5.1 1.7 - - - +
1645B ILE* 4.6 7.6 - - - +
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Residues in contact with GLN1638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1634B SER* 3.3 11.9 + - - +
1635B LYS* 3.0 47.0 + - - +
1637B ASN* 1.3 77.3 - - - +
1639B THR* 1.3 69.3 + - + +
1718B ASN* 4.8 7.9 - - - +
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Residues in contact with THR1639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1635B LYS 5.4 0.3 + - - -
1636B PHE 3.5 1.2 + - - -
1637B ASN 4.3 0.2 - - - -
1638B GLN* 1.3 85.4 - - + +
1640B CYS* 1.3 62.6 + - - +
1641B SER 3.8 1.8 - - - -
1642B HIS* 3.4 17.7 + - - -
1718B ASN* 3.8 28.0 - - + +
1719B ALA* 3.4 12.6 + - - +
1720B ASN* 3.1 44.2 + - - +
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Residues in contact with CYS1640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1636B PHE* 3.1 45.8 + - + +
1637B ASN* 3.7 5.4 + - - +
1639B THR* 1.3 80.9 - - - +
1641B SER* 1.3 62.5 + - - +
1642B HIS* 3.2 9.0 - - - -
1643B PHE* 3.2 23.2 + - + +
1719B ALA* 3.7 11.2 - - - -
1720B ASN* 3.5 37.9 - - - -
1723B ALA* 3.8 16.8 - - - -
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Residues in contact with SER1641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1637B ASN* 3.3 36.0 + - - -
1639B THR 3.8 1.2 - - - -
1640B CYS* 1.3 77.0 - - - +
1642B HIS* 1.3 61.1 + - - +
1643B PHE 3.2 9.0 - - - +
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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