Contacts of the strand formed by residues 1623 - 1630 (chain A) in PDB entry 3ZQK
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 ILE1623 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1586A SER* 3.8 37.7 - - - +
1590A PHE* 3.9 27.8 - - + -
1602A ASN* 3.9 12.3 - - - +
1604A VAL* 3.8 27.4 - - + -
1618A ARG* 5.3 3.6 + - - -
1619A LEU* 3.9 27.3 - - + +
1620A PRO* 3.1 15.1 + - + +
1621A GLY* 2.9 9.3 - - - +
1622A ASP* 1.3 94.0 - - - +
1624A GLN* 1.3 59.9 + - - +
1625A VAL* 3.7 8.7 + - + +
2676A GOL 5.8 0.2 - - - +
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Residues in contact with GLN1624 (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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1601A PRO* 4.3 12.8 - - - +
1602A ASN 2.9 16.5 + - - +
1603A LEU* 3.5 24.7 - - + +
1604A VAL* 2.9 24.9 + - - +
1618A ARG* 6.2 1.3 - - - +
1621A GLY 4.4 9.4 - - - +
1622A ASP 5.2 1.3 - - - -
1623A ILE* 1.3 75.4 - - - +
1625A VAL* 1.3 61.8 + - - +
1626A VAL* 3.9 4.7 + - + +
1646A ASN* 5.6 5.3 - - - +
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Residues in contact with VAL1625 (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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1582A LEU* 4.3 11.7 - - + -
1604A VAL* 3.7 29.4 - - + -
1606A MET* 4.7 7.4 - - + -
1619A LEU* 4.1 18.6 - - + +
1623A ILE* 3.7 20.0 + - + +
1624A GLN* 1.3 75.1 - - - +
1626A VAL* 1.3 73.9 + - - +
1627A PRO* 3.4 8.9 - - + +
1642A ILE* 3.3 35.9 + - + +
1643A GLY* 3.5 17.7 - - - +
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Residues in contact with VAL1626 (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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1603A LEU* 6.5 0.7 - - + -
1604A VAL 2.8 11.0 + - - +
1605A TYR* 3.5 33.9 - - + +
1606A MET 3.2 18.4 + - - -
1624A GLN* 5.1 5.4 - - + +
1625A VAL* 1.3 76.9 - - - +
1627A PRO* 1.3 67.1 - - + +
1628A ILE* 3.7 2.4 + - + +
1646A ASN* 5.6 4.9 - - + +
1647A ALA 5.2 1.1 - - - +
1649A ILE* 3.6 36.3 - - + +
1668A ARG* 3.7 31.2 - - + +
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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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1606A MET* 3.6 18.2 - - + +
1608A THR* 5.6 0.2 - - + -
1625A VAL* 3.4 11.2 - - + +
1626A VAL* 1.3 86.9 - - - +
1628A ILE* 1.3 61.2 + - - +
1629A GLY 3.9 0.4 - - - -
1639A LEU* 3.4 52.7 - - + +
1642A ILE* 4.1 11.0 - - + -
1643A GLY* 3.9 13.0 - - - +
1647A ALA 5.4 0.9 - - - +
1648A PRO* 3.7 12.4 - - + +
1649A ILE* 3.0 26.0 + - - +
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Residues in contact with ILE1628 (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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1520A PHE* 3.6 33.0 - - + -
1605A TYR* 4.2 14.8 - - + -
1606A MET 2.8 12.5 + - - +
1607A VAL* 3.5 10.5 - - + -
1608A THR* 3.1 24.4 + - - +
1626A VAL 4.0 6.1 - - - +
1627A PRO* 1.3 76.7 - - - +
1629A GLY* 1.3 59.8 + - - +
1630A VAL* 3.7 5.4 + - + +
1639A LEU* 4.6 1.1 - - - -
1649A ILE* 3.2 22.0 - - + +
1651A ILE* 3.8 28.5 - - + -
1657A LEU* 3.8 16.8 - - + -
1661A ALA* 4.8 2.0 - - + -
1665A VAL* 4.0 16.2 - - + -
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Residues in contact with GLY1629 (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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1608A THR 3.5 5.2 - - - -
1628A ILE* 1.3 72.8 - - - +
1630A VAL* 1.3 60.7 + - - +
1631A GLY 5.2 0.2 - - - -
1634A ALA* 3.9 8.1 - - - -
1639A LEU* 3.5 28.3 - - - +
1649A ILE 2.9 10.0 + - - -
1650A LEU* 3.5 8.1 - - - +
1651A ILE* 2.8 27.0 + - - +
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Residues in contact with VAL1630 (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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1607A VAL* 3.9 20.6 - - + -
1608A THR 3.0 8.5 + - - +
1609A GLY* 3.4 20.6 - - - +
1628A ILE* 3.8 22.9 - - + +
1629A GLY* 1.3 78.6 - - - +
1631A GLY* 1.3 68.8 + - - +
1634A ALA* 3.8 2.0 - - - +
1651A ILE* 3.4 9.0 - - + +
1653A ASP* 3.5 31.6 - - - +
1654A PHE* 3.6 34.4 - - + +
1657A LEU* 4.2 9.6 - - + -
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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