Contacts of the strand formed by residues 1602 - 1608 (chain B) 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 ASN1602 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1497B LEU* 4.7 0.7 - - - -
1498B ASP* 3.5 4.6 - - - +
1590B PHE* 3.3 32.0 - - + +
1596B ASP* 3.0 9.4 + - - +
1600B ALA 3.4 1.6 + - - +
1601B PRO* 1.3 75.2 - - - +
1603B LEU* 1.3 61.6 + - - +
1622B ASP* 3.4 33.7 + - - +
1623B ILE* 4.0 14.5 - - + +
1624B GLN* 3.1 26.6 + - - +
4675B CA 2.4 30.0 - - - -
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Residues in contact with LEU1603 (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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1497B LEU* 4.1 29.4 - - + -
1498B ASP 3.0 7.3 + - - +
1499B VAL* 3.2 7.7 - - + +
1500B ALA 2.8 25.5 + - - +
1590B PHE* 4.1 1.3 - - - -
1602B ASN* 1.3 75.7 - - - +
1604B VAL* 1.3 71.9 + - - +
1605B TYR* 3.6 33.2 - - + +
1624B GLN* 3.4 35.9 - - + +
1626B VAL* 4.2 18.8 - - + -
1669B CYS* 3.9 21.1 - - + -
1670B CYS* 4.2 0.4 - - - -
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Residues in contact with VAL1604 (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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1500B ALA* 3.3 10.1 - - + +
1502B VAL* 4.0 11.4 - - + -
1582B LEU* 5.6 1.3 - - + -
1585B LEU* 3.9 24.9 - - + -
1590B PHE* 3.8 15.9 - - + -
1603B LEU* 1.3 79.1 - - - +
1605B TYR* 1.3 75.2 + - - +
1606B MET* 4.4 3.1 - - + +
1619B LEU* 4.4 1.3 - - + -
1623B ILE* 3.4 31.0 - - + -
1624B GLN 2.8 11.7 + - - +
1625B VAL* 3.5 16.9 - - + +
1626B VAL* 2.8 31.0 + - - +
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Residues in contact with TYR1605 (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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1499B VAL* 3.8 28.0 - - + -
1500B ALA 2.9 8.9 + - - +
1501B PHE* 3.5 33.3 - + + +
1502B VAL* 2.9 25.6 + - - +
1520B PHE* 5.0 4.3 - + + -
1524B VAL* 4.8 4.7 - - + -
1528B MET* 5.1 4.4 - - - -
1603B LEU* 3.6 15.0 - - + +
1604B VAL* 1.3 74.8 - - - +
1606B MET* 1.3 60.5 + - - +
1607B VAL* 4.1 2.7 + - + +
1626B VAL* 3.5 37.3 - - + +
1628B ILE* 4.4 10.1 - - + -
1665B VAL* 3.1 41.7 + - + +
1669B CYS* 3.0 33.3 - - - +
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Residues in contact with MET1606 (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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1502B VAL* 3.3 25.1 - - + +
1542B TYR* 4.7 5.8 - - + +
1578B THR* 3.7 25.4 - - + +
1581B ALA* 5.9 0.7 - - - -
1582B LEU* 4.0 15.9 - - + -
1604B VAL* 4.0 4.1 + - + -
1605B TYR* 1.3 74.6 - - - +
1607B VAL* 1.3 65.0 + - - +
1608B THR* 3.9 7.4 + - + +
1625B VAL* 4.5 7.4 - - + -
1626B VAL 3.3 7.3 + - - -
1627B PRO* 4.4 15.7 - - + -
1628B ILE* 2.7 34.6 + - - +
1639B LEU* 4.5 7.0 - - + -
1642B ILE* 3.7 42.8 - - + -
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Residues in contact with VAL1607 (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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1502B VAL 2.9 7.5 + - - +
1503B LEU* 3.7 27.4 - - + -
1504B GLU* 3.1 25.2 + - - +
1517B SER* 3.8 20.6 - - - +
1520B PHE* 3.9 28.3 - - + -
1542B TYR* 4.7 0.3 - - - -
1605B TYR 4.9 2.7 - - - +
1606B MET* 1.3 77.4 - - - +
1608B THR* 1.3 64.2 + - - +
1628B ILE* 3.4 11.7 - - + +
1630B VAL* 4.0 22.9 - - + -
1654B PHE* 4.2 5.8 - - + -
1657B LEU* 4.1 7.6 - - + -
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Residues in contact with THR1608 (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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1504B GLU* 2.7 21.9 + - - -
1509B ILE* 5.3 0.2 - - - -
1542B TYR* 3.3 19.6 + - - +
1576B THR* 4.0 1.4 - - - +
1578B THR* 4.4 3.8 + - + +
1606B MET* 4.8 11.9 - - + +
1607B VAL* 1.3 78.2 - - - +
1609B GLY* 1.3 57.2 + - - +
1610B ASN 3.4 17.2 + - - +
1628B ILE 3.0 8.2 + - - +
1629B GLY* 3.5 1.9 - - - -
1630B VAL* 2.9 25.8 + - - +
1634B ALA* 4.5 2.4 - - + +
1639B LEU* 3.7 33.0 - - + -
1654B PHE* 4.8 2.7 - - - -
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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