Contacts of the helix formed by residues 1577 - 1588 (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 ASN1577 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1542B TYR* 3.5 12.3 - - + +
1543B SER 2.7 19.7 + - - +
1544B TYR* 2.9 37.1 + - - +
1545B MET 6.2 0.2 - - - -
1575B ARG* 3.8 11.4 - - - +
1576B THR* 1.3 69.1 - - - +
1578B THR* 1.3 62.5 - - - +
1579B GLY 3.3 2.9 - - - -
1580B LEU* 3.3 15.6 + - + +
1581B ALA 3.1 16.8 + - - -
1613B SER* 3.5 13.9 - - - -
1614B ASP* 3.4 30.1 - - - +
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Residues in contact with THR1578 (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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1542B TYR* 2.8 27.0 + - - +
1576B THR* 2.9 18.9 + - - +
1577B ASN* 1.3 70.0 - - - +
1579B GLY* 1.3 66.5 + - - +
1581B ALA* 3.2 2.4 + - + +
1582B LEU* 2.9 28.5 + - + +
1606B MET* 3.7 28.5 - - - -
1608B THR* 4.4 6.1 + - + +
1610B ASN 5.0 0.3 + - - -
1612B ALA* 3.8 17.4 + - - +
1614B ASP* 3.3 1.2 + - - -
1616B ILE* 3.9 16.2 - - + -
1639B LEU* 6.3 0.2 - - + -
1642B ILE* 4.2 4.7 - - + -
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Residues in contact with GLY1579 (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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1578B THR* 1.3 80.1 - - - +
1580B LEU* 1.3 55.9 + - - +
1582B LEU* 3.4 5.4 + - - +
1583B ARG* 3.0 29.1 + - - +
1614B ASP* 2.8 10.5 + - - -
1615B GLU 3.3 25.4 - - - -
1616B ILE* 4.0 13.5 - - - +
1617B LYS 5.1 1.9 + - - -
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Residues in contact with LEU1580 (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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1544B TYR 3.6 23.8 - - - +
1545B MET* 4.2 12.1 - - + -
1546B VAL* 4.1 12.1 - - + +
1577B ASN* 3.4 15.5 - - + +
1579B GLY* 1.3 74.9 - - - +
1581B ALA* 1.3 60.5 + - - +
1583B ARG* 3.5 10.1 + - + +
1584B TYR* 3.0 31.0 + - + +
1614B ASP* 2.9 13.9 + - - +
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Residues in contact with ALA1581 (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* 4.1 13.7 - - + -
1540B LEU* 4.2 3.1 - - + +
1542B TYR* 3.6 41.7 - - + -
1546B VAL* 3.8 13.4 - - + +
1577B ASN 3.1 3.7 + - - +
1578B THR* 3.2 8.7 + - + +
1580B LEU* 1.3 80.4 - - - +
1582B LEU* 1.3 62.7 + - + +
1584B TYR* 3.1 12.7 + - - +
1585B LEU* 3.3 17.0 + - - +
1606B MET* 5.9 0.4 - - - -
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Residues in contact with LEU1582 (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* 6.3 0.9 - - + -
1578B THR* 2.9 26.7 + - + +
1579B GLY* 3.8 4.9 - - - +
1581B ALA* 1.3 75.3 - - - +
1583B ARG* 1.3 64.6 + - - +
1585B LEU* 3.1 28.4 + - + +
1586B SER 3.8 0.5 + - - -
1604B VAL* 5.6 1.1 - - + -
1606B MET* 4.0 22.9 - - + -
1616B ILE* 3.9 27.8 - - + -
1617B LYS 4.1 12.8 - - - +
1618B ARG* 6.0 0.2 - - - -
1619B LEU* 3.1 41.2 - - + +
1625B VAL* 5.0 4.5 - - + -
1642B ILE* 4.0 27.4 - - + -
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Residues in contact with ARG1583 (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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1579B GLY 3.0 17.6 + - - +
1580B LEU* 3.9 11.4 - - + +
1582B LEU* 1.3 75.8 - - - +
1584B TYR* 1.3 63.6 + - - +
1586B SER* 3.2 13.7 + - - +
1587B ASP* 2.7 58.0 + - - +
1619B LEU* 5.1 0.9 - - - -
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Residues in contact with TYR1584 (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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1540B LEU* 4.0 11.4 - - + -
1546B VAL* 3.7 42.7 + - + -
1548B VAL* 3.5 33.2 + - + +
1580B LEU* 3.0 15.6 + - + +
1581B ALA 3.1 11.6 + - - +
1583B ARG* 1.3 76.9 - - - +
1585B LEU* 1.3 58.0 + - - +
1587B ASP* 4.5 0.9 - - - -
1588B HIS* 2.9 68.0 + + + +
1589B SER* 3.2 9.7 + - - -
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Residues in contact with LEU1585 (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* 3.9 21.1 - - + -
1502B VAL* 3.8 15.5 - - + -
1540B LEU* 3.6 22.9 - - + -
1581B ALA 3.7 7.2 - - - +
1582B LEU* 3.1 22.9 + - + +
1584B TYR* 1.3 78.8 - - - +
1586B SER* 1.3 57.7 + - - +
1589B SER* 3.3 15.4 + - - +
1590B PHE* 2.9 46.4 + - + +
1604B VAL* 3.9 30.7 - - + -
1619B LEU* 4.0 18.6 - - + -
1623B ILE* 4.8 0.7 - - + -
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Residues in contact with SER1586 (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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1582B LEU 3.8 3.0 + - - -
1583B ARG* 3.2 19.8 + - - +
1585B LEU* 1.3 78.3 - - - +
1587B ASP* 1.3 67.3 + - - +
1588B HIS 3.4 0.4 + - - -
1590B PHE* 5.1 3.8 + - - +
1591B LEU* 3.9 14.4 - - - +
1619B LEU* 4.4 3.4 - - - +
1620B PRO* 4.0 32.1 - - - +
1623B ILE* 4.3 10.3 - - - -
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Residues in contact with ASP1587 (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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1583B ARG* 2.7 68.4 + - - +
1584B TYR* 5.1 0.2 - - - -
1586B SER* 1.3 80.1 + - - +
1588B HIS* 1.3 86.0 + - + +
1591B LEU* 3.2 19.8 - - - +
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Residues in contact with HIS1588 (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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1548B VAL* 5.8 0.7 - - + -
1584B TYR* 2.9 61.9 + + + +
1586B SER 3.4 0.8 - - - -
1587B ASP* 1.3 101.5 + - + +
1589B SER* 1.3 66.4 + - - +
1590B PHE 3.3 2.1 + - - -
1591B LEU* 3.3 22.0 + - - +
1594B GLN* 3.4 19.4 - - + +
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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