Contacts of the helix formed by residues 1635 - 1644 (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 ASN1635 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1610B ASN 4.8 1.6 + - - +
1611B PRO* 4.1 25.4 - - + +
1633B ASN 3.5 2.0 + - - -
1634B ALA* 1.3 69.3 - - - +
1636B VAL* 1.3 63.7 + - - +
1637B GLN* 3.4 15.5 + - - +
1638B GLU* 3.2 51.3 + - + +
1639B LEU* 3.1 26.9 + - + +
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Residues in contact with VAL1636 (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 ALA* 3.5 11.6 + - + +
1635B ASN* 1.3 73.6 + - - +
1637B GLN* 1.3 72.6 + - - +
1639B LEU* 3.3 7.8 + - - +
1640B GLU* 2.8 52.0 + - + +
1648B PRO* 5.3 2.0 - - + -
1650B LEU* 4.1 38.1 - - + -
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Residues in contact with GLN1637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1635B ASN* 3.3 11.8 - - - +
1636B VAL* 1.3 93.3 + - - +
1638B GLU* 1.3 61.1 + - - +
1640B GLU* 3.4 15.0 + - - +
1641B ARG* 3.1 23.8 + - - +
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Residues in contact with GLU1638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1610B ASN 4.8 0.5 - - - +
1611B PRO* 3.7 4.0 - - - +
1612B ALA* 2.8 46.7 + - - +
1614B ASP 5.1 1.4 - - - +
1616B ILE* 3.6 20.0 - - + +
1635B ASN* 3.2 37.8 + - + +
1637B GLN* 1.3 77.3 - - - +
1639B LEU* 1.3 64.8 + - + +
1641B ARG* 3.2 26.7 + - - +
1642B ILE* 3.0 30.6 + - + +
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Residues in contact with LEU1639 (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* 6.3 0.2 - - + -
1606B MET* 4.5 2.5 - - + -
1608B THR* 3.7 25.4 - - + -
1627B PRO* 3.4 28.3 - - + +
1628B ILE 4.7 0.2 - - - -
1629B GLY* 3.5 33.4 - - - +
1634B ALA* 4.1 13.2 - - + -
1635B ASN 3.1 21.7 + - - +
1636B VAL* 3.7 5.4 - - - +
1638B GLU* 1.3 80.9 - - + +
1640B GLU* 1.3 56.2 + - - +
1642B ILE* 3.4 15.3 + - + +
1643B GLY* 3.0 24.6 + - - -
1648B PRO* 3.8 15.3 - - + +
1650B LEU* 4.3 12.1 - - + -
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Residues in contact with GLU1640 (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 VAL* 2.8 36.3 + - + +
1637B GLN* 3.8 15.7 + - - +
1638B GLU 3.2 0.2 - - - -
1639B LEU* 1.3 78.3 - - - +
1641B ARG* 1.3 56.7 + - - +
1644B TRP* 3.0 38.7 + - + +
1646B ASN 4.8 0.7 - - - +
1648B PRO* 3.6 27.9 - - + +
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Residues in contact with ARG1641 (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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1616B ILE* 3.2 41.4 + - - +
1617B LYS* 5.2 1.2 - - - +
1618B ARG* 2.9 46.0 + - + +
1637B GLN 3.1 13.9 + - - +
1638B GLU* 3.2 33.0 + - - +
1640B GLU* 1.3 77.5 - - - +
1642B ILE* 1.3 58.7 - - + +
1644B TRP* 4.0 3.3 - - - +
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Residues in contact with ILE1642 (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* 4.2 4.0 - - + -
1582B LEU* 4.0 16.8 - - + -
1606B MET* 3.7 34.5 - - + -
1616B ILE* 3.4 46.0 - - + -
1618B ARG* 3.7 17.0 + - - +
1619B LEU* 5.8 1.6 + - + -
1625B VAL* 3.9 26.6 - - + +
1627B PRO* 4.3 2.0 - - + -
1638B GLU* 3.0 24.6 + - + +
1639B LEU* 3.7 11.9 - - + +
1640B GLU 3.3 0.2 - - - -
1641B ARG* 1.3 79.5 - - + +
1643B GLY* 1.3 60.3 + - - +
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Residues in contact with GLY1643 (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 VAL* 3.6 14.2 + - - +
1627B PRO* 3.6 20.6 - - - -
1639B LEU 3.0 11.8 + - - -
1642B ILE* 1.3 77.4 - - - +
1644B TRP* 1.3 67.3 + - - +
1645B PRO* 4.0 0.7 - - - +
1646B ASN* 2.7 33.0 + - - +
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Residues in contact with TRP1644 (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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1618B ARG* 2.7 43.8 + - - +
1640B GLU* 3.0 23.9 + - + +
1641B ARG* 4.0 3.8 - - - +
1642B ILE 3.5 1.2 - - - -
1643B GLY* 1.3 75.6 - - - +
1645B PRO* 1.4 88.1 - - + +
1646B ASN 3.6 4.0 + - - +
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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