Contacts of the helix formed by residues 1635 - 1644 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1610C ASN 4.9 1.6 + - - -
1611C PRO* 4.3 24.9 - - + +
1633C ASN 3.5 1.6 + - - +
1634C ALA* 1.3 71.3 - - - +
1636C VAL* 1.3 62.5 + - - +
1637C GLN* 3.4 12.0 + - - +
1638C GLU* 3.0 50.4 + - + +
1639C LEU* 3.0 26.6 + - - +
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Residues in contact with VAL1636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1634C ALA* 3.5 10.0 + - + +
1635C ASN* 1.3 71.7 + - - +
1637C GLN* 1.3 58.3 + - - +
1639C LEU* 3.2 8.3 + - - +
1640C GLU* 2.8 51.8 + - + +
1648C PRO* 5.3 1.3 - - + -
1650C LEU* 4.0 38.1 - - + -
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Residues in contact with GLN1637 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1635C ASN* 3.3 9.1 + - - +
1636C VAL* 1.3 78.5 - - - +
1638C GLU* 1.3 61.6 + - + +
1640C GLU* 3.3 14.3 + - - +
1641C ARG* 3.0 49.5 + - + +
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Residues in contact with GLU1638 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1610C ASN 4.9 0.7 - - - +
1611C PRO* 3.7 7.8 - - - +
1612C ALA* 2.9 46.3 + - - +
1614C ASP 5.4 0.9 - - - +
1616C ILE* 5.0 6.3 - - + +
1635C ASN* 3.0 33.3 + - - +
1637C GLN* 1.3 75.0 - - - +
1639C LEU* 1.3 65.8 + - + +
1641C ARG* 3.2 32.1 + - - +
1642C ILE* 3.0 35.1 + - + +
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Residues in contact with LEU1639 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1606C MET* 5.1 0.7 - - + -
1608C THR* 3.6 27.6 - - + -
1627C PRO* 3.4 26.4 - - + +
1629C GLY* 3.5 31.6 - - - +
1634C ALA* 4.1 13.2 - - + -
1635C ASN 3.0 21.7 + - - +
1636C VAL* 3.6 6.3 - - - +
1638C GLU* 1.3 77.7 - - + +
1640C GLU* 1.3 62.7 + - - +
1642C ILE* 3.3 12.5 + - + -
1643C GLY* 3.0 20.1 + - - -
1648C PRO* 3.8 17.4 - - + +
1650C LEU* 4.1 15.5 - - + -
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Residues in contact with GLU1640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1636C VAL* 2.8 38.2 + - + +
1637C GLN* 3.6 12.6 - - - +
1639C LEU* 1.3 76.4 - - - +
1641C ARG* 1.3 56.9 + - + +
1644C TRP* 3.0 40.8 + - + +
1646C ASN 4.8 0.7 - - - +
1648C PRO* 3.7 26.7 - - + +
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Residues in contact with ARG1641 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1616C ILE* 5.5 15.3 + - + +
1618C ARG* 3.6 20.7 + - + +
1637C GLN* 3.0 47.0 + - + +
1638C GLU* 3.4 37.2 + - - +
1640C GLU* 1.3 78.8 - - - +
1642C ILE* 1.3 63.5 + - + +
1644C TRP* 3.7 9.9 + - - +
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Residues in contact with ILE1642 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1578C THR* 4.1 12.1 - - + -
1582C LEU* 4.1 12.6 - - + -
1606C MET* 3.9 29.4 - - + -
1616C ILE* 3.5 34.8 - - + -
1618C ARG* 3.5 22.1 - - - +
1619C LEU 5.1 0.9 + - - +
1625C VAL* 3.9 32.0 - - + +
1627C PRO* 4.1 4.3 - - + -
1638C GLU* 3.0 28.1 + - + +
1639C LEU* 3.7 11.7 - - + +
1641C ARG* 1.3 77.2 - - + +
1643C GLY* 1.3 63.6 + - - +
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Residues in contact with GLY1643 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1625C VAL* 3.6 20.0 + - - +
1627C PRO* 3.6 13.5 - - - -
1639C LEU 3.0 11.8 + - - -
1642C ILE* 1.3 77.7 - - - +
1644C TRP* 1.3 69.0 + - - +
1646C ASN* 2.8 35.8 + - - +
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Residues in contact with TRP1644 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1618C ARG* 3.9 42.0 - - - +
1640C GLU* 3.0 26.1 + - + +
1641C ARG* 3.7 11.4 - - - +
1642C ILE 3.3 1.6 - - - -
1643C GLY* 1.3 79.6 - - - +
1645C PRO* 1.4 88.8 - - + +
1646C ASN 3.8 0.9 + - - -
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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