Contacts of the helix formed by residues 1684 - 1693 (chain A) in PDB entry 5G04
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 THR1684 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1660A LEU* 4.1 9.5 - - - +
1678A ILE 4.6 4.0 + - - -
1679A ASP* 3.7 53.1 + - + +
1680A LEU* 4.2 10.5 - - - +
1685A GLN* 1.3 70.4 + - - +
1686A HIS* 3.2 21.1 + - - +
1687A LEU* 3.6 16.3 + - - +
1688A LYS* 3.9 3.6 + - - +
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Residues in contact with GLN1685 (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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1684A THR* 1.3 82.0 + - - +
1686A HIS* 1.3 63.1 + - - +
1688A LYS* 3.5 23.0 + - + +
1689A SER* 3.2 20.2 + - - -
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Residues in contact with HIS1686 (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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1677A LEU* 3.5 29.4 - - + +
1684A THR* 3.2 10.4 + - - +
1685A GLN* 1.3 76.2 - - - +
1687A LEU* 1.3 65.7 + - - +
1689A SER* 3.0 23.3 + - - -
1690A ILE* 3.3 34.4 + - + +
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Residues in contact with LEU1687 (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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1619A LEU* 4.1 19.1 - - + -
1657A LEU* 4.2 7.0 - - + -
1660A LEU* 3.6 27.8 - - + +
1663A LEU* 4.9 3.4 - - + -
1666A ILE* 3.8 21.8 - - + -
1677A LEU* 3.9 25.1 - - + -
1679A ASP* 3.8 20.4 - - - +
1684A THR 3.6 11.7 + - - +
1685A GLN 3.4 0.2 - - - -
1686A HIS* 1.3 82.2 - - + +
1688A LYS* 1.3 61.2 + - - +
1690A ILE* 3.3 14.7 + - + +
1691A LEU* 3.2 33.6 + - + +
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Residues in contact with LYS1688 (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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1615A GLU* 5.9 5.2 - - - +
1616A PRO* 5.9 10.0 - - + +
1660A LEU* 3.7 20.5 - - + +
1685A GLN* 3.5 29.3 + - + +
1686A HIS 3.3 0.2 - - - -
1687A LEU* 1.3 77.7 - - - +
1689A SER* 1.3 52.4 + - - +
1691A LEU* 3.2 9.5 + - + +
1692A SER* 2.7 43.7 + - - +
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Residues in contact with SER1689 (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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1685A GLN* 3.2 10.5 + - - -
1686A HIS* 3.0 14.4 + - - -
1688A LYS* 1.3 77.1 - - - +
1690A ILE* 1.3 63.5 + - - +
1692A SER* 3.3 20.7 + - - -
1693A LYS* 3.5 25.7 + - - +
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Residues in contact with ILE1690 (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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1619A LEU* 4.8 12.1 - - + -
1677A LEU* 3.9 20.0 - - + -
1686A HIS* 3.3 43.3 + - + +
1687A LEU* 3.3 13.9 + - + +
1689A SER* 1.3 77.5 - - - +
1691A LEU* 1.3 59.5 + - - +
1693A LYS* 3.2 27.8 + - - +
1695A GLY* 3.3 7.6 + - - +
1696A VAL* 3.2 32.2 + - - +
1697A LEU* 4.9 11.2 - - + -
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Residues in contact with LEU1691 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1571A ARG* 5.9 0.5 - - - -
1616A PRO* 3.6 35.2 - - + +
1617A ARG* 3.9 11.9 - - + +
1618A LEU 3.0 34.7 - - - +
1619A LEU* 3.8 18.8 - - + -
1657A LEU* 5.1 0.9 - - + -
1660A LEU* 3.9 23.3 - - + -
1687A LEU* 3.2 37.1 + - + +
1688A LYS* 3.6 8.1 - - + +
1689A SER 3.2 0.2 - - - -
1690A ILE* 1.3 77.2 - - - +
1692A SER* 1.3 65.6 + - - +
1693A LYS 3.2 1.0 + - - -
1694A ASP* 3.7 3.3 + - - -
1695A GLY* 3.6 16.0 + - - -
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Residues in contact with SER1692 (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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1150A ALA* 4.9 13.8 - - - +
1572A TYR* 5.6 2.1 + - - -
1616A PRO* 4.8 8.3 - - - +
1688A LYS* 2.7 26.5 + - - +
1689A SER* 3.3 16.4 + - - -
1691A LEU* 1.3 75.1 - - - +
1693A LYS* 1.3 60.1 + - - +
1694A ASP 3.5 3.1 + - - -
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Residues in contact with LYS1693 (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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1150A ALA* 6.0 3.1 - - + -
1689A SER* 3.5 26.3 + - - +
1690A ILE* 3.2 12.0 - - - +
1691A LEU 3.2 0.4 - - - -
1692A SER* 1.3 76.9 + - - +
1694A ASP* 1.3 67.6 + - - +
1695A GLY 2.9 15.0 + - - -
1696A VAL* 3.9 10.5 + - + +
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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