Contacts of the helix formed by residues 1622 - 1627 (chain A) in PDB entry 6J8H
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 ARG1622 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1521A ILE* 4.4 7.3 - - - +
1522A MET* 4.5 5.0 - - - +
1525A ILE* 4.2 18.8 - - + +
1558A PHE* 4.1 29.3 - - - +
1561A GLU* 2.6 30.1 + - - +
1565A LYS* 5.0 0.6 - - - +
1578A TRP* 4.5 5.2 - - + -
1581A PHE* 4.1 19.7 - - + -
1582A ASP* 2.5 40.1 + - - +
1585A VAL* 4.0 14.5 - - + +
1586A VAL* 5.3 1.0 - - - +
1618A GLY 4.0 4.0 - - - +
1619A ARG* 2.8 37.8 + - - +
1621A LEU* 1.3 73.6 - - - +
1623A LEU* 1.3 63.2 + - - +
1624A VAL 3.1 0.7 - - - -
1625A LYS* 3.1 28.9 + - + +
1626A GLY 4.1 1.0 + - - -
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Residues in contact with LEU1623 (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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254A PHE* 4.4 16.4 - - + -
1522A MET* 2.6 41.2 - - + +
1525A ILE* 3.9 21.5 - - + +
1526A CYS* 4.1 26.7 - - - -
1529A MET* 4.4 21.3 - - - -
1619A ARG 4.3 0.2 + - - -
1620A ILE* 3.2 16.6 + - + +
1621A LEU 3.0 0.4 - - - -
1622A ARG* 1.3 78.8 - - - +
1624A VAL* 1.3 62.8 + - - +
1626A GLY* 3.1 13.2 + - - -
1627A ALA* 3.6 10.2 + - - +
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Residues in contact with VAL1624 (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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254A PHE* 3.6 29.6 - - + -
1578A TRP* 4.2 12.6 - - + -
1621A LEU* 3.3 19.1 - - + +
1622A ARG 3.1 0.2 - - - -
1623A LEU* 1.3 77.7 - - - +
1625A LYS* 1.3 62.3 + - - +
1626A GLY 3.3 0.3 + - - -
1627A ALA* 3.4 14.0 + - - +
1630A ILE* 4.9 9.9 - - + -
1631A ARG* 3.3 33.5 - - + +
1634A LEU* 3.6 29.8 - - + -
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Residues in contact with LYS1625 (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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1518A ASP* 4.9 18.1 - - - +
1522A MET* 5.8 4.3 - - - -
1565A LYS* 5.1 8.5 - - - +
1576A VAL* 6.0 0.6 - - - +
1578A TRP* 3.7 58.9 - - + +
1579A ASN* 4.1 18.2 + - - -
1582A ASP* 5.8 3.2 + - + +
1622A ARG* 3.1 19.9 + - + +
1624A VAL* 1.3 81.2 - - - +
1626A GLY* 1.3 61.5 + - - +
1631A ARG* 3.7 21.6 + - - +
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Residues in contact with GLY1626 (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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1522A MET* 4.1 22.4 - - - -
1622A ARG 4.1 1.2 + - - -
1623A LEU 3.1 9.6 + - - -
1625A LYS* 1.3 83.3 - - - +
1627A ALA* 1.3 59.0 + - - +
1628A LYS* 3.5 3.1 + - - +
1631A ARG* 5.6 0.7 + - - -
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Residues in contact with ALA1627 (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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250A ILE* 5.7 1.3 - - + -
1623A LEU 3.6 7.3 + - - +
1624A VAL* 3.4 14.1 + - - +
1626A GLY* 1.3 73.8 - - - +
1628A LYS* 1.3 65.9 + - - +
1629A GLY 3.3 1.3 - - - +
1630A ILE* 4.2 28.9 - - + +
1631A ARG* 3.3 19.2 + - - +
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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