Contacts of the helix formed by residues 7018 - 7033 (chain A) in PDB entry 6W4H
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 ASP7018 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6817A ARG* 4.3 14.7 + - - +
7016A GLN 4.2 1.2 + - - -
7017A ILE* 1.3 71.7 - - - +
7019A GLY* 1.3 52.9 + - - +
7020A TYR* 3.0 21.2 + - - +
7021A VAL* 3.1 30.5 + - + +
7022A MET* 2.9 34.0 + - - +
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Residues in contact with GLY7019 (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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6974A TRP* 3.8 0.9 - - - -
6976A ALA* 3.3 36.1 + - - +
6979A TYR* 3.6 20.2 - - - -
6980A LYS* 5.0 1.2 - - - +
7017A ILE 3.6 5.5 + - - -
7018A ASP* 1.3 69.1 + - - +
7020A TYR* 1.3 60.0 + - - +
7022A MET 4.4 0.2 - - - -
7023A HIS* 3.0 30.3 + - - +
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Residues in contact with TYR7020 (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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6820A LEU* 5.4 10.4 - - + +
6940A GLU* 5.3 1.8 - - - -
6941A ASN 4.7 2.5 - - - -
6942A ASP* 3.6 22.5 + - - +
6943A SER* 2.9 41.2 + - - -
6974A TRP* 3.6 21.8 - + - -
6976A ALA* 3.7 13.9 - - + +
7018A ASP* 3.0 8.9 + - - +
7019A GLY* 1.3 75.3 - - - +
7021A VAL* 1.3 63.8 + - + +
7023A HIS* 3.5 2.3 + - - +
7024A ALA* 3.2 22.0 + - - +
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Residues in contact with VAL7021 (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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6816A GLN 3.8 9.6 - - - +
6817A ARG* 3.7 60.6 - - + +
6818A MET 4.5 4.5 - - - +
7018A ASP* 3.1 32.2 + - + +
7020A TYR* 1.3 74.9 - - + +
7022A MET* 1.3 61.3 + - + +
7024A ALA* 3.1 8.9 + - - +
7025A ASN* 2.9 29.6 + - - +
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Residues in contact with MET7022 (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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6809A MET* 4.4 2.9 - - + -
6814A LYS* 3.2 37.0 - - + +
6979A TYR* 3.5 21.8 - - + -
6988A TRP* 3.5 42.4 - - + -
7015A GLU* 5.9 0.9 - - - +
7017A ILE* 3.8 30.1 - - + -
7018A ASP 2.9 16.1 + - - +
7019A GLY 3.4 0.2 + - - -
7021A VAL* 1.3 78.8 - - + +
7023A HIS* 1.3 58.2 + - - +
7025A ASN* 3.2 12.7 + - - +
7026A TYR* 2.9 27.2 + - - +
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Residues in contact with HIS7023 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6820A LEU* 4.2 15.9 - - + -
6969A ILE* 4.4 2.2 - - + -
6970A THR 3.3 20.2 - - - -
6971A GLU* 2.8 26.5 + - - -
6974A TRP* 3.3 46.0 - + + -
6979A TYR* 2.8 40.7 + - + -
7019A GLY 3.0 14.0 + - - +
7020A TYR 4.0 2.0 - - - +
7022A MET* 1.3 77.5 - - - +
7024A ALA* 1.3 57.7 + - - +
7026A TYR* 3.1 18.9 + + - +
7027A ILE* 2.9 32.9 + - + +
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Residues in contact with ALA7024 (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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6818A MET* 3.2 30.8 - - - +
6819A LEU 3.5 4.8 - - - +
6820A LEU* 3.5 36.7 - - + +
6821A GLU 5.6 0.2 + - - -
7020A TYR 3.2 12.4 + - - +
7021A VAL* 3.1 6.6 + - - +
7023A HIS* 1.3 76.2 - - - +
7025A ASN* 1.3 56.8 + - - +
7027A ILE* 3.4 3.0 + - - +
7028A PHE* 2.9 29.8 + - - +
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Residues in contact with ASN7025 (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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6809A MET* 3.6 9.6 - - + +
6813A TYR* 3.3 22.2 + - - +
6814A LYS 3.5 17.2 + - - -
6816A GLN* 2.8 24.7 + - - -
6818A MET* 3.0 39.0 + - - +
7021A VAL* 2.9 22.3 + - - +
7022A MET* 3.4 15.9 - - - +
7024A ALA* 1.3 75.7 - - - +
7026A TYR* 1.3 57.7 + - - +
7028A PHE* 3.3 2.8 + - - +
7029A TRP* 3.0 29.1 + - - +
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Residues in contact with TYR7026 (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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6809A MET* 3.6 13.8 - - - +
6969A ILE* 4.6 4.7 - - + -
6970A THR 5.1 1.3 - - - -
6979A TYR* 3.6 25.1 - - + +
6990A ALA* 3.8 17.3 - - + -
7000A SER* 2.6 30.0 + - - -
7002A ALA* 3.1 30.5 - - + +
7022A MET 2.9 9.4 + - - +
7023A HIS* 3.1 16.8 + + - +
7025A ASN* 1.3 76.3 - - - +
7027A ILE* 1.3 80.4 + - + +
7029A TRP* 3.2 19.8 + + - +
7030A ARG* 3.0 65.7 + - + +
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Residues in contact with ILE7027 (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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6820A LEU* 4.0 17.9 - - + -
6821A GLU* 3.5 26.2 - - + +
6823A CYS* 4.0 20.0 - - + -
6971A GLU* 3.9 34.1 - - + -
7000A SER* 5.2 0.4 - - - -
7023A HIS* 2.9 25.0 + - - +
7024A ALA 3.8 4.0 - - - +
7026A TYR* 1.3 95.0 - - + +
7028A PHE* 1.3 52.8 + - - +
7030A ARG* 3.2 4.7 + - - +
7031A ASN* 2.7 50.9 + - - +
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Residues in contact with PHE7028 (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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6813A TYR* 3.8 30.7 - + - -
6816A GLN* 5.3 7.0 - - + -
6818A MET* 3.6 48.9 - - + -
6819A LEU 5.9 0.7 - - - +
6821A GLU* 4.5 15.0 - - - +
7024A ALA 2.9 17.4 + - - +
7025A ASN* 3.6 4.7 - - - +
7026A TYR 3.3 0.2 - - - -
7027A ILE* 1.3 77.8 - - - +
7029A TRP* 1.3 58.7 + - - +
7031A ASN* 3.3 6.7 + - + +
7032A THR* 2.8 53.2 + - + +
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Residues in contact with TRP7029 (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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6807A VAL* 3.6 38.8 - - + +
6808A ALA 3.8 0.7 - - - -
6809A MET* 3.5 43.7 - - + -
6810A PRO* 3.3 23.4 - - + +
6813A TYR* 3.7 30.3 - + + -
6990A ALA 3.8 5.4 - - - -
6992A VAL* 3.7 12.6 - - + -
7025A ASN 3.0 13.6 + - - +
7026A TYR* 3.2 26.2 + + - +
7028A PHE* 1.3 77.0 - - - +
7030A ARG* 1.3 78.8 + - - +
7032A THR 3.2 1.0 + - - -
7033A ASN* 2.9 59.8 + - + +
7035A ILE* 4.2 8.3 - - + -
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Residues in contact with ARG7030 (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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6823A CYS* 4.3 9.0 - - - -
6825A LEU* 3.5 34.5 - - + +
6992A VAL* 3.5 18.1 - - - +
6997A ALA 2.9 29.7 + - - -
6999A SER 3.0 23.0 + - - -
7000A SER* 3.7 4.8 - - - +
7001A GLU 3.3 8.5 + - - -
7026A TYR* 3.0 54.6 + - + +
7027A ILE* 3.6 6.1 - - - +
7029A TRP* 1.3 106.5 - - - +
7031A ASN* 1.3 61.6 + - - +
7032A THR 3.4 0.5 + - - -
7033A ASN 3.6 16.5 + - - +
7034A PRO* 4.5 2.1 - - - +
7035A ILE* 4.0 13.7 - - - +
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Residues in contact with ASN7031 (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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6821A GLU* 4.3 16.6 + - - +
6822A LYS 3.0 21.8 + - - -
6823A CYS* 3.3 8.5 - - - -
6824A ASP* 2.8 43.3 + - - +
6826A GLN 5.9 0.3 + - - -
7027A ILE* 2.7 32.1 + - - +
7028A PHE* 3.8 8.3 - - + +
7029A TRP 3.3 0.2 - - - -
7030A ARG* 1.3 73.2 - - - +
7032A THR* 1.3 64.4 + - + +
7033A ASN 3.6 0.2 - - - -
7034A PRO* 5.2 3.3 - - - +
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Residues in contact with THR7032 (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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6813A TYR* 3.9 12.2 + - - -
7028A PHE* 2.8 49.1 + - + +
7029A TRP 3.5 0.2 + - - -
7031A ASN* 1.3 81.8 - - + +
7033A ASN* 1.3 74.9 + - - +
7034A PRO* 3.6 10.4 - - - +
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Residues in contact with ASN7033 (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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6810A PRO* 5.4 2.4 - - - +
6813A TYR* 2.9 31.7 + - - -
7029A TRP* 2.9 36.8 + - - +
7030A ARG* 3.8 12.0 + - - +
7031A ASN 3.6 1.2 - - - -
7032A THR* 1.3 91.9 + - - +
7034A PRO* 1.3 68.2 - - - +
7035A ILE* 3.3 15.8 + - + +
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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