Contacts of the helix formed by residues 6946 - 6958 (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 GLY6946 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6945A GLU* 1.3 76.9 - - - +
6947A PHE* 1.3 63.8 + - - -
6949A THR* 3.1 19.3 + - - -
6950A TYR* 3.8 3.3 + - - +
7104A ACT 3.4 11.9 - - - -
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Residues in contact with PHE6947 (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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6912A ASP* 5.8 0.2 - - - -
6913A CYS* 3.5 28.7 - - - -
6927A SER* 5.1 2.5 - - - -
6929A MET* 3.3 45.1 - - + -
6930A TYR* 3.8 18.4 - - - -
6931A ASP 4.5 0.2 - - - -
6946A GLY* 1.3 70.8 - - - -
6948A PHE* 1.3 100.1 + + - +
6950A TYR* 3.2 6.5 + - - +
6951A ILE* 3.0 30.7 + - + +
6967A ILE* 5.9 0.9 - - + -
6968A LYS 5.2 0.9 - - - -
6973A SER* 3.9 9.0 - - - -
7102A SAM 3.7 27.8 + - - +
7104A ACT 3.1 39.1 + - - -
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Residues in contact with PHE6948 (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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6944A LYS* 3.9 8.7 - - + -
6945A GLU 2.9 9.3 + - - +
6947A PHE* 1.3 99.5 - + - +
6949A THR* 1.3 63.4 + - - +
6951A ILE* 3.3 5.6 + - + +
6952A CYS* 3.0 30.5 + - - -
6967A ILE* 4.3 6.3 - - + -
6968A LYS 4.1 10.8 - - - -
6969A ILE* 4.1 8.3 - - + -
6973A SER* 3.4 39.7 - - - -
6974A TRP* 3.5 18.2 - - - -
6975A ASN* 3.4 29.8 - - + +
6978A LEU* 3.9 27.1 - - + -
7104A ACT 3.7 22.4 - - + -
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Residues in contact with THR6949 (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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6945A GLU* 3.5 30.7 + - - +
6946A GLY 3.1 9.3 + - - -
6948A PHE* 1.3 78.0 - - - +
6950A TYR* 1.3 63.3 - - - +
6952A CYS* 3.5 6.1 + - - +
6953A GLY* 3.2 17.8 + - - -
6975A ASN* 4.7 3.7 + - - +
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Residues in contact with TYR6950 (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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6868A PHE* 3.8 24.8 - + - -
6913A CYS* 3.0 48.0 + - + -
6914A ALA* 3.6 20.4 - - + -
6916A VAL* 2.8 33.8 + - - +
6917A HIS* 6.0 2.0 - + - -
6946A GLY 3.8 1.3 + - - +
6947A PHE* 3.2 11.7 + - - +
6949A THR* 1.3 80.1 - - - +
6951A ILE* 1.3 59.9 + - + +
6953A GLY* 3.2 3.0 + - - -
6954A PHE* 2.8 67.3 + + + +
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Residues in contact with ILE6951 (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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6868A PHE* 3.8 28.0 - - + -
6925A ILE* 4.7 4.3 - - + -
6927A SER* 4.3 11.9 - - - +
6929A MET* 3.6 27.1 - - + -
6947A PHE* 3.0 23.2 + - + +
6948A PHE* 3.3 7.2 + - + +
6950A TYR* 1.3 81.6 - - + +
6952A CYS* 1.3 59.6 + - - +
6954A PHE* 3.7 4.3 - - + +
6955A ILE* 2.9 49.2 + - + +
6967A ILE* 3.9 25.6 - - + -
6978A LEU* 4.4 9.2 - - + -
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Residues in contact with CYS6952 (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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6948A PHE 3.0 21.1 + - - +
6949A THR* 3.8 6.1 - - - +
6951A ILE* 1.3 77.0 - - - +
6953A GLY* 1.3 62.8 + - - +
6955A ILE* 3.5 1.1 + - - -
6956A GLN* 3.2 33.8 + - - +
6975A ASN* 3.7 10.8 - - - -
6977A ASP* 3.9 10.1 - - + -
6978A LEU* 3.5 41.7 - - - -
6981A LEU* 3.6 21.1 - - + +
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Residues in contact with GLY6953 (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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6949A THR 3.2 7.6 + - - -
6950A TYR* 3.2 6.4 + - - -
6952A CYS* 1.3 75.5 - - - +
6954A PHE* 1.3 60.2 + - - +
6956A GLN* 3.4 7.8 + - - -
6957A GLN* 2.9 52.5 + - - +
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Residues in contact with PHE6954 (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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6866A ILE* 3.9 19.7 - - + -
6868A PHE* 4.1 17.5 - + - -
6916A VAL* 5.0 2.2 - - + -
6918A THR* 3.9 19.5 - - + -
6922A TRP* 3.7 31.0 - + - -
6925A ILE* 3.5 27.6 - - + -
6950A TYR* 2.8 58.7 + + + +
6951A ILE* 3.7 8.1 - - + +
6953A GLY* 1.3 70.7 - - - +
6955A ILE* 1.3 56.9 + - - +
6957A GLN* 4.9 0.7 - - - -
6958A LYS* 2.7 53.8 + - + +
6959A LEU 3.5 0.3 + - - -
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Residues in contact with ILE6955 (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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6925A ILE* 4.1 9.2 - - + -
6951A ILE* 2.9 39.8 + - + +
6952A CYS* 3.8 6.1 - - - +
6954A PHE* 1.3 76.2 - - + +
6956A GLN* 1.3 62.2 + - + +
6959A LEU* 3.1 50.0 + - + +
6965A VAL* 4.1 30.7 - - + -
6967A ILE* 4.7 1.6 - - + -
6978A LEU* 4.0 18.4 - - + -
6981A LEU* 4.8 11.4 - - + -
6982A MET* 5.1 1.6 - - + -
6985A PHE* 4.1 14.8 - - + -
7009A TYR* 3.8 17.6 - - + +
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Residues in contact with GLN6956 (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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6921A LYS* 5.2 4.3 + - - -
6952A CYS* 3.2 23.5 + - - +
6953A GLY* 3.9 7.0 - - - +
6955A ILE* 1.3 76.7 - - + +
6957A GLN* 1.3 63.2 + - + +
6959A LEU 5.0 0.9 - - - +
6981A LEU* 3.5 35.1 - - + +
6984A HIS* 4.8 8.5 - - - +
7009A TYR* 3.5 21.8 + - - +
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Residues in contact with GLN6957 (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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6921A LYS* 3.5 22.5 + - - +
6953A GLY* 2.9 33.0 + - - +
6954A PHE* 4.9 0.6 - - - -
6956A GLN* 1.3 84.9 - - + +
6958A LYS* 1.3 84.0 + - + +
6959A LEU 3.8 0.9 - - - -
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Residues in contact with LYS6958 (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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6918A THR* 2.8 32.6 + - - +
6919A ALA* 3.9 14.1 + - - +
6920A ASN 3.7 14.6 - - - +
6921A LYS* 3.1 10.6 - - + +
6922A TRP* 2.7 38.6 + - + +
6954A PHE* 2.7 51.0 + - + +
6957A GLN* 1.3 96.1 + - + +
6959A LEU* 1.3 54.4 + - - +
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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