Contacts of the helix formed by residues 7066 - 7075 (chain A) in PDB entry 6W75
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 ASN7066 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7064A GLN 3.1 10.4 + - - +
7065A ILE* 1.3 74.5 - - - +
7067A ASP* 1.3 61.7 + - - +
7068A MET* 2.9 16.9 + - - +
7069A ILE* 2.8 32.9 + - - +
7070A LEU* 3.1 29.6 + - - +
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Residues in contact with ASP7067 (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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7012A LYS* 5.2 2.1 + - - -
7066A ASN* 1.3 75.3 - - - +
7068A MET* 1.3 61.3 + - - +
7070A LEU* 3.4 18.7 + - - +
7071A SER* 3.0 29.2 + - - -
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Residues in contact with MET7068 (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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7066A ASN* 2.9 15.8 + - - +
7067A ASP* 1.3 78.6 - - - +
7069A ILE* 1.3 67.1 + - + +
7071A SER* 3.3 8.4 + - - -
7072A LEU* 3.1 46.0 + - + +
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Residues in contact with ILE7069 (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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7058A MET* 5.9 3.1 - - + -
7060A LEU* 4.0 17.7 - - + -
7064A GLN 3.9 8.5 - - - +
7065A ILE* 4.4 8.3 - - + -
7066A ASN* 2.8 37.4 + - - +
7068A MET* 1.3 82.0 - - + +
7070A LEU* 1.3 59.7 + - - +
7072A LEU* 3.0 15.2 + - + +
7073A LEU* 2.9 36.7 + - + +
7078A LEU* 3.8 13.5 - - + -
7080A ILE* 3.4 33.7 - - + -
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Residues in contact with LEU7070 (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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7010A LEU* 4.1 31.7 - - + +
7012A LYS* 3.5 36.1 - - - +
7065A ILE* 3.8 22.9 - - + +
7066A ASN 3.1 19.9 + - - +
7067A ASP* 3.7 22.4 - - - +
7068A MET 3.4 0.2 - - - -
7069A ILE* 1.3 75.3 - - - +
7071A SER* 1.3 54.5 + - - +
7073A LEU* 3.4 13.9 + - + +
7074A SER* 2.8 38.2 + - - +
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Residues in contact with SER7071 (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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7067A ASP 3.0 13.9 + - - -
7068A MET* 3.4 12.6 - - - -
7069A ILE 3.1 0.2 - - - -
7070A LEU* 1.3 74.7 - - - +
7072A LEU* 1.3 65.7 + - - +
7074A SER* 3.3 14.7 + - - -
7075A LYS* 2.9 46.9 + - - +
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Residues in contact with LEU7072 (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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7068A MET* 3.1 42.2 + - + +
7069A ILE* 3.0 14.6 + - + +
7071A SER* 1.3 73.5 - - - +
7073A LEU* 1.3 66.7 + - - +
7075A LYS* 3.1 10.8 + - + +
7077A ARG* 3.1 65.9 + - + +
7078A LEU* 4.0 28.9 - - + -
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Residues in contact with LEU7073 (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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6961A LEU* 3.7 28.9 - - + +
6962A GLY* 3.7 20.4 - - - +
7008A ASN* 3.2 19.3 + - - +
7009A TYR 4.4 4.7 - - - +
7010A LEU* 4.0 10.8 - - + -
7065A ILE* 4.9 0.4 - - + -
7069A ILE* 2.9 23.4 + - + +
7070A LEU* 3.5 27.6 - - + +
7072A LEU* 1.3 75.1 - - - +
7074A SER* 1.3 57.1 + - - +
7076A GLY* 3.1 17.2 + - - -
7078A LEU* 3.4 38.8 - - + +
7080A ILE* 4.0 15.0 - - + -
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Residues in contact with SER7074 (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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6856A THR* 4.0 4.5 + - - +
6986A ALA* 3.5 32.1 - - - +
7008A ASN* 3.4 13.1 - - - +
7010A LEU* 3.6 10.8 - - - +
7070A LEU* 2.8 22.5 + - - +
7071A SER* 3.6 8.7 - - - -
7072A LEU 3.2 0.6 - - - -
7073A LEU* 1.3 75.3 - - - +
7075A LYS* 1.3 59.8 + - - +
7076A GLY 3.4 0.2 - - - -
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Residues in contact with LYS7075 (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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6856A THR* 3.7 19.3 - - - +
7053A ARG* 3.7 12.6 + - - -
7071A SER* 2.9 37.2 + - - +
7072A LEU* 3.1 12.5 + - + +
7074A SER* 1.3 77.4 - - - +
7076A GLY* 1.3 62.3 + - - +
7077A ARG* 3.4 36.3 + - - +
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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