Contacts of the helix formed by residues 6975 - 6983 (chain C) 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 ASN6975 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6943C SER* 3.3 10.7 + - - -
6944C LYS 2.9 20.0 + - - +
6945C GLU* 4.4 11.1 - - - +
6948C PHE* 3.3 37.3 - - + +
6949C THR* 4.6 4.2 - - - +
6952C CYS* 3.7 5.2 - - - -
6969C ILE* 5.4 1.2 - - - +
6974C TRP* 1.3 82.8 - - - +
6976C ALA* 1.3 63.4 + - - +
6977C ASP* 2.8 37.2 + - - +
6978C LEU* 2.8 25.4 + - + +
6979C TYR* 3.4 16.9 + - - -
7004C LEU* 5.6 0.4 - - - +
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Residues in contact with ALA6976 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6943C SER* 2.8 12.3 + - - +
6974C TRP* 3.6 6.9 - - + -
6975C ASN* 1.3 68.6 + - - +
6977C ASP* 1.3 63.1 + - - +
6979C TYR 3.3 1.9 + - - -
6980C LYS* 3.0 25.8 + - - +
7019C GLY* 3.3 17.5 + - - +
7020C TYR* 3.5 58.1 - - + +
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Residues in contact with ASP6977 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6943C SER* 4.8 0.2 + - - -
6952C CYS* 3.8 15.3 - - + -
6975C ASN* 2.8 21.7 + - - +
6976C ALA* 1.3 72.4 - - - +
6978C LEU* 1.3 57.3 + - - -
6980C LYS* 3.2 23.7 + - + +
6981C LEU* 2.9 33.1 + - + +
7020C TYR* 6.2 0.2 - - - -
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Residues in contact with LEU6978 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6948C PHE* 3.9 20.6 - - + -
6951C ILE* 4.3 9.4 - - + -
6952C CYS* 3.5 12.3 - - - -
6955C ILE* 3.8 29.4 - - + -
6967C ILE* 3.5 32.5 - - + -
6969C ILE* 4.4 2.5 - - + -
6975C ASN* 2.8 24.5 + - + +
6976C ALA 3.2 0.2 - - - -
6977C ASP* 1.3 74.5 - - - +
6979C TYR* 1.3 65.4 + - - +
6981C LEU* 3.0 14.4 + - + +
6982C MET* 3.1 22.5 + - + +
7004C LEU* 3.9 23.6 - - + -
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Residues in contact with TYR6979 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6809C MET* 6.2 0.2 - - - -
6969C ILE* 3.1 22.0 - - + +
6974C TRP* 4.1 8.5 - + + -
6975C ASN 3.4 19.3 + - - -
6976C ALA 3.3 1.6 + - - +
6978C LEU* 1.3 77.3 - - - +
6980C LYS* 1.3 64.4 + - - +
6982C MET* 3.0 23.6 + - - +
6988C TRP* 4.4 10.7 - + - -
7004C LEU* 3.6 30.7 - - + -
7017C ILE* 3.7 12.2 - - + +
7019C GLY* 3.5 29.2 - - - -
7022C MET* 3.5 34.5 - - + -
7023C HIS* 2.8 45.9 + + + -
7026C TYR* 3.6 15.0 - - + +
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Residues in contact with LYS6980 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6976C ALA 3.0 13.8 + - - +
6977C ASP* 3.4 26.7 - - - +
6978C LEU 3.2 0.2 - - - -
6979C TYR* 1.3 74.5 - - - +
6981C LEU* 1.3 58.4 + - + +
6983C GLY* 3.1 20.6 + - - -
6984C HIS* 3.6 14.8 - - - +
7015C GLU 4.7 1.9 - - - +
7016C GLN* 4.6 18.7 - - + +
7017C ILE* 3.0 43.9 + - - +
7018C ASP* 4.6 4.8 - - - +
7019C GLY 5.4 1.8 - - - +
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Residues in contact with LEU6981 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6952C CYS* 3.6 52.3 - - + +
6955C ILE* 4.3 20.9 - - + -
6956C GLN* 3.7 32.1 - - + +
6977C ASP* 2.9 14.1 + - + +
6978C LEU* 3.0 11.8 + - + +
6980C LYS* 1.3 72.1 - - + +
6982C MET* 1.3 63.0 + - + +
6983C GLY 3.0 2.0 - - - -
6984C HIS* 2.8 46.9 + - + +
6985C PHE* 3.2 14.3 - - - -
7009C TYR* 5.9 0.4 - - + -
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Residues in contact with MET6982 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6955C ILE* 5.0 1.1 - - + -
6965C VAL* 4.0 21.8 - - + -
6967C ILE* 5.5 0.4 - - + -
6978C LEU* 3.1 36.6 + - + +
6979C TYR* 3.0 22.6 + - - +
6981C LEU* 1.3 77.2 - - - +
6983C GLY* 1.3 57.4 + - - +
6984C HIS 3.1 3.7 + - - -
6985C PHE* 3.3 31.9 + - + +
6988C TRP* 3.6 44.1 - - + +
7004C LEU* 4.2 20.2 - - + -
7005C ILE 3.8 9.9 - - - +
7006C GLY* 3.8 22.0 - - - -
7014C ARG* 4.5 0.2 + - - -
7017C ILE* 4.3 3.1 - - + -
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Residues in contact with GLY6983 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6980C LYS 3.1 9.9 + - - -
6981C LEU 3.0 2.0 - - - -
6982C MET* 1.3 76.1 - - - +
6984C HIS* 1.3 54.7 + - - +
6985C PHE 3.2 5.4 - - - -
7014C ARG* 2.7 36.4 + - - +
7015C GLU* 3.2 37.5 + - - +
7017C ILE* 3.7 7.9 - - - +
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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