Contacts of the helix formed by residues 65 - 73 (chain L) in PDB entry 6FF7
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 ARG 65 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64L SER* 1.3 75.0 - - - +
66L GLU* 1.3 65.0 + - - +
67L GLU 3.4 0.4 - - - -
68L GLU* 3.5 3.6 + - - +
69L GLU* 3.1 24.8 + - - +
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Residues in contact with GLU 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64L SER* 4.3 3.6 - - - -
65L ARG* 1.3 75.8 - - - +
67L GLU* 1.3 61.0 + - - +
69L GLU* 3.6 4.1 + - - +
70L LYS* 2.9 28.4 + - - +
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Residues in contact with GLU 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64L SER* 4.7 12.3 - - - +
65L ARG 3.4 1.6 - - - +
66L GLU* 1.3 76.0 - - - +
68L GLU* 1.3 60.4 + - - +
70L LYS* 3.3 8.3 + - - +
71L LEU* 2.9 29.8 + - - +
89L ILE* 5.1 20.6 - - + +
91L ARG* 6.4 1.3 - - + -
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Residues in contact with GLU 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64L SER 3.8 18.4 + - - +
65L ARG* 3.5 5.6 + - - +
66L GLU 3.3 0.2 - - - -
67L GLU* 1.3 78.8 - - - +
69L GLU* 1.3 57.8 + - - +
71L LEU* 3.1 6.1 + - - +
72L LEU* 2.9 30.2 + - - +
100L TYR* 6.4 1.3 - - + -
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Residues in contact with GLU 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65L ARG 3.1 16.9 + - - +
66L GLU* 4.2 4.5 - - - +
68L GLU* 1.3 73.2 - - - +
70L LYS* 1.3 63.7 + - - +
72L LEU* 3.9 11.3 + - - +
73L HIS* 4.1 10.0 + - - +
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Residues in contact with LYS 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L GLU 2.9 19.8 + - - +
67L GLU* 3.4 10.1 - - - +
68L GLU 3.1 0.2 - - - -
69L GLU* 1.3 79.2 - - - +
71L LEU* 1.3 61.4 + - - +
73L HIS* 3.8 3.5 + - - +
74L LEU* 3.3 20.4 + - - +
89L ILE* 6.2 4.7 - - + -
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Residues in contact with LEU 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L GLU 2.9 15.9 + - - +
68L GLU* 3.1 5.3 + - - +
70L LYS* 1.3 75.4 - - - +
72L LEU* 1.3 59.4 + - - +
73L HIS 3.3 0.2 - - - -
74L LEU* 3.5 9.6 - - + -
75L ALA* 2.8 34.7 + - + +
89L ILE* 5.7 9.2 - - + -
97L LEU* 6.4 1.8 - - + -
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Residues in contact with LEU 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L GLU 2.9 15.9 + - - +
69L GLU* 4.4 7.9 - - - +
70L LYS 3.4 0.8 - - - -
71L LEU* 1.3 77.4 - - - +
73L HIS* 1.3 57.7 + - - +
74L LEU 3.3 0.6 + - - -
75L ALA* 4.7 3.1 - - - +
76L LYS* 3.9 16.1 + - - +
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Residues in contact with HIS 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L GLU 4.1 7.3 + - - +
70L LYS 3.8 7.7 + - - +
71L LEU 3.3 0.2 - - - -
72L LEU* 1.3 76.7 - - - +
74L LEU* 1.3 56.9 + - - +
76L LYS* 4.3 12.1 - - + -
77L LEU* 4.4 10.4 + - - +
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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