Contacts of the helix formed by residues 75 - 84 (chain O) in PDB entry 6CNB
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 SER 75 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74O LEU* 1.3 79.2 - - - +
76O VAL* 1.3 70.2 + - - +
77O ARG* 3.5 4.5 + - - +
78O GLU* 2.9 19.2 + - - -
79O LEU* 2.8 25.9 + - - +
117O THR* 3.7 8.8 + - - -
118O THR* 3.3 14.6 + - - -
119O TYR* 3.2 29.4 - - - +
120O TYR* 4.8 0.2 - - - -
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Residues in contact with VAL 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75O SER* 1.3 78.4 + - - +
77O ARG* 1.3 67.3 + - - +
79O LEU* 3.1 24.8 + - - +
80O VAL* 4.1 3.3 + - - +
87O ASP* 4.8 3.9 - - - +
88O VAL* 5.7 5.2 - - + -
91O VAL* 3.9 21.3 - - + +
92O LYS* 4.8 20.0 - - + +
95O LEU* 4.6 4.9 - - + -
118O THR* 3.1 25.5 + - + +
120O TYR* 3.3 22.8 - - + +
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Residues in contact with ARG 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75O SER* 4.4 2.7 + - - +
76O VAL* 1.3 81.5 - - + +
78O GLU* 1.3 64.3 + - - +
79O LEU 3.1 1.2 + - - -
80O VAL* 3.2 16.6 + - - +
81O GLU* 3.7 19.8 + - + +
87O ASP* 4.4 13.2 - - - +
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Residues in contact with GLU 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 5.5 2.1 + - - -
128A ARG* 3.1 35.5 + - - +
73O ARG 5.6 0.6 - - - +
74O LEU* 3.5 22.5 - - + +
75O SER* 2.9 33.7 + - - +
77O ARG* 1.3 76.0 - - - +
79O LEU* 1.3 68.1 + - - +
81O GLU* 3.0 30.9 + - + +
82O LYS* 4.2 11.8 + - - +
119O TYR* 4.5 5.7 - - - -
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Residues in contact with LEU 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64O VAL* 3.6 30.3 - - + -
68O LEU* 6.2 1.1 - - + -
74O LEU* 3.6 32.4 - - + +
75O SER 2.8 38.3 + - - +
76O VAL* 3.1 12.7 + - - +
78O GLU* 1.3 74.2 - - - +
80O VAL* 1.3 53.3 + - - +
81O GLU 2.8 0.2 + - - -
82O LYS* 2.7 30.0 + - - +
83O ILE* 3.1 27.6 - - + +
91O VAL* 3.7 32.1 - - + -
95O LEU* 5.7 6.1 - - + -
120O TYR* 5.2 9.2 - - + -
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Residues in contact with VAL 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76O VAL 4.4 1.1 - - - +
77O ARG 3.2 8.1 + - - +
79O LEU* 1.3 72.8 - - + +
81O GLU* 1.3 60.5 + - - +
82O LYS 2.9 3.2 + - - -
83O ILE* 4.5 7.2 - - + +
84O ASP* 4.0 14.5 + - - +
85O GLY* 4.3 15.3 - - - +
86O MET 4.4 2.0 - - - +
87O ASP* 3.2 59.9 - - + +
91O VAL* 3.7 24.2 - - + -
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Residues in contact with GLU 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77O ARG* 3.7 17.2 + - + +
78O GLU* 3.0 32.4 + - + +
79O LEU 2.8 1.0 + - - -
80O VAL* 1.3 78.4 - - - +
82O LYS* 1.3 70.5 + - + +
84O ASP* 4.9 3.6 - - - +
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Residues in contact with LYS 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ARG* 4.9 9.4 - - - +
247A THR* 6.2 1.3 - - - -
67O MET* 3.6 37.0 - - + -
71O LEU* 3.7 25.8 - - + +
74O LEU* 5.3 4.8 - - + +
78O GLU* 4.7 19.0 + - - +
79O LEU 2.7 10.5 + - - +
80O VAL 2.9 1.2 - - - -
81O GLU* 1.3 94.3 - - + +
83O ILE* 1.3 67.1 + - + +
84O ASP* 2.9 15.2 + - - +
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Residues in contact with ILE 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63O SER* 4.2 28.0 - - - +
64O VAL* 4.7 6.7 - - + +
67O MET* 4.1 35.2 - - + -
79O LEU* 3.1 56.6 + - + +
80O VAL* 4.3 1.8 - - + +
82O LYS* 1.3 75.5 - - - +
84O ASP* 1.3 64.7 + - - +
85O GLY* 3.7 20.9 - - - +
90O SER* 5.9 0.7 - - - +
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Residues in contact with ASP 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80O VAL* 4.0 14.2 + - - +
81O GLU 4.9 2.6 - - - +
82O LYS* 2.9 18.1 + - - +
83O ILE* 1.3 79.2 - - - +
85O GLY* 1.3 58.8 + - - +
86O MET* 3.5 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