Contacts of the helix formed by residues 58 - 72 (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 GLY 58 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53O VAL 2.8 8.1 + - - -
54O LYS* 2.7 26.9 + - - -
57O LEU* 1.3 73.5 - - - +
59O GLU* 1.3 79.9 + - - +
61O ALA* 3.1 19.9 + - - +
62O ALA* 3.9 3.1 - - - -
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Residues in contact with GLU 59 (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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54O LYS* 4.7 6.7 - - - +
57O LEU 5.4 1.1 - - - +
58O GLY* 1.3 77.6 - - - +
60O ARG* 1.3 89.2 + - + +
61O ALA* 5.4 0.4 - - + -
62O ALA* 2.9 16.7 + - - +
63O SER* 3.2 12.0 + - - -
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Residues in contact with ARG 60 (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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59O GLU* 1.3 95.6 + - + +
61O ALA* 1.3 72.8 + - + +
62O ALA 3.2 1.0 + - - -
63O SER* 3.2 16.5 + - - +
64O VAL* 3.5 12.5 + - - +
85O GLY 5.3 1.8 + - - -
86O MET* 4.8 18.0 - - - +
89O ASP* 4.4 6.7 - - - +
90O SER* 3.4 38.2 - - - +
93O THR* 5.4 7.1 + - - +
94O THR* 3.7 22.7 + - + +
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Residues in contact with ALA 61 (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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53O VAL* 3.6 9.8 - - - +
57O LEU* 4.1 24.7 - - + -
58O GLY 3.1 12.2 + - - +
59O GLU* 5.4 0.4 - - + -
60O ARG* 1.3 82.3 - - + +
62O ALA* 1.3 60.9 + - - +
64O VAL* 3.1 18.0 - - - +
94O THR* 3.7 21.1 - - + -
97O SER* 6.4 1.3 - - - -
98O LEU* 4.4 8.3 - - + +
70Q PHE 5.0 9.0 - - - +
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Residues in contact with ALA 62 (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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50O LYS* 4.5 6.1 - - + +
53O VAL* 3.5 18.0 - - + +
54O LYS* 3.5 45.3 - - + +
58O GLY 3.3 4.0 + - - -
59O GLU 2.9 16.2 + - - +
61O ALA* 1.3 71.6 - - - +
63O SER* 1.3 55.8 + - - +
64O VAL 2.7 16.7 + - - -
65O ILE* 2.8 18.9 + - - +
66O GLY 3.6 5.6 + - - -
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Residues in contact with SER 63 (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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50O LYS* 5.7 6.5 - - - -
59O GLU 3.2 7.0 + - - -
60O ARG* 3.2 12.8 + - - -
62O ALA* 1.3 76.3 - - - +
64O VAL* 1.3 64.6 + - - +
66O GLY* 3.5 4.5 + - - +
67O MET* 3.3 16.1 + - - +
83O ILE* 4.2 21.5 - - - +
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Residues in contact with VAL 64 (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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60O ARG 3.5 8.2 + - - +
61O ALA 3.1 22.4 - - - +
62O ALA 2.7 4.4 + - - -
63O SER* 1.3 73.2 - - - +
65O ILE* 1.3 63.0 + - + +
67O MET* 2.7 31.1 + - + +
68O LEU* 2.9 18.2 + - + -
74O LEU* 6.3 0.9 - - + -
79O LEU* 3.6 30.7 - - + -
83O ILE* 4.7 10.6 - - + +
91O VAL* 6.0 1.3 - - + -
94O THR* 4.4 15.3 - - - +
95O LEU* 5.5 9.0 - - + +
98O LEU* 4.1 18.8 - - + -
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Residues in contact with ILE 65 (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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49O TYR* 4.7 16.6 - - + -
53O VAL* 3.7 36.6 - - + -
62O ALA 2.8 10.9 + - - +
64O VAL* 1.3 78.3 - - + +
66O GLY* 1.3 63.3 + - - +
68O LEU* 3.0 11.3 + - + -
69O VAL* 2.9 40.9 + - + +
98O LEU* 3.7 35.4 - - + -
103O CYS* 4.5 16.4 - - + +
104O VAL* 4.9 5.8 - - + -
122O TYR* 5.0 7.4 - - + -
127O ILE* 4.8 8.5 - - + -
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Residues in contact with GLY 66 (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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46O LEU* 3.2 24.1 - - - +
49O TYR* 6.4 0.4 - - - -
50O LYS* 4.9 20.3 - - - +
53O VAL* 5.4 1.8 - - - +
62O ALA 3.6 4.6 + - - -
63O SER* 3.5 6.9 + - - -
64O VAL 3.1 1.6 - - - -
65O ILE* 1.3 80.1 - - - +
67O MET* 1.3 61.5 + - - +
69O VAL* 5.3 0.2 - - - -
70O ALA* 3.1 19.6 + - - +
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Residues in contact with MET 67 (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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247A THR* 3.7 28.7 - - - +
63O SER 3.3 10.4 + - - +
64O VAL* 2.7 14.9 + - + +
66O GLY* 1.3 71.4 - - - +
68O LEU* 1.3 62.1 + - - +
70O ALA* 3.7 4.2 - - - +
71O LEU* 2.9 38.0 + - + +
74O LEU* 4.0 21.5 - - + -
82O LYS* 3.6 43.1 - - + -
83O ILE* 4.1 26.7 - - + +
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Residues in contact with LEU 68 (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* 2.9 18.3 + - + +
65O ILE* 3.0 15.0 + - + +
67O MET* 1.3 75.2 - - - +
69O VAL* 1.3 55.7 + - - +
72O GLY* 2.6 59.7 + - - +
74O LEU* 4.2 19.2 - - + +
79O LEU* 6.2 0.7 - - + -
95O LEU* 6.2 0.7 - - + -
104O VAL* 4.6 12.3 - - + -
120O TYR* 3.3 28.3 - - + +
121O TYR* 3.3 10.8 - - - +
122O TYR* 3.3 37.7 - - + +
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Residues in contact with VAL 69 (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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236A SER* 3.1 25.5 + - - +
237A ALA 3.7 2.1 + - - -
45O ASP* 4.9 7.9 - - - +
46O LEU* 4.0 28.7 - - + -
49O TYR* 5.1 16.4 - - + -
65O ILE* 2.9 29.2 + - + +
68O LEU* 1.3 73.8 - - - +
70O ALA* 1.3 64.5 + - - +
72O GLY* 3.6 5.8 + - - -
122O TYR* 3.5 50.8 - - + -
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Residues in contact with ALA 70 (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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236A SER* 3.2 17.3 - - - +
237A ALA 3.2 18.9 + - - +
239A CYS* 4.6 4.7 - - - +
246A ALA* 4.1 19.2 - - + +
247A THR* 5.3 4.7 - - - -
248A VAL* 5.2 11.4 - - + -
252A ARG* 5.4 1.8 - - - +
46O LEU* 3.6 13.1 - - + +
66O GLY 3.1 21.5 + - - +
67O MET* 3.7 5.6 - - - +
68O LEU 3.2 0.2 - - - -
69O VAL* 1.3 80.1 - - - +
71O LEU* 1.3 58.9 + - + +
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Residues in contact with LEU 71 (chain O).
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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124A LEU* 5.5 3.5 - - - +
128A ARG* 3.3 29.7 + - - +
237A ALA 3.8 12.3 - - - +
239A CYS* 6.5 0.2 - - - -
240A GLU* 3.8 21.5 - - - +
246A ALA 4.8 13.9 - - - +
247A THR* 6.3 1.6 - - - -
67O MET* 2.9 27.4 + - + +
68O LEU 3.6 0.2 - - - -
70O ALA* 1.3 73.8 - - - +
72O GLY* 1.3 61.4 + - - +
73O ARG 3.8 14.4 + - - +
74O LEU* 4.5 16.8 - - + -
82O LYS* 3.7 32.8 - - + +
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Residues in contact with GLY 72 (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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237A ALA* 4.7 10.8 - - - -
68O LEU* 2.6 42.8 + - - +
69O VAL* 3.6 5.5 + - - -
70O ALA 3.4 3.0 + - - -
71O LEU* 1.3 70.2 - - - +
73O ARG* 1.3 67.9 + - - +
74O LEU* 3.9 2.8 - - - +
120O TYR 4.9 0.2 - - - -
121O TYR* 5.1 4.0 - - - -
122O TYR* 6.1 3.6 - - - -
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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