Contacts of the helix formed by residues 46 - 57 (chain O) in PDB entry 6CNC
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 LEU 46 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A SER* 4.8 4.0 - - - -
248A VAL* 4.3 8.5 - - + -
252A ARG* 4.0 19.3 - - - +
43O ASN* 6.0 0.7 - - - +
44O PRO 2.7 4.7 + - - +
45O ASP* 1.3 80.3 - - + +
47O PHE* 1.3 65.6 + - - +
49O TYR* 2.9 26.0 + - + +
50O LYS* 3.5 26.9 + - + +
66O GLY* 3.4 32.3 - - - +
69O VAL* 3.4 34.8 - - + -
70O ALA* 3.6 24.9 - - + -
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Residues in contact with PHE 47 (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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39O GLN* 4.5 8.3 - - - -
43O ASN* 3.3 41.7 - - + +
44O PRO 2.9 5.7 + - - -
45O ASP 2.9 1.6 + - - -
46O LEU* 1.3 80.6 - - - +
48O LEU* 1.3 73.1 + - + +
49O TYR 3.1 0.7 + - - -
50O LYS* 3.3 24.9 + - + +
51O GLU* 3.3 21.7 + - + -
582O GLU* 3.1 21.8 - - - +
585O MET 4.8 0.2 - - - -
586O ALA* 3.3 37.0 - - + -
590O PHE* 3.1 39.7 - + - -
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Residues in contact with LEU 48 (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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45O ASP 3.4 10.1 + - - +
46O LEU 3.0 0.8 + - - -
47O PHE* 1.3 88.9 - - + +
49O TYR* 1.3 76.7 + - + +
51O GLU* 3.3 2.8 + - - +
52O LEU* 2.9 41.2 + - + +
131O LEU* 3.5 26.2 - - + -
581O LEU* 3.4 34.3 - - + +
582O GLU* 4.0 2.8 + - - +
585O MET* 3.6 39.5 - - + +
586O ALA 4.7 0.2 - - - +
589O LEU* 5.1 1.6 - - + -
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Residues in contact with TYR 49 (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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45O ASP* 3.9 23.1 - - - -
46O LEU* 2.9 20.0 + - + +
48O LEU* 1.3 86.7 - - + +
50O LYS* 1.3 59.0 + - - +
52O LEU* 2.7 28.5 + - + +
53O VAL* 3.0 16.4 + - - +
65O ILE* 4.5 16.4 - - + -
69O VAL* 4.7 12.8 - - + -
122O TYR* 4.4 30.8 - + + -
123O ASN 5.7 0.2 - - - -
124O GLU 4.9 0.2 + - - -
125O GLU* 3.9 29.7 + - - +
127O ILE* 3.9 26.9 - - + +
128O HIS 5.1 1.3 - - - -
581O LEU* 5.5 5.2 - - + +
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Residues in contact with LYS 50 (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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248A VAL* 4.8 17.2 - - - +
43O ASN* 4.7 14.0 - - - +
46O LEU* 3.5 30.6 + - + +
47O PHE* 3.3 24.6 + - + +
49O TYR* 1.3 78.1 - - - +
51O GLU* 1.3 58.4 + - - +
53O VAL* 3.7 12.5 - - + +
54O LYS* 3.0 35.3 + - - +
62O ALA* 4.3 6.7 - - + +
63O SER* 5.5 4.9 - - - -
65O ILE* 5.6 0.2 - - - -
66O GLY* 3.9 34.8 - - - +
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Residues in contact with GLU 51 (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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47O PHE* 3.3 21.0 + - + +
48O LEU* 3.3 7.4 + - + +
49O TYR 2.9 1.0 + - - -
50O LYS* 1.3 79.1 - - - +
52O LEU* 1.3 55.9 + - - +
53O VAL 3.4 0.2 - - - -
54O LYS* 2.9 10.8 + - + +
55O ALA* 2.3 41.0 + - + +
585O MET 4.7 0.6 - - - +
586O ALA* 3.2 19.2 - - - +
589O LEU* 3.0 22.2 - - + +
590O PHE* 2.7 61.5 + - + -
593O GLU* 4.0 6.7 - - + +
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Residues in contact with LEU 52 (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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48O LEU* 2.9 48.5 + - + +
49O TYR* 2.7 14.9 + - + +
51O GLU* 1.3 71.1 - - - +
53O VAL* 1.3 52.3 + - - +
55O ALA* 2.9 2.3 + - - +
56O HIS* 2.6 41.3 + - + +
127O ILE* 3.7 28.5 - - + +
128O HIS 5.1 0.2 - - - +
130O LEU* 5.7 2.7 - - + -
131O LEU* 3.7 34.5 - - + +
589O LEU* 3.6 24.4 - - + +
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Residues in contact with VAL 53 (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 3.0 15.0 + - - +
50O LYS* 3.7 11.4 - - - -
52O LEU* 1.3 75.4 - - - +
54O LYS* 1.3 56.4 + - - +
56O HIS* 4.1 3.6 - - - -
57O LEU* 2.5 43.8 + - + +
58O GLY 2.4 27.6 + - - -
61O ALA 3.8 7.6 - - - +
62O ALA* 3.6 33.0 - - + +
65O ILE* 4.5 21.3 - - + -
127O ILE* 4.3 13.5 - - + +
130O LEU* 5.3 1.8 - - + -
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Residues in contact with LYS 54 (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* 3.0 32.1 + - - +
51O GLU* 2.9 12.6 + - + +
53O VAL* 1.3 82.4 - - - +
55O ALA* 1.3 62.2 + - - +
56O HIS 3.1 1.4 + - - -
57O LEU 4.2 0.3 - - - -
58O GLY* 3.2 28.7 + - - -
59O GLU 5.2 1.3 - - - +
62O ALA* 3.6 9.2 - - + -
590O PHE* 6.0 5.4 - - + -
593O GLU* 5.1 2.6 - - + +
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Residues in contact with ALA 55 (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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51O GLU* 2.3 31.2 + - + +
52O LEU 3.2 3.8 - - - +
54O LYS* 1.3 68.5 - - - +
56O HIS* 1.3 58.6 + - - +
589O LEU* 3.9 24.5 - - + -
592O LYS* 4.6 7.2 + - - -
593O GLU* 3.2 46.3 - - + +
66Q LYS* 5.9 3.1 - - - +
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Residues in contact with HIS 56 (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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52O LEU* 2.6 20.0 + - + +
53O VAL* 2.9 2.9 + - - +
54O LYS 4.3 0.2 - - - -
55O ALA* 1.3 77.5 - - - +
57O LEU* 1.3 69.8 + - + +
101O LEU* 5.0 2.9 - - + -
130O LEU* 3.3 45.2 - - + +
61Q PHE* 3.7 23.9 - + - -
62Q GLY* 4.4 15.0 - - - +
65Q VAL* 3.3 41.1 - - + +
66Q LYS* 4.3 25.1 + - - +
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Residues in contact with LEU 57 (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* 2.5 22.9 + - + +
54O LYS 4.2 0.2 - - - -
56O HIS* 1.3 84.8 - - + +
58O GLY* 1.3 62.5 + - - +
59O GLU* 4.2 9.9 - - - +
61O ALA* 4.0 15.7 - - + -
97O SER* 5.0 6.1 - - - +
98O LEU* 3.7 30.7 - - + -
101O LEU* 4.0 22.2 - - + -
103O CYS* 4.6 2.2 - - - -
130O LEU* 5.3 2.2 - - + -
65Q VAL* 3.6 30.5 - - + +
66Q LYS* 5.9 1.8 - - - +
70Q PHE* 4.1 27.7 - - + +
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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