Contacts of the helix formed by residues 63 - 74 (chain T) in PDB entry 6CP3
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 63 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64S PHE* 4.5 11.9 - - + -
59T GLU* 2.9 26.2 + - + +
60T ALA* 4.9 2.9 - - - -
61T THR 3.3 0.4 + - - -
62T GLY* 1.3 78.3 - - - +
64T PHE* 1.3 68.7 + - + +
65T CYS 3.3 1.6 - - - -
66T LEU* 2.9 41.6 + - + +
67T MET* 2.9 13.4 + - + +
168X ALA* 4.4 16.8 - - + +
171X ILE* 3.8 20.9 - - + -
172X SER* 3.7 37.5 - - - +
175X LEU* 5.1 5.4 - - + -
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Residues in contact with PHE 64 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K LEU* 5.1 2.0 - - + -
63K LEU* 5.9 5.2 - - + -
66K LEU* 3.8 25.1 - - + -
60T ALA* 3.1 42.8 - - + -
61T THR 4.0 3.4 + - - +
63T LEU* 1.3 78.7 - - + +
65T CYS* 1.3 55.5 + - - +
67T MET* 3.0 29.2 + - + +
68T VAL* 2.5 39.3 + - - +
164X LEU* 3.6 57.9 - - + -
167X PHE* 5.0 7.6 - + - -
168X ALA* 4.1 14.8 - - + -
171X ILE* 6.5 0.7 - - + -
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Residues in contact with CYS 65 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K THR* 3.8 16.6 - - - -
17K ILE* 3.7 18.6 - - - -
19K LEU* 3.7 33.0 - - + +
15T SER* 3.2 25.5 - - - +
16T THR 5.1 0.4 - - - -
18T GLY* 3.6 26.7 - - - -
62T GLY 5.2 1.1 - - - -
63T LEU 4.5 0.6 - - - +
64T PHE* 1.3 78.1 - - - +
66T LEU* 1.3 51.4 + - - +
68T VAL* 3.0 10.4 + - - +
69T SER 2.7 29.6 + - - -
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Residues in contact with LEU 66 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64S PHE* 3.7 33.4 - - + -
65S CYS* 5.3 0.9 - - - -
68S VAL* 3.9 27.6 - - + -
15T SER 4.4 1.1 - - - -
16T THR* 5.0 6.5 + - - +
19T LEU* 3.8 23.2 - - + +
62T GLY 4.3 6.1 + - - +
63T LEU* 2.9 32.7 + - + +
65T CYS* 1.3 78.3 - - - +
67T MET* 1.3 55.7 + - - +
69T SER* 2.8 30.2 + - - -
70T PHE* 3.0 31.3 + - + -
175X LEU* 4.6 7.4 - - + -
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Residues in contact with MET 67 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66K LEU* 4.7 7.0 - - + -
70K PHE* 6.5 1.1 - - + -
63T LEU* 2.9 12.2 + - + +
64T PHE* 3.0 47.3 + - + +
66T LEU* 1.3 72.2 - - - +
68T VAL* 1.3 74.3 + - + +
69T SER 3.1 0.7 - - - -
70T PHE* 2.9 29.0 + - + +
71T LEU* 3.0 39.8 + - + +
171X ILE* 6.0 6.5 - - + -
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Residues in contact with VAL 68 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K ALA* 4.2 8.1 - - + +
13K GLY* 5.2 0.2 - - - -
16K THR* 3.4 36.1 - - + +
66K LEU* 4.6 10.5 - - + +
69K SER* 4.6 4.7 - - - +
73K LEU* 6.2 6.5 - - + -
15T SER* 3.9 14.0 + - - -
64T PHE 2.5 22.1 + - - +
65T CYS* 3.1 13.9 - - - +
67T MET* 1.3 85.1 - - + +
69T SER* 1.3 59.7 + - - +
71T LEU* 5.0 5.3 - - + +
72T LEU* 3.2 30.7 + - + +
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Residues in contact with SER 69 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68S VAL* 3.3 29.4 - - - +
12T ALA* 3.5 22.8 + - - +
15T SER* 3.3 29.8 + - - -
16T THR* 4.4 0.8 + - - -
65T CYS 2.7 8.9 + - - -
66T LEU* 2.8 20.9 - - - -
68T VAL* 1.3 74.9 - - - +
70T PHE* 1.3 60.8 + - - +
73T LEU* 3.5 15.4 + - - +
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Residues in contact with PHE 70 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67S MET* 5.3 7.0 - - + -
68S VAL* 4.6 18.6 - - + -
71S LEU* 4.9 17.3 - - + -
66T LEU* 3.0 46.2 + - + -
67T MET* 2.9 20.8 + - + +
69T SER* 1.3 76.7 - - - +
71T LEU* 1.3 62.9 + - - +
73T LEU* 2.7 39.3 + - + +
74T PHE* 3.4 13.5 + + + -
175X LEU* 4.1 29.8 - - + -
179X SER* 5.8 2.0 - - - -
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Residues in contact with LEU 71 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K PHE* 6.0 4.0 - - + -
73K LEU* 3.7 29.4 - - + -
74K PHE* 4.6 10.8 - - + -
67T MET* 3.0 42.1 + - + +
68T VAL* 5.0 4.7 - - + +
70T PHE* 1.3 74.5 - - + +
72T LEU* 1.3 61.8 + - - +
73T LEU 3.2 0.2 - - - -
74T PHE* 2.9 32.8 + - + +
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Residues in contact with LEU 72 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K TYR* 3.5 52.9 - - + +
12K ALA* 5.0 3.6 - - + -
13K GLY* 4.6 5.2 - - - +
73K LEU* 3.7 18.8 - - + -
8T LYS* 3.2 37.4 - - + +
11T GLY* 3.5 32.8 - - - +
12T ALA* 3.5 3.1 - - + +
15T SER* 4.5 2.2 - - - +
68T VAL* 3.2 23.9 + - + +
69T SER 4.3 2.7 - - - +
70T PHE 3.2 0.8 - - - -
71T LEU* 1.3 77.6 - - + +
73T LEU* 1.3 63.1 + - - +
74T PHE 3.2 2.2 - - - +
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Residues in contact with LEU 73 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71S LEU* 3.8 32.1 - - + +
72S LEU* 5.0 8.5 - - + -
8T LYS* 3.8 9.7 + - - -
9T TYR* 3.6 41.4 + - + +
12T ALA* 4.6 8.0 - - + +
69T SER 3.5 12.5 + - - +
70T PHE* 2.7 23.9 + - + +
72T LEU* 1.3 79.7 - - - +
74T PHE* 1.3 83.8 + - + +
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Residues in contact with PHE 74 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8T LYS* 3.1 29.9 + - - +
70T PHE* 3.4 18.1 + + + -
71T LEU* 2.9 26.2 + - + +
72T LEU* 3.5 2.1 - - - +
73T LEU* 1.3 102.5 - - + +
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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