Contacts of the helix formed by residues 23 - 32 (chain G) in PDB entry 1CVJ
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 THR 23 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E PRO 5.6 1.6 - - - +
21E ASP* 4.8 14.2 + - - +
22E VAL 5.9 0.2 - - - +
23E THR* 3.7 24.9 - - + -
44E ARG* 6.1 3.6 - - - -
21G ASP 3.4 14.1 + - - +
22G VAL* 1.3 76.7 - - - +
24G GLU* 1.3 65.2 + - - +
25G ALA* 3.4 11.5 + - - +
26G MET* 3.0 40.8 + - - +
27G LEU* 3.1 16.3 + - - +
42G VAL* 4.0 7.0 - - - -
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Residues in contact with GLU 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E ARG* 3.6 15.8 + - - +
49E ARG* 2.6 51.3 + - + +
23G THR* 1.3 73.8 - - - +
25G ALA* 1.3 57.1 + - - +
27G LEU* 3.4 2.3 + - - +
28G TYR* 3.0 28.4 + - - +
40G ILE* 3.4 26.2 - - + +
41G ARG* 3.6 2.1 - - - -
42G VAL* 3.2 36.1 + - + +
44G ARG* 3.3 11.8 + - - +
7S A 3.2 25.8 + - - -
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Residues in contact with ALA 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E PRO 5.6 5.4 - - - +
44E ARG* 5.5 1.5 - - - +
48E THR 3.9 3.8 - - - +
49E ARG* 3.5 31.8 + - - +
50E ARG* 4.0 9.4 - - - -
51E SER 4.8 2.2 - - - +
23G THR* 3.0 11.3 - - - +
24G GLU* 1.3 79.8 - - - +
26G MET* 1.3 62.1 + - + +
28G TYR* 3.5 2.8 + - - +
29G GLU* 3.3 29.2 + - - +
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Residues in contact with MET 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ASP* 4.5 17.0 - - - +
21G ASP 4.0 6.3 - - - +
22G VAL* 3.7 20.2 - - + -
23G THR* 3.0 33.8 + - - +
25G ALA* 1.3 76.3 - - + +
27G LEU* 1.3 62.2 + - - +
29G GLU* 3.7 12.2 + - - +
30G LYS* 3.0 27.2 + - - +
77G ILE* 4.1 11.8 - - + +
78G LYS* 3.3 42.2 - - + +
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Residues in contact with LEU 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G VAL* 4.5 15.0 - - + -
18G LEU* 4.2 8.5 - - + -
22G VAL* 3.8 15.9 - - + -
23G THR 3.1 8.3 + - - +
24G GLU 3.9 4.9 - - - +
26G MET* 1.3 74.4 - - - +
28G TYR* 1.3 57.1 + - - +
30G LYS* 4.0 0.4 - - - -
31G PHE* 2.6 66.5 + - + +
40G ILE* 3.9 17.7 - - + -
42G VAL* 3.9 17.0 - - + -
55G ALA* 3.4 33.2 - - + -
57G VAL* 4.5 1.1 - - + -
77G ILE* 4.2 15.5 - - + -
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Residues in contact with TYR 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ASP* 2.5 34.1 + - - -
91B PRO 4.6 0.2 - - - -
92B SER* 3.7 10.6 + - - -
47E ILE* 3.7 20.2 - - + +
48E THR* 3.4 48.5 - - + +
49E ARG* 4.8 1.6 - - + -
24G GLU 3.0 14.5 + - - +
25G ALA 3.6 2.5 - - - +
27G LEU* 1.3 78.0 - - - +
29G GLU* 1.3 65.7 + - + +
31G PHE 3.0 0.3 + - - -
32G SER* 2.4 67.8 + - - -
37G ILE* 3.6 28.7 - - + -
40G ILE* 4.7 4.9 - - + +
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Residues in contact with GLU 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LYS* 5.2 4.9 + - - -
50E ARG* 5.2 8.1 + - - -
25G ALA* 3.3 16.4 + - - +
26G MET* 3.9 12.9 - - - +
28G TYR* 1.3 89.6 - - + +
30G LYS* 1.3 65.1 + - - +
32G SER* 4.3 2.7 - - - -
33G PRO* 3.0 24.3 - - - +
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Residues in contact with LYS 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G MET 3.0 17.8 + - - +
27G LEU* 3.5 7.2 - - - +
29G GLU* 1.3 81.3 - - - +
31G PHE* 1.3 71.8 + - + +
33G PRO* 3.9 5.2 - - - +
72G MET* 3.1 37.8 - - - +
75G ASP* 3.4 32.7 + - - -
76G VAL 4.7 4.3 - - - +
77G ILE* 3.5 34.3 - - + -
82G VAL* 6.0 0.4 - - + -
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Residues in contact with PHE 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LEU* 4.9 4.9 - - + -
15G VAL* 4.2 14.8 - - + -
27G LEU* 2.6 59.9 + - + +
30G LYS* 1.3 88.2 - - + +
32G SER* 1.3 62.8 + - - +
33G PRO* 3.2 4.0 - - - -
34G ALA* 3.0 22.1 + - - +
37G ILE* 3.9 9.0 - - + -
57G VAL* 4.1 20.0 - - + -
59G PHE* 3.5 18.1 - + + -
68G ALA* 4.1 15.9 - - + -
72G MET* 3.6 24.0 - - + -
77G ILE* 4.9 1.1 - - + -
82G VAL* 4.8 4.3 - - + -
84G ILE* 3.4 34.8 - - + -
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Residues in contact with SER 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ASP* 4.5 0.5 + - - -
92B SER* 3.6 19.4 - - - -
28G TYR* 2.4 67.9 + - - -
29G GLU* 3.9 3.4 - - - -
31G PHE* 1.3 66.8 - - - +
33G PRO* 1.3 64.7 - - - +
34G ALA 3.1 5.2 + - - -
35G GLY* 3.3 17.7 + - - +
37G ILE* 3.7 11.1 - - - +
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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