Contacts of the strand formed by residues 36 - 45 (chain G) in PDB entry 4CDC
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 GLN 36 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18G GLN* 2.9 40.3 + - + +
19G VAL 3.5 13.2 - - - +
20G GLY* 3.8 1.1 - - - +
33G MET* 3.2 36.4 - - - +
34G GLY 4.1 5.4 - - - +
35G PRO* 1.3 80.2 - - + +
37G GLU* 1.3 62.2 + - - +
38G LYS 3.8 0.7 - - - +
114G THR* 3.3 19.6 + - - +
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Residues in contact with GLU 37 (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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19G VAL 2.8 10.0 + - - +
20G GLY* 3.7 3.6 - - - -
21G SER* 3.7 6.6 + - - -
22G SER* 3.0 36.4 + - - +
35G PRO* 3.0 35.6 - - + +
36G GLN* 1.3 74.4 - - - +
38G LYS* 1.3 60.1 + - + +
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Residues in contact with LYS 38 (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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18G GLN* 3.6 4.6 - - - +
19G VAL* 2.7 45.9 + - + +
36G GLN* 3.8 1.0 - - - +
37G GLU* 1.3 82.5 - - + +
39G LYS* 1.3 74.4 + - - +
40G VAL* 4.5 11.3 - - + +
255K GLN* 5.7 9.0 - - - +
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Residues in contact with LYS 39 (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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16G VAL* 4.1 21.7 - - + +
17G PHE 3.2 6.5 - - - +
18G GLN* 3.7 18.6 - - - +
38G LYS* 1.3 89.4 + - - +
40G VAL* 1.3 68.2 - - - +
41G VAL* 4.6 16.5 - - + +
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Residues in contact with VAL 40 (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 TRP 3.8 0.7 - - - +
16G VAL* 3.6 1.3 - - - -
17G PHE* 2.8 34.9 + - + +
19G VAL* 4.6 7.6 - - + -
38G LYS* 4.5 14.6 - - + +
39G LYS* 1.3 79.5 - - - +
41G VAL* 1.3 69.5 + - - +
42G VAL* 4.0 20.5 + - + -
52G ASP* 5.6 4.7 - - + -
72G LEU* 6.1 1.1 - - + -
77G TRP* 4.0 32.5 - - + -
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Residues in contact with VAL 41 (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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14G THR* 3.6 29.4 - - + -
15G TRP 3.4 5.6 - - - +
16G VAL* 4.6 13.9 - - + -
39G LYS* 4.6 24.0 - - + +
40G VAL* 1.3 75.4 - - - +
42G VAL* 1.3 65.5 + - - +
43G TYR* 3.7 19.5 - - + +
52G ASP* 3.8 23.0 - - - +
53G ASP* 3.8 21.5 + - - +
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Residues in contact with VAL 42 (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 GLY 3.8 0.7 - - - +
14G THR 3.7 0.7 - - - -
15G TRP* 2.8 41.1 + - + +
17G PHE* 3.8 32.5 - - + -
40G VAL* 4.0 13.5 - - + -
41G VAL* 1.3 78.6 - - - +
43G TYR* 1.3 65.0 + - - +
44G LEU* 3.7 26.0 + - + -
50G ALA* 4.7 1.1 - - + -
51G TYR 3.5 8.3 - - - +
70G ILE* 4.1 13.7 - - + -
72G LEU* 4.2 23.3 - - + -
77G TRP* 5.2 4.9 - - - +
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Residues in contact with TYR 43 (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 GLY 3.5 4.7 - - - +
14G THR* 3.2 37.0 - - + -
41G VAL* 3.7 18.2 - - + +
42G VAL* 1.3 73.7 - - - +
44G LEU* 1.3 63.7 + - - +
45G GLN* 4.1 3.1 - - + +
49G THR 3.8 0.2 - - - +
50G ALA* 3.4 4.9 - - - -
51G TYR* 2.7 89.1 + + + +
52G ASP* 4.2 11.0 - - - -
53G ASP* 2.6 31.3 + - - -
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Residues in contact with LEU 44 (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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11G LEU* 3.5 49.8 - - + +
12G LEU* 3.8 7.4 - - - +
13G GLY* 2.9 27.3 + - - +
15G TRP* 3.9 16.2 - - + -
42G VAL* 3.7 20.6 - - + -
43G TYR* 1.3 80.6 - - - +
45G GLN* 1.3 64.8 + - - +
49G THR 3.5 1.6 - - - -
50G ALA* 4.0 8.5 - - + -
60G PHE* 3.9 32.3 - - + -
68G PHE* 5.6 0.2 - - + -
70G ILE* 3.8 21.8 - - + -
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Residues in contact with GLN 45 (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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332E ASN* 3.4 21.0 - - + +
333E GLU* 3.1 36.5 + - - +
334E ALA* 3.1 27.2 + - - +
420F GLY 5.1 5.7 + - - -
12G LEU* 4.0 4.7 - - - -
43G TYR* 5.0 2.5 - - + +
44G LEU* 1.3 80.6 - - - +
46G LYS* 1.3 62.4 + - - +
49G THR* 2.9 37.2 + - - +
51G TYR* 3.4 27.4 + - + -
60G PHE* 3.3 3.3 - - - -
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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