Contacts of the strand formed by residues 17 - 24 (chain G) in PDB entry 1M06
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 ARG 17 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G THR* 4.0 6.7 - - - +
12G ALA 2.8 24.2 + - - -
13G ILE* 4.6 0.2 - - - +
14G GLN* 3.4 14.5 - - - +
15G THR* 3.0 33.6 + - - +
16G SER* 1.3 78.7 - - - +
18G PHE* 1.3 66.0 + - - +
41G ILE* 4.6 3.8 - - - +
47G VAL* 3.4 39.5 - - + +
49G ASN* 4.5 10.3 - - - +
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Residues in contact with PHE 18 (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 SER 5.3 0.9 - - - +
17G ARG* 1.3 79.2 - - - +
19G SER* 1.3 79.9 + - - +
20G VAL* 3.7 23.5 + - + -
36G ILE 4.7 3.4 - - - -
37G ASN* 4.0 17.0 - - - -
38G GLY 5.1 1.6 - - - -
39G GLY* 4.2 38.4 - - - +
41G ILE* 5.3 5.2 - - + -
47G VAL 3.2 6.0 + - - +
48G VAL* 3.4 11.1 - - + -
49G ASN* 2.8 26.6 + - - +
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Residues in contact with SER 19 (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 PHE* 1.3 93.2 - - - +
20G VAL* 1.3 62.6 + - - +
21G THR* 4.0 10.3 + - - +
49G ASN* 3.5 21.1 + - - +
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Residues in contact with VAL 20 (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 PHE* 3.7 16.6 - - + -
19G SER* 1.3 75.4 - - - +
21G THR* 1.3 73.0 + - - +
23G ASN 5.9 1.6 - - - +
24G VAL* 6.4 0.9 - - + -
36G ILE* 3.6 40.6 - - + +
37G ASN* 4.3 0.4 - - - +
48G VAL* 3.5 26.5 - - + -
49G ASN 2.8 9.3 + - - +
50G LEU* 3.6 21.8 - - + +
51G TYR* 3.2 25.6 + - - +
52G ALA* 4.7 2.9 - - + -
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Residues in contact with THR 21 (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 SER* 4.0 10.3 + - - +
20G VAL* 1.3 89.1 - - - +
22G GLY* 1.3 67.6 + - - +
23G ASN 3.9 4.3 + - - +
51G TYR* 3.6 27.4 - - + +
52G ALA* 4.0 3.1 - - - -
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Residues in contact with GLY 22 (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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21G THR* 1.3 79.3 - - - +
23G ASN* 1.3 60.8 + - - -
51G TYR 4.3 0.4 + - - -
52G ALA* 2.9 8.2 - - - +
53G ASN* 2.7 33.5 + - - +
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Residues in contact with ASN 23 (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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21G THR 3.9 4.2 + - - +
22G GLY* 1.3 79.0 - - - +
24G VAL* 1.3 61.6 + - - +
25G ILE* 4.2 10.8 - - + -
36G ILE* 5.5 2.3 - - - +
52G ALA* 5.0 0.6 - - - +
53G ASN* 3.3 16.8 + - - +
55G ASN* 3.2 38.7 - - + +
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Residues in contact with VAL 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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23G ASN* 1.3 75.4 - - - +
25G ILE* 1.3 62.3 + - - +
26G PRO* 2.9 13.8 - - - +
34G PRO* 5.7 0.2 - - + -
36G ILE* 4.1 22.0 - - + -
50G LEU* 6.3 1.6 - - + -
52G ALA* 4.6 11.4 - - + -
53G ASN 3.0 18.8 + - - +
54G MET* 3.3 39.7 - - + +
55G ASN 3.1 11.6 + - - -
64G PHE* 3.9 30.7 - - + -
167G VAL* 4.8 3.1 - - + -
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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