Contacts of the strand formed by residues 102 - 107 (chain G) in PDB entry 43C9
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 102 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6G GLN* 3.6 16.2 + - - +
7G THR 4.2 2.4 + - - -
8G PRO 2.8 27.5 + - - +
9G SER 3.7 1.6 - - - -
10G SER 4.6 0.4 - - - +
11G LEU* 4.5 15.7 - - + -
21G MET* 4.0 37.8 - - + +
22G SER 4.9 0.2 + - - -
85G ASP* 3.4 5.9 - - - +
86G TYR* 3.0 36.3 + - - +
101G GLY* 1.3 75.5 + - - -
103G LYS* 1.3 69.8 + - - +
104G LEU* 3.5 2.5 + - - +
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Residues in contact with LYS 103 (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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9G SER 3.0 17.0 + - - +
10G SER* 3.5 7.5 - - - -
11G LEU 3.1 28.2 + - - +
84G ALA 4.5 2.2 - - - +
85G ASP* 3.0 40.9 + - - +
102G THR* 1.3 71.4 - - - +
104G LEU* 1.3 59.8 + - - +
105G GLU* 3.6 34.4 + - + +
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Residues in contact with LEU 104 (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* 3.2 31.9 - - + +
13G MET* 4.4 1.8 - - + -
19G VAL* 4.0 13.7 - - + -
21G MET* 4.5 5.4 - - + -
75G ILE* 3.8 19.7 - - + -
78G VAL* 4.9 1.8 - - + -
82G ASP* 3.1 28.3 - - + +
83G GLN* 3.3 4.8 - - - +
84G ALA 2.8 31.6 + - - +
86G TYR* 3.3 31.0 - - + +
102G THR* 3.5 2.9 + - + +
103G LYS* 1.3 72.2 - - - +
105G GLU* 1.3 64.6 + - - +
106G ILE* 4.0 22.2 - - + -
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Residues in contact with GLU 105 (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 3.0 11.8 + - - +
12G ALA* 3.0 15.5 - - + +
13G MET 3.0 22.0 + - - -
83G GLN* 3.4 26.1 + - + +
103G LYS* 3.6 35.7 + - + +
104G LEU* 1.3 78.9 - - - +
106G ILE* 1.3 62.6 + - - +
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Residues in contact with ILE 106 (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 MET* 3.0 22.7 - - + +
14G SER* 4.8 2.0 - - - -
15G VAL* 5.0 5.4 - - + +
78G VAL* 4.2 14.4 - - + -
79G GLN 3.0 22.0 - - - +
80G ALA* 3.0 35.0 - - - +
82G ASP* 4.4 1.6 - - + -
83G GLN* 3.6 32.4 + - + +
104G LEU* 4.0 20.0 - - + -
105G GLU* 1.3 78.0 - - - +
107G LYS* 1.3 66.2 + - - +
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Residues in contact with LYS 107 (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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12G ALA* 4.1 23.2 + - + -
13G MET* 3.0 22.6 + - - +
14G SER* 3.3 31.3 + - - +
15G VAL* 4.2 20.1 - - - +
17G GLN* 4.6 3.6 - - - +
106G ILE* 1.3 76.5 - - - +
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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