Contacts of the strand formed by residues 73 - 79 (chain G) in PDB entry 3KDO
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 LYS 73 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11G TYR* 2.6 64.5 + - - +
12G TYR* 3.8 6.9 - - - +
14G ASP* 4.5 17.5 - - + +
17G TYR* 4.3 36.8 - - + -
68G ALA 5.5 2.0 - - - -
71G SER* 4.5 10.7 - - - +
72G ALA* 1.3 85.2 + - - +
74G ALA* 1.3 64.0 + - - +
75G TYR* 3.3 6.8 + - - -
89G ILE* 3.3 4.6 - - - -
90G ALA 2.9 34.5 + - - +
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Residues in contact with ALA 74 (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 TYR 3.0 19.1 + - - +
13G VAL* 3.8 3.4 - - - -
14G ASP 2.9 27.9 + - - +
43G ALA* 4.3 15.7 - - + +
47G ALA* 4.3 1.5 - - + +
73G LYS* 1.3 68.5 - - - +
75G TYR* 1.3 59.2 + - - +
76G ASP 3.8 1.1 - - - -
77G PHE* 3.8 26.5 - - + -
87G VAL* 4.2 6.5 - - + -
88G ARG 3.8 6.7 - - - -
89G ILE* 4.0 16.9 - - + +
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Residues in contact with TYR 75 (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 ASP 3.1 17.0 - - - +
15G LYS* 3.3 27.0 - - - +
17G TYR* 3.3 24.9 - + + +
19G PRO* 3.6 30.1 - - + +
26G ILE* 3.2 32.2 - - + +
73G LYS 3.5 12.1 - - - +
74G ALA* 1.3 75.4 - - - +
76G ASP* 1.3 74.2 + - + +
77G PHE* 4.4 2.0 - - - -
88G ARG* 3.2 43.0 + - + +
89G ILE 3.8 11.7 - - - -
90G ALA* 3.8 15.5 - - + -
352G LEU* 4.8 0.5 - - - +
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Residues in contact with ASP 76 (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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74G ALA 3.8 0.6 - - - -
75G TYR* 1.3 102.1 - - + +
77G PHE* 1.3 77.5 + - - +
78G HIS* 4.2 5.4 + - - +
86G ILE 4.5 1.9 - - - +
87G VAL* 3.2 10.0 - - - +
88G ARG* 3.1 61.2 + - + +
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Residues in contact with PHE 77 (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 VAL* 4.0 23.6 - - + -
15G LYS* 5.0 11.7 - - + -
39G ILE* 3.5 52.9 - - + -
40G GLU* 4.2 12.3 - - + +
43G ALA* 3.7 19.3 - - + -
74G ALA* 3.8 29.6 - - + -
75G TYR 4.4 2.2 - - - -
76G ASP* 1.3 88.5 + - - +
78G HIS* 1.3 61.3 + - - +
79G ASP 4.2 0.2 - - - -
85G TRP* 4.1 15.4 - - + -
86G ILE 3.6 2.0 - - - -
87G VAL* 3.9 7.9 - - + -
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Residues in contact with HIS 78 (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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76G ASP* 4.6 6.3 - - - +
77G PHE* 1.3 75.4 - - - +
79G ASP* 1.3 75.8 + - - +
80G MET* 3.4 24.9 + - - -
85G TRP* 3.3 5.6 - - - -
86G ILE* 2.8 48.7 + - + +
349G VAL* 3.8 31.3 - - + +
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Residues in contact with ASP 79 (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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78G HIS* 1.3 86.1 + - - +
80G MET* 1.3 62.8 + - - +
81G GLY* 2.3 41.2 + - - -
82G ASP 4.3 0.5 + - - -
83G GLY 5.1 1.7 + - - -
84G SER 4.1 2.6 - - - +
85G TRP* 3.0 52.1 + - + -
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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