Contacts of the strand formed by residues 73 - 79 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I TYR* 2.9 54.6 + - - -
12I TYR* 3.5 3.6 - - - +
14I ASP* 4.1 29.2 + - + +
17I TYR* 4.6 26.7 - - + -
68I ALA 5.8 1.2 + - - -
71I SER* 3.9 10.1 - - - +
72I ALA* 1.3 105.1 - - - +
74I ALA* 1.3 62.5 + - - +
75I TYR* 3.3 6.9 + - - -
89I ILE* 3.8 4.0 - - - -
90I ALA* 2.9 36.0 + - + +
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Residues in contact with ALA 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I TYR 2.8 16.8 + - - +
13I VAL* 3.8 4.4 - - + -
14I ASP 3.0 23.1 + - - +
43I ALA* 4.3 15.0 - - + +
47I ALA* 4.5 1.1 - - + +
73I LYS* 1.3 69.1 - - - +
75I TYR* 1.3 59.3 + - - +
76I ASP 3.8 0.7 - - - -
77I PHE* 3.7 18.8 - - + -
87I VAL* 4.0 22.2 - - + -
88I ARG 3.5 7.2 - - - -
89I ILE* 4.0 11.8 - - + +
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Residues in contact with TYR 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ASP 3.3 16.8 - - - +
15I LYS* 3.5 25.0 - - - +
17I TYR* 3.5 24.1 - + + +
18I GLU* 5.7 0.7 - - - -
19I PRO* 3.5 31.3 - - + +
26I ILE* 3.0 32.2 - - + +
73I LYS 3.6 11.7 - - - +
74I ALA* 1.3 73.5 - - - +
76I ASP* 1.3 74.2 + - + +
77I PHE* 4.4 2.9 - - - -
88I ARG* 3.0 48.0 + - + +
89I ILE 4.0 1.8 - - - -
90I ALA* 3.9 24.0 - - + -
352I LEU* 5.4 0.5 - - - +
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Residues in contact with ASP 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I ALA 3.8 0.6 - - - -
75I TYR* 1.3 94.8 - - + +
77I PHE* 1.3 77.4 + - - +
78I HIS* 4.6 5.5 + - - +
86I ILE* 4.9 1.2 - - - +
87I VAL* 3.3 9.2 - - - +
88I ARG* 3.1 68.1 + - + +
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Residues in contact with PHE 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I VAL* 4.0 15.7 - - + -
15I LYS* 4.0 37.9 - - + +
39I ILE* 3.7 32.5 - - + -
40I GLU* 4.3 9.2 - - + -
43I ALA* 3.6 32.5 - - + -
74I ALA* 3.7 30.7 - - + -
76I ASP* 1.3 89.6 - - - +
78I HIS* 1.3 60.7 + - - +
79I ASP 4.2 0.8 + - - -
85I TRP* 4.2 14.4 - - + -
86I ILE 3.5 3.1 - - - -
87I VAL* 3.9 8.1 - - + -
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Residues in contact with HIS 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I ASP* 4.9 6.1 - - - +
77I PHE* 1.3 74.6 - - - +
79I ASP* 1.3 79.4 + - - +
80I MET* 3.4 23.8 + - - -
85I TRP* 3.3 6.2 - - - -
86I ILE* 2.8 48.9 + - + +
88I ARG* 6.3 0.7 - - - +
349I VAL* 3.8 31.2 - - + +
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Residues in contact with ASP 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I HIS* 1.3 88.2 + - - +
80I MET* 1.3 63.1 + - - +
81I GLY* 2.9 27.0 + - - -
82I ASP 4.6 0.5 + - - -
83I GLY* 5.1 2.3 + - - -
84I SER 3.7 6.4 - - - +
85I TRP* 3.3 48.0 + - + -
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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