Contacts of the strand formed by residues 85 - 92 (chain E) 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 TRP 85 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E PHE 3.4 0.7 - - - +
30E ARG* 3.2 4.4 - - - -
31E VAL* 2.6 37.3 + - - +
33E PRO* 4.5 5.5 - - + +
39E ILE* 3.5 56.3 - - + +
40E GLU* 5.9 0.2 - - - -
77E PHE* 4.2 17.3 - - + -
78E HIS 3.3 12.8 - - - -
79E ASP* 3.5 52.6 + - + -
80E MET* 4.2 1.6 - - - -
83E GLY* 4.1 10.4 + - - -
84E SER* 1.3 96.3 + - - +
86E ILE* 1.3 64.1 + - - +
87E VAL* 3.8 4.9 + - + -
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Residues in contact with ILE 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E VAL* 3.6 21.8 - - + -
29E PHE 3.3 1.8 - - - +
30E ARG* 3.9 27.4 - - + +
76E ASP* 3.5 3.4 - - - +
77E PHE* 3.5 3.1 - - - -
78E HIS* 2.8 48.9 + - + +
80E MET* 3.6 23.1 - - - -
85E TRP* 1.3 71.7 - - - +
87E VAL* 1.3 63.3 + - - +
88E ARG* 4.3 7.1 + - + +
124E GLU* 4.5 2.5 - - + -
349E VAL* 3.2 28.5 - - + +
350E PHE* 3.6 32.1 - - + -
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Residues in contact with VAL 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E ALA 3.6 1.7 - - - +
28E VAL* 3.7 0.6 - - - -
29E PHE* 2.7 39.8 + - + +
31E VAL* 4.0 17.0 - - + -
39E ILE* 4.0 22.4 - - + -
43E ALA* 4.0 18.8 - - + -
74E ALA* 4.1 7.0 - - + -
76E ASP 3.1 9.0 - - - +
77E PHE* 3.9 23.1 - - + -
85E TRP* 4.3 3.4 - - + -
86E ILE* 1.3 78.3 - - - +
88E ARG* 1.3 72.4 + - - +
89E ILE* 4.0 16.2 - - + +
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Residues in contact with ARG 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ILE* 4.2 3.8 - - + -
27E ALA 3.6 4.5 - - - -
28E VAL* 4.5 18.2 - - + +
74E ALA* 3.5 3.5 - - - -
75E TYR* 3.0 62.0 + - + +
76E ASP* 3.0 45.2 + - + +
86E ILE* 5.1 5.3 - - + +
87E VAL* 1.3 75.2 - - - +
89E ILE* 1.3 60.7 + - - +
348E ASP 5.4 2.0 + - - -
349E VAL* 4.9 15.8 + - - +
351E HIS 5.8 0.8 + - - -
352E LEU* 3.7 30.8 - - - +
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Residues in contact with ILE 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ILE* 3.4 2.8 - - - -
27E ALA 2.9 32.7 + - - +
29E PHE* 3.7 18.6 - - + -
43E ALA* 4.5 4.0 - - - +
46E VAL* 3.5 33.0 - - + -
47E ALA* 4.0 17.0 - - + +
72E ALA* 3.9 11.9 - - + -
73E LYS 3.2 16.4 - - - +
74E ALA* 4.1 4.0 - - - -
75E TYR* 4.0 2.5 - - - -
87E VAL* 4.0 16.8 - - + +
88E ARG* 1.3 79.8 - - - +
90E ALA* 1.3 62.2 + - - +
91E TYR* 3.3 31.6 - - + +
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Residues in contact with ALA 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E TYR* 3.9 26.2 - - + -
19E PRO* 4.4 2.7 - - + -
24E ASP* 4.2 15.0 - - + +
25E ILE 3.3 5.2 - - - +
26E ILE* 4.6 1.8 - - + -
72E ALA* 3.2 7.8 - - - +
73E LYS* 2.8 38.1 + - + +
75E TYR* 3.8 19.9 - - + -
89E ILE* 1.3 72.3 - - - +
91E TYR* 1.3 61.4 + - - +
92E PRO* 4.3 1.3 - - - +
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Residues in contact with TYR 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ASP* 3.4 4.3 - - - -
25E ILE* 2.5 53.8 + - + +
27E ALA* 3.8 9.4 - - + -
29E PHE* 3.9 10.0 - - - -
50E SER* 2.8 40.4 + - - -
51E SER* 4.5 4.0 - - - -
70E LEU 6.0 0.2 - - - -
72E ALA* 3.4 20.9 - - + -
89E ILE* 3.3 39.6 - - + +
90E ALA* 1.3 75.0 - - - +
92E PRO* 1.3 69.2 - - + +
95E ALA* 5.6 0.2 - - + -
96E PHE* 3.7 28.5 - + + -
108E ILE* 2.5 37.2 - - + +
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Residues in contact with PRO 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E ARG* 3.8 6.5 - - + +
24E ASP* 3.9 7.8 - - - +
69E ASP 3.7 18.6 - - - +
70E LEU* 3.9 20.9 - - - +
71E SER 4.1 11.2 - - - +
72E ALA* 4.8 0.2 - - - -
73E LYS* 5.8 2.9 - - + -
90E ALA 4.3 1.6 - - - +
91E TYR* 1.3 85.9 - - + +
93E PHE* 1.3 66.6 + - - +
94E HIS* 3.6 24.2 - - + -
95E ALA* 3.0 27.6 + - + +
96E PHE* 3.6 5.1 - - - -
23H ARG* 3.9 15.5 - - - +
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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