Contacts of the strand formed by residues 24 - 33 (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 ASP 24 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E TYR* 2.5 25.5 + - - -
19E PRO* 3.1 13.6 - - + +
20E SER* 2.5 41.2 + - - +
23E ARG* 1.3 82.2 - - - +
25E ILE* 1.3 64.1 + - - +
26E ILE* 4.3 3.5 - - + +
90E ALA* 4.2 10.4 - - + +
91E TYR 3.4 14.6 - - - +
92E PRO* 3.9 8.1 - - - +
127E TYR* 3.6 16.3 - - - -
129E PRO* 3.3 16.9 - - - +
23H ARG* 5.4 2.9 + - - -
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Residues in contact with ILE 25 (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 3.9 0.4 + - - -
24E ASP* 1.3 73.7 - - - +
26E ILE* 1.3 63.1 + - - +
27E ALA 4.2 0.2 - - - -
90E ALA* 3.3 2.6 - - - -
91E TYR* 2.5 56.3 + - + +
93E PHE* 4.3 9.6 - - - -
96E PHE* 3.4 34.1 - - + -
104E LEU* 4.0 10.8 - - + -
108E ILE* 5.6 0.9 - - + -
126E LEU* 4.2 13.9 - - + -
127E TYR 3.5 12.6 - - - +
128E PHE* 4.0 12.1 - - + -
129E PRO* 3.9 13.0 - - + -
132E LEU* 3.3 35.0 - - + -
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Residues in contact with ILE 26 (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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19E PRO* 3.9 23.3 - - + -
20E SER 5.7 1.3 - - - +
21E LYS* 6.4 0.4 - - - -
24E ASP* 3.9 7.4 + - + +
25E ILE* 1.3 78.2 - - - +
27E ALA* 1.3 69.7 + - - +
28E VAL* 4.0 0.4 + - + -
75E TYR* 3.2 28.5 - - + +
88E ARG* 4.2 8.3 - - + -
89E ILE 3.4 9.6 - - - +
90E ALA* 4.6 3.1 - - - -
125E ASP 4.0 0.7 - - - +
126E LEU* 3.4 6.1 - - - -
127E TYR* 2.7 53.5 + - + +
352E LEU* 3.5 32.0 - - + +
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Residues in contact with ALA 27 (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* 1.3 73.0 - - - +
28E VAL* 1.3 61.5 + - - +
29E PHE* 3.6 26.8 + - + -
87E VAL 3.6 1.7 - - - +
88E ARG* 3.6 1.2 - - - -
89E ILE* 2.9 31.5 + - - -
91E TYR* 3.8 9.0 - - + -
108E ILE* 3.6 26.2 - - + -
123E LEU* 4.0 8.7 - - + -
125E ASP 3.6 4.7 - - - -
126E LEU* 4.1 3.1 - - + -
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Residues in contact with VAL 28 (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* 4.4 3.6 - - + +
27E ALA* 1.3 73.4 - - - +
29E PHE* 1.3 56.9 + - - +
86E ILE* 3.6 27.8 - - + -
87E VAL 3.7 4.0 - - - +
88E ARG* 4.5 12.1 - - + +
123E LEU* 3.6 3.9 - - - +
124E GLU* 2.7 38.9 + - + +
125E ASP* 3.0 21.3 + - + +
349E VAL 4.5 0.9 - - - +
350E PHE 3.3 26.9 - - - +
352E LEU* 3.7 37.0 - - + -
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Residues in contact with PHE 29 (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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27E ALA* 3.6 24.5 - - + -
28E VAL* 1.3 73.2 - - - +
30E ARG* 1.3 58.9 + - - +
31E VAL* 3.6 9.1 + - + -
46E VAL* 4.0 6.3 - - + -
85E TRP 3.4 0.9 - - - +
86E ILE* 3.3 4.9 - - - +
87E VAL* 2.7 41.0 + - + +
89E ILE* 3.7 30.3 - - + -
91E TYR* 3.9 7.4 - - - -
108E ILE 3.4 22.2 - - - -
112E ILE* 3.6 22.4 - - + -
113E PHE* 5.0 2.2 - + - -
121E LEU* 3.6 30.7 - - + -
122E ARG 3.3 1.3 - - - -
123E LEU* 3.6 37.0 - - + -
124E GLU* 4.3 2.7 - - - -
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Residues in contact with ARG 30 (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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29E PHE* 1.3 70.1 - - - +
31E VAL* 1.3 61.0 + - - +
32E THR* 3.9 1.0 + - - +
80E MET* 3.7 22.9 - - - +
82E ASP* 2.8 27.3 + - - -
84E SER* 3.1 23.5 + - - +
85E TRP 3.2 7.0 - - - +
86E ILE* 3.9 13.9 - - + -
120E GLY 3.8 1.7 - - - +
121E LEU* 3.6 5.0 + - - -
122E ARG* 2.8 37.3 + - + +
124E GLU* 3.2 26.1 + - - +
292E PRO* 3.5 24.9 + - - +
293E TYR* 3.5 23.8 + - + +
350E PHE* 3.7 20.2 - - - -
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Residues in contact with VAL 31 (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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29E PHE* 3.8 13.2 - - + +
30E ARG* 1.3 73.0 - - - +
32E THR* 1.3 64.2 + - - +
33E PRO* 3.3 9.6 - - - +
39E ILE* 3.9 22.2 - - + -
42E ALA* 3.9 24.7 - - + -
43E ALA* 5.4 3.1 - - - -
46E VAL* 4.8 8.3 - - + -
84E SER* 3.3 1.6 - - - -
85E TRP* 2.6 38.2 + - - +
87E VAL* 4.0 18.4 - - + -
89E ILE* 6.3 0.2 - - + -
118E VAL* 4.3 12.6 - - + -
120E GLY 3.9 2.9 - - - +
121E LEU* 3.7 20.2 - - + -
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Residues in contact with THR 32 (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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30E ARG* 4.9 1.0 + - - +
31E VAL* 1.3 73.3 - - - +
33E PRO* 1.3 59.9 - - - +
83E GLY* 3.7 20.6 - - - +
84E SER* 3.2 17.9 - - - -
118E VAL* 3.4 1.2 - - - -
119E LYS* 2.5 57.0 + - + +
120E GLY* 3.0 24.5 + - - -
293E TYR* 4.1 19.4 + - + +
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Residues in contact with PRO 33 (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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31E VAL* 3.3 16.1 - - + +
32E THR* 1.3 90.2 - - - +
34E ALA* 1.3 63.9 + - - +
37E TYR* 3.5 25.1 - - + +
38E THR 3.9 13.2 - - - +
39E ILE* 4.3 14.6 - - + +
42E ALA* 3.9 14.1 - - + -
83E GLY 3.6 15.2 - - - +
85E TRP* 4.5 6.5 - - + +
117E ARG 3.8 7.0 - - - +
118E VAL* 4.4 0.4 - - - -
119E LYS* 4.0 11.1 + - - -
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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