Contacts of the strand formed by residues 24 - 33 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B TYR* 2.7 25.9 + - - -
19B PRO* 3.2 8.7 - - + +
20B SER* 2.6 41.6 + - - +
22B LYS 3.9 0.4 - - - -
23B ARG* 1.3 84.1 - - - +
25B ILE* 1.3 69.6 + - - +
26B ILE* 4.2 3.1 - - + +
90B ALA* 4.2 14.4 - - + +
91B TYR 3.4 10.4 - - - +
92B PRO* 3.8 10.6 - - - +
127B TYR* 3.5 25.5 - - - -
129B PRO* 3.5 5.2 - - - +
23F ARG* 5.5 2.6 + - - -
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Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ASP* 1.3 72.4 - - - +
26B ILE* 1.3 63.5 + - - +
90B ALA* 3.3 3.6 - - - -
91B TYR* 2.6 59.1 + - + +
92B PRO 4.4 0.2 - - - -
93B PHE* 3.4 40.4 - - + -
96B PHE* 4.5 11.9 - - + -
104B LEU* 4.7 4.9 - - + -
108B ILE* 5.1 4.7 - - + -
126B LEU* 4.2 19.5 - - + -
127B TYR 3.5 10.8 - - - +
128B PHE* 4.2 7.4 - - + -
129B PRO* 3.7 15.0 - - + -
132B LEU* 3.6 25.4 - - + -
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Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PRO* 3.9 19.5 - - + -
20B SER 5.8 0.7 - - - +
21B LYS* 6.4 0.9 - - - -
24B ASP* 3.8 10.7 + - + +
25B ILE* 1.3 78.1 - - - +
27B ALA* 1.3 69.3 + - - +
28B VAL* 4.0 3.1 + - + +
75B TYR* 3.3 26.5 - - + +
88B ARG* 4.4 5.6 - - + -
89B ILE 3.4 9.0 - - - +
90B ALA* 4.7 2.9 - - - -
125B ASP 3.9 0.7 - - - +
126B LEU* 3.5 7.0 - - - +
127B TYR* 2.7 63.5 + - + -
352B LEU* 3.5 25.6 - - + -
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE 4.2 0.6 - - - -
26B ILE* 1.3 72.3 - - - +
28B VAL* 1.3 63.4 + - - +
29B PHE* 3.4 32.9 + - + -
87B VAL 3.6 1.7 - - - +
88B ARG* 3.6 1.4 - - - -
89B ILE 2.9 31.1 + - - -
91B TYR* 3.8 17.6 - - + +
108B ILE* 4.6 4.5 - - + -
123B LEU* 4.1 3.8 - - + -
125B ASP 3.7 4.5 - - - -
126B LEU* 4.0 14.8 - - + -
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ILE* 4.4 1.3 - - + +
27B ALA* 1.3 73.2 - - - +
29B PHE* 1.3 57.8 + - - +
86B ILE* 3.7 27.1 - - + -
87B VAL 3.7 3.4 - - - +
88B ARG* 4.2 11.9 - - + +
123B LEU* 3.6 3.8 - - - +
124B GLU* 2.7 38.5 + - + +
125B ASP* 3.0 23.6 + - + +
349B VAL 4.3 1.1 - - - +
350B PHE 3.4 23.1 - - - +
352B LEU* 3.5 40.6 - - + -
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Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ALA* 3.4 27.1 - - + -
28B VAL* 1.3 72.2 - - - +
30B ARG* 1.3 58.1 + - - +
31B VAL* 3.7 18.3 + - + -
46B VAL* 4.1 5.4 - - + -
85B TRP 3.5 0.9 - - - +
86B ILE* 3.3 4.3 - - - +
87B VAL* 2.6 44.8 + - + +
89B ILE* 3.7 30.3 - - + -
91B TYR* 3.9 7.6 - - - -
108B ILE 3.4 21.3 - - - -
112B ILE* 3.6 25.1 - - + -
113B PHE* 5.1 2.2 - + - -
121B LEU* 3.7 22.4 - - + -
122B ARG 3.4 1.3 - - - -
123B LEU* 3.4 34.8 - - + -
124B GLU* 4.4 2.9 - - - -
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Residues in contact with ARG 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PHE* 1.3 69.5 - - - +
31B VAL* 1.3 61.3 + - - +
32B THR* 3.9 0.7 + - - +
80B MET* 3.9 19.4 - - - +
82B ASP* 2.8 28.9 + - - -
84B SER* 3.1 23.0 + - - +
85B TRP 3.3 4.5 - - - +
86B ILE* 3.8 14.8 - - + -
120B GLY 3.7 2.1 - - - +
121B LEU* 3.7 5.2 - - - -
122B ARG* 2.8 37.7 + - + +
124B GLU* 3.4 21.4 + - - +
292B PRO* 3.4 28.9 + - - +
293B TYR* 3.3 26.7 + - + +
350B PHE* 3.6 23.2 - - - -
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PHE* 3.9 13.0 - - + -
30B ARG* 1.3 73.2 - - - +
32B THR* 1.3 63.3 + - - +
33B PRO* 3.3 7.8 - - - +
39B ILE* 3.7 22.7 - - + +
42B ALA* 3.8 23.6 - - + -
43B ALA* 4.7 5.6 - - - +
46B VAL* 4.9 7.4 - - + -
84B SER* 3.2 1.7 - - - -
85B TRP 2.6 38.2 + - - +
87B VAL* 3.9 20.0 - - + -
89B ILE* 6.4 0.4 - - + -
118B VAL* 4.1 15.3 - - + -
120B GLY 4.0 2.0 - - - -
121B LEU* 3.8 17.7 - - + -
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Residues in contact with THR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ARG* 3.9 1.6 + - - +
31B VAL* 1.3 73.0 - - - +
33B PRO* 1.3 59.6 - - - +
83B GLY 3.9 14.8 - - - +
84B SER* 3.2 19.3 - - - -
118B VAL* 3.5 2.1 - - - -
119B LYS* 2.7 49.5 + - + -
120B GLY* 3.0 24.8 + - - -
293B TYR* 4.1 16.8 + - + +
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Residues in contact with PRO 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B VAL* 3.3 16.6 - - + +
32B THR* 1.3 92.5 - - - +
34B ALA* 1.3 65.4 + - - +
37B TYR* 3.6 23.3 - - + +
38B THR 4.1 1.8 - - - +
39B ILE* 4.2 18.8 - - + +
42B ALA* 3.7 23.6 - - + -
83B GLY 3.6 14.2 - - - +
85B TRP* 4.7 4.7 - - + +
117B ARG 3.8 6.7 - - - +
118B VAL* 4.4 0.4 - - - -
119B LYS* 4.5 1.2 - - - +
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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