Contacts of the strand formed by residues 24 - 33 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B ARG* 5.6 2.3 + - - -
17F TYR* 2.4 31.6 + - - -
19F PRO* 3.2 13.7 - - + +
20F SER* 2.7 34.7 + - - +
23F ARG* 1.3 85.5 - - - +
25F ILE* 1.3 65.8 + - - +
26F ILE* 4.5 2.6 - - + +
90F ALA* 4.2 11.2 - - + +
91F TYR 3.6 2.7 - - - +
92F PRO* 3.8 17.8 - - - +
127F TYR* 3.5 18.2 - - - -
129F PRO* 3.4 14.8 - - - +
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Residues in contact with ILE 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F ARG 4.0 0.2 + - - -
24F ASP* 1.3 73.2 - - - +
26F ILE* 1.3 68.6 + - - +
90F ALA* 3.4 3.5 - - - -
91F TYR* 2.8 48.6 + - + +
93F PHE* 4.2 12.6 - - - +
96F PHE* 3.8 31.9 - - + -
104F LEU* 3.9 7.9 - - + -
108F ILE* 5.8 1.3 - - + -
126F LEU* 4.5 9.2 - - + -
127F TYR 3.3 14.1 - - - +
128F PHE* 4.0 13.5 - - + -
129F PRO* 3.6 13.5 - - + -
132F LEU* 3.0 37.2 - - + -
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Residues in contact with ILE 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F PRO* 3.7 24.2 - - + -
20F SER 5.8 0.9 - - - +
21F LYS* 6.5 0.7 - - - -
24F ASP* 4.0 7.2 + - + +
25F ILE* 1.3 80.4 - - - +
27F ALA* 1.3 63.7 + - - +
28F VAL 4.1 0.3 + - - -
75F TYR* 3.4 30.3 - - + +
88F ARG* 4.1 13.2 - - + -
89F ILE 3.3 10.5 - - - +
90F ALA* 4.6 3.6 - - + -
125F ASP 3.8 0.9 - - - +
126F LEU* 3.4 5.0 - - - +
127F TYR* 2.8 54.3 + - + +
352F LEU* 3.6 29.2 - - + +
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Residues in contact with ALA 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F ILE 4.2 0.6 + - - -
26F ILE* 1.3 73.3 - - - +
28F VAL* 1.3 62.5 + - - +
29F PHE* 3.6 30.9 + - + -
87F VAL 3.7 1.7 - - - +
88F ARG* 3.5 1.9 - - - -
89F ILE* 2.9 32.0 + - - -
91F TYR* 3.9 17.8 - - + -
108F ILE* 4.3 3.4 - - + -
123F LEU* 4.2 3.1 - - + -
125F ASP 3.6 4.7 - - - -
126F LEU* 3.9 17.0 - - + -
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Residues in contact with VAL 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ILE* 4.6 0.2 - - + -
27F ALA* 1.3 73.4 - - - +
29F PHE* 1.3 58.7 + - - +
86F ILE* 3.6 28.7 - - + -
87F VAL 3.9 2.5 - - - +
88F ARG* 4.2 15.9 - - + +
123F LEU* 3.7 2.6 - - - +
124F GLU* 2.7 38.1 + - + +
125F ASP* 3.0 20.1 + - + +
349F VAL 4.4 0.9 - - - +
350F PHE 3.4 28.3 - - - +
352F LEU* 3.6 35.7 - - + -
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Residues in contact with PHE 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F ALA* 3.6 30.5 - - + -
28F VAL* 1.3 72.6 - - - +
30F ARG* 1.3 59.7 - - - +
31F VAL* 3.6 10.6 + - + +
46F VAL* 3.8 5.6 - - + -
85F TRP 3.4 1.2 - - - +
86F ILE* 3.3 4.8 - - - +
87F VAL* 2.8 40.5 + - + +
89F ILE* 3.6 31.9 - - + -
91F TYR* 3.9 8.3 - - - -
108F ILE 3.3 27.6 - - - -
112F ILE* 3.6 21.1 - - + -
113F PHE* 5.2 1.6 - + - -
121F LEU* 3.5 31.0 - - + -
122F ARG 3.4 1.3 - - - -
123F LEU* 3.7 26.5 - - + -
124F GLU* 4.5 2.0 - - - -
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Residues in contact with ARG 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F PHE* 1.3 70.7 - - - +
31F VAL* 1.3 60.3 + - - +
32F THR* 3.9 1.0 + - - +
80F MET* 3.8 18.5 - - - +
82F ASP* 2.7 30.9 + - - -
84F SER* 3.1 23.1 + - - +
85F TRP 3.2 4.5 - - - +
86F ILE* 3.6 17.3 - - + -
120F GLY 3.6 5.9 - - - +
121F LEU* 3.7 0.5 - - - -
122F ARG* 2.8 35.5 + - + +
124F GLU* 3.4 21.7 + - - +
292F PRO* 3.4 26.8 + - - +
293F TYR* 3.5 24.6 + - + +
350F PHE* 3.6 26.3 - - - -
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Residues in contact with VAL 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F PHE* 3.8 22.0 - - + -
30F ARG* 1.3 74.1 - - - +
32F THR* 1.3 63.1 + - - +
33F PRO* 3.4 8.1 - - - +
39F ILE* 3.7 21.1 - - + -
42F ALA* 3.9 22.7 - - + -
43F ALA* 4.7 3.8 - - - +
46F VAL* 4.8 7.6 - - + -
84F SER* 3.2 1.3 - - - -
85F TRP* 2.5 39.7 + - - +
87F VAL* 3.9 21.5 - - + -
118F VAL* 4.2 14.1 - - + -
120F GLY 3.9 2.7 - - - +
121F LEU* 3.9 9.0 - - + -
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Residues in contact with THR 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ARG* 3.9 1.4 + - - +
31F VAL* 1.3 71.7 - - - +
33F PRO* 1.3 60.2 - - - +
82F ASP 6.1 0.2 - - - +
83F GLY 3.9 13.5 - - - +
84F SER* 3.0 19.8 - - - -
118F VAL* 3.6 2.3 - - - -
119F LYS* 2.7 74.1 + - + +
120F GLY* 3.0 23.9 + - - +
293F TYR* 3.9 17.6 + - + +
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Residues in contact with PRO 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F VAL* 3.4 11.9 - - - +
32F THR* 1.3 93.8 - - - +
34F ALA* 1.3 65.1 + - - +
37F TYR* 3.5 23.6 - - + +
39F ILE* 3.7 33.0 - - + +
42F ALA* 4.1 14.8 - - + -
83F GLY 3.4 16.3 - - - +
85F TRP* 3.9 11.4 - - + -
117F ARG 4.0 5.8 - - - +
118F VAL* 4.5 0.2 - - - -
119F LYS* 4.0 4.5 + - - +
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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