Contacts of the strand formed by residues 24 - 33 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A TYR* 2.6 33.7 + - - -
19A PRO 3.4 0.5 - - - -
20A SER* 2.4 46.6 + - - +
23A ARG* 1.3 83.5 - - - +
25A ILE* 1.3 63.1 + - - +
26A ILE* 4.2 15.7 - - + -
90A ALA* 4.2 4.9 - - + +
91A TYR 3.4 13.9 - - - +
92A PRO* 4.2 4.5 - - - +
127A TYR* 3.7 13.1 - - - -
129A PRO* 3.1 19.8 - - - +
23G ARG* 5.6 2.6 + - - -
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASP* 1.3 75.6 - - - +
26A ILE* 1.3 60.5 + - - +
90A ALA* 3.2 1.6 - - - -
91A TYR* 2.6 56.5 + - + +
93A PHE* 3.9 15.7 - - + -
96A PHE* 3.4 36.6 - - + -
104A LEU* 4.4 7.2 - - + -
108A ILE* 5.5 1.3 - - + -
126A LEU* 4.5 13.7 - - + -
127A TYR 3.2 17.0 - - - +
128A PHE* 4.1 14.6 - - + -
129A PRO* 4.0 7.0 - - + -
132A LEU* 3.5 30.1 - - + -
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Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PRO* 4.1 15.3 - - + -
24A ASP* 4.2 6.7 - - + -
25A ILE* 1.3 74.4 - - - +
27A ALA* 1.3 61.4 + - - +
28A VAL* 4.0 3.3 + - + -
75A TYR* 3.9 23.6 - - + +
88A ARG* 4.1 13.7 - - + -
89A ILE 3.2 4.0 - - - +
90A ALA* 3.2 35.4 - - + -
125A ASP 3.9 0.7 - - - +
126A LEU* 3.3 4.7 - - - +
127A TYR* 2.5 61.0 + - + +
352A LEU* 3.2 26.7 - - + +
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE 4.0 0.6 + - - -
26A ILE* 1.3 71.4 - - - +
28A VAL* 1.3 60.9 + - - +
29A PHE* 2.8 45.5 + - + -
89A ILE 2.9 25.5 + - - -
91A TYR* 4.0 15.9 - - + -
108A ILE* 4.4 2.7 - - + -
123A LEU* 4.2 0.4 - - + -
125A ASP 3.3 5.6 - - - +
126A LEU* 3.4 22.4 - - + -
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Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 4.4 0.7 - - + +
27A ALA* 1.3 70.9 - - - +
29A PHE* 1.3 56.0 + - - +
86A ILE* 3.6 30.3 - - + -
87A VAL 3.6 5.8 - - - +
88A ARG* 4.2 13.0 - - + +
123A LEU* 3.5 4.5 - - - +
124A GLU* 2.7 41.1 + - + -
125A ASP* 2.9 25.7 + - + +
350A PHE 3.7 19.5 - - - +
352A LEU* 3.5 38.1 - - + -
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Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 2.8 50.3 - - + -
28A VAL* 1.3 71.8 - - - +
30A ARG* 1.3 57.9 + - - +
31A VAL* 3.2 21.0 + - + +
46A VAL* 4.8 5.2 - - + -
85A TRP 3.1 2.6 - - - +
86A ILE* 4.5 1.3 - - - -
87A VAL* 2.6 42.6 + - + +
89A ILE* 4.3 15.9 - - + -
91A TYR* 4.2 12.3 - - - -
108A ILE* 3.1 30.7 - - + -
112A ILE* 3.7 17.5 - - + -
113A PHE* 5.2 1.1 - + - -
121A LEU* 3.6 21.8 - - + -
122A ARG 3.5 1.6 - - - -
123A LEU* 3.7 30.7 - - + -
124A GLU* 4.5 0.2 - - - -
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE* 1.3 68.1 - - - +
31A VAL* 1.3 60.1 + - - +
32A THR* 5.1 0.6 + - - +
80A MET* 4.0 28.1 - - - +
82A ASP* 2.7 29.3 + - - -
84A SER* 2.9 24.9 + - - +
85A TRP 3.1 10.8 - - - +
86A ILE* 4.4 4.9 - - + +
120A GLY 3.6 4.5 - - - +
122A ARG* 2.9 32.3 + - + +
124A GLU* 3.2 29.3 - - + +
292A PRO* 3.6 23.7 + - - +
293A TYR* 3.0 32.7 + - + +
350A PHE* 4.0 18.4 - - - -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE* 3.3 28.9 - - + +
30A ARG* 1.3 74.6 - - - +
32A THR* 1.3 65.3 + - - +
33A PRO* 3.9 4.2 - - + +
42A ALA* 3.6 32.8 - - + -
43A ALA* 5.1 6.5 - - - -
46A VAL* 5.1 4.7 - - + -
84A SER* 3.0 6.8 - - - -
85A TRP* 2.7 37.5 + - + +
87A VAL* 4.1 20.0 - - + -
118A VAL* 4.1 17.5 - - + -
120A GLY 3.9 2.0 - - - +
121A LEU* 4.0 12.3 - - + -
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Residues in contact with THR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ARG* 5.1 0.9 + - - +
31A VAL* 1.3 74.8 + - - +
33A PRO* 1.3 70.9 - - - +
83A GLY* 3.7 12.1 - - - +
84A SER* 3.2 23.2 - - - -
118A VAL* 3.6 2.3 - - - +
119A LYS* 2.8 41.6 + - + -
120A GLY* 3.0 23.4 + - - +
293A TYR* 4.8 10.6 + - - +
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Residues in contact with PRO 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.9 5.8 - - + +
32A THR* 1.3 97.8 - - - +
34A ALA* 1.3 67.6 + - - +
37A TYR* 3.4 26.9 - - + +
38A THR 3.7 12.6 - - - +
39A ILE* 4.0 10.8 - - + +
42A ALA* 3.6 25.1 - - + -
83A GLY 3.6 14.6 - - - +
85A TRP* 5.0 9.6 - - + -
117A ARG 3.8 6.7 - - - +
118A VAL* 4.4 0.9 - - - -
119A LYS* 4.1 2.3 - - - +
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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