Contacts of the strand formed by residues 85 - 92 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C PHE 3.5 0.7 - - - +
30C ARG* 3.3 3.4 - - - -
31C VAL* 2.6 41.3 + - - +
33C PRO* 4.5 5.7 - - + +
39C ILE* 3.4 56.4 - - + +
40C GLU* 6.0 0.2 - - - -
77C PHE* 4.4 12.8 - - + -
78C HIS* 3.4 13.5 - - - +
79C ASP* 3.1 60.4 - - + -
80C MET* 4.2 0.9 - - - -
83C GLY* 4.3 9.6 + - - -
84C SER* 1.3 84.3 + - - +
86C ILE* 1.3 65.4 + - - +
87C VAL* 3.7 4.8 + - + -
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Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C VAL* 3.6 25.4 - - + -
29C PHE 3.3 2.7 - - - +
30C ARG* 4.1 18.2 - - + -
76C ASP* 3.5 6.1 - - - +
77C PHE* 3.5 1.0 - - - -
78C HIS* 2.9 40.7 + - + +
80C MET* 3.4 35.0 - - + -
85C TRP* 1.3 72.8 - - - +
87C VAL* 1.3 60.4 + - - +
88C ARG* 4.2 6.6 + - + +
124C GLU* 4.9 0.7 - - + +
349C VAL* 3.2 28.5 - - + +
350C PHE* 3.8 26.0 - - + -
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Residues in contact with VAL 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ALA 3.6 1.6 - - - +
28C VAL* 3.7 0.8 - - - -
29C PHE* 2.8 41.0 + - + +
31C VAL* 3.9 24.9 - - + -
39C ILE* 4.0 15.9 - - + -
43C ALA* 4.0 10.8 - - + -
74C ALA* 4.0 15.5 - - + -
76C ASP 3.2 6.5 - - - +
77C PHE* 3.9 24.2 - - + -
85C TRP* 4.4 2.2 - - + -
86C ILE* 1.3 77.0 - - - +
88C ARG* 1.3 73.0 + - - +
89C ILE* 3.9 15.9 + - + -
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Residues in contact with ARG 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 4.2 3.8 - - + -
27C ALA 3.5 4.3 - - - -
28C VAL* 4.3 19.9 - - + +
74C ALA* 3.5 3.6 - - - -
75C TYR* 3.1 58.6 + - + +
76C ASP* 3.0 43.9 + - + +
86C ILE* 5.2 5.3 - - + +
87C VAL* 1.3 74.9 - - - +
89C ILE* 1.3 60.5 + - - +
348C ASP 5.4 2.2 + - - -
349C VAL* 5.0 18.8 + - - +
351C HIS 5.8 0.8 + - - -
352C LEU* 4.1 27.5 - - - +
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Residues in contact with ILE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 3.3 3.5 - - - -
27C ALA 2.9 33.2 + - - +
29C PHE* 3.7 17.5 - - + -
43C ALA 4.6 0.4 - - - +
46C VAL* 3.6 32.8 - - + -
47C ALA* 4.0 16.8 - - + +
72C ALA* 3.9 10.8 - - + -
73C LYS 3.3 17.7 - - - +
74C ALA* 4.0 6.1 - - + +
75C TYR* 4.1 2.7 - - - -
87C VAL* 3.9 17.7 - - + -
88C ARG* 1.3 80.8 - - - +
90C ALA* 1.3 61.8 + - - +
91C TYR* 3.4 31.1 - - + +
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Residues in contact with ALA 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C TYR* 3.8 29.6 - - + -
19C PRO* 4.4 3.1 - - + -
24C ASP* 4.1 15.0 - - + -
25C ILE 3.3 6.5 - - - +
26C ILE* 4.6 1.3 - - + +
72C ALA* 3.1 7.3 - - - +
73C LYS* 2.9 36.4 + - + +
75C TYR* 3.9 15.0 - - + -
89C ILE* 1.3 71.2 - - - +
91C TYR* 1.3 63.8 + - - +
92C PRO* 4.3 0.8 - - - +
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Residues in contact with TYR 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ASP* 3.5 4.1 - - - -
25C ILE* 2.7 56.4 + - + +
27C ALA* 3.8 9.4 - - + -
29C PHE* 3.9 10.9 - - - -
50C SER* 2.7 39.4 + - - -
51C SER* 4.4 4.3 - - - -
70C LEU 6.0 0.4 - - - -
72C ALA* 3.3 21.5 - - + -
89C ILE* 3.4 36.5 - - + +
90C ALA* 1.3 74.5 - - - +
92C PRO* 1.3 69.8 - - + +
95C ALA* 5.6 0.2 - - + -
96C PHE* 3.6 28.3 - + + -
108C ILE* 3.6 36.1 - - + +
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Residues in contact with PRO 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ARG* 4.0 1.8 - - + +
24C ASP* 3.8 13.9 - - - +
69C ASP 3.7 18.4 - - - +
70C LEU* 3.7 24.5 - - - +
71C SER 3.9 12.3 - - - +
73C LYS* 5.7 3.4 - - + -
90C ALA 4.3 1.6 - - - +
91C TYR* 1.3 85.3 - - + +
93C PHE* 1.3 66.7 + - - +
94C HIS* 3.5 24.7 - - + +
95C ALA* 3.0 25.0 + - + +
96C PHE* 3.8 4.9 - - - -
23J ARG* 3.8 13.0 - - - +
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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