Contacts of the strand formed by residues 85 - 92 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29J PHE 3.4 1.0 - - - +
30J ARG* 3.3 3.4 - - - -
31J VAL* 2.7 36.6 + - - +
33J PRO* 4.6 4.3 - - + +
39J ILE* 3.3 55.5 - - + +
40J GLU* 5.9 0.7 - - - -
77J PHE* 4.1 19.7 - - + -
78J HIS 3.3 13.7 - - - -
79J ASP* 3.2 54.7 + - + -
80J MET* 4.3 1.8 - - - -
83J GLY* 4.2 9.5 + - - -
84J SER* 1.3 94.7 + - - +
86J ILE* 1.3 65.3 + - - +
87J VAL* 3.6 4.6 + - + -
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Residues in contact with ILE 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J VAL* 3.6 24.9 - - + -
29J PHE 3.3 2.0 - - - +
30J ARG* 4.1 21.3 - - + +
76J ASP* 3.5 7.3 - - - +
77J PHE* 3.5 1.0 - - - -
78J HIS* 2.9 48.8 + - + +
80J MET* 3.5 24.2 - - - -
85J TRP* 1.3 73.0 - - - +
87J VAL* 1.3 60.3 + - - +
88J ARG* 4.2 7.6 + - + +
124J GLU* 4.8 1.6 - - + +
349J VAL* 3.2 28.7 - - + +
350J PHE* 3.8 31.4 - - + -
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Residues in contact with VAL 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J ALA 3.6 2.1 - - - +
28J VAL* 4.7 0.7 - - - -
29J PHE* 2.8 41.3 + - + +
31J VAL* 3.7 28.0 - - + -
39J ILE* 4.0 21.1 - - + -
43J ALA* 3.9 21.5 - - + -
74J ALA* 4.0 18.6 - - + -
76J ASP 3.2 8.5 - - - +
77J PHE* 4.0 16.4 - - + -
85J TRP* 4.2 2.5 - - + +
86J ILE* 1.3 77.5 - - - +
88J ARG* 1.3 65.1 + - - +
89J ILE* 3.9 9.6 + - + -
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Residues in contact with ARG 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J ILE* 4.4 3.6 - - + -
27J ALA 3.5 4.5 - - - -
28J VAL* 4.2 19.0 - - + +
74J ALA* 3.6 2.4 - - - -
75J TYR* 3.0 60.9 + - + +
76J ASP* 3.0 43.9 + - + +
86J ILE* 5.1 5.5 - - + +
87J VAL* 1.3 73.7 - - - +
89J ILE* 1.3 60.3 + - - +
348J ASP 5.3 2.8 + - - -
349J VAL* 4.7 20.0 + - - +
351J HIS 5.6 1.0 + - - -
352J LEU* 3.8 31.9 - - - +
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Residues in contact with ILE 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J ILE* 3.4 3.3 - - - -
27J ALA 2.9 34.4 + - - +
29J PHE* 3.7 16.8 - - + -
31J VAL* 6.3 0.4 - - + -
43J ALA 4.5 4.0 - - - +
46J VAL* 3.6 33.4 - - + -
47J ALA* 3.9 17.0 - - + +
72J ALA* 3.9 11.7 - - + -
73J LYS 3.3 17.5 - - - +
74J ALA* 4.0 9.4 - - + -
75J TYR* 4.1 2.2 - - - -
87J VAL* 4.1 12.3 - - + -
88J ARG* 1.3 79.2 - - - +
90J ALA* 1.3 61.3 + - - +
91J TYR* 3.3 30.0 - - + +
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Residues in contact with ALA 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J TYR* 3.9 29.2 - - + -
19J PRO* 4.3 4.3 - - + -
24J ASP* 4.1 14.4 - - + +
25J ILE 3.4 5.8 - - - +
26J ILE* 4.7 1.8 - - + +
71J SER 4.7 0.2 - - - +
72J ALA* 3.2 7.4 - - - +
73J LYS* 2.9 33.8 + - + +
75J TYR* 3.9 15.0 - - + -
89J ILE* 1.3 70.8 - - - +
91J TYR* 1.3 65.0 + - - +
92J PRO* 4.4 1.3 - - - +
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Residues in contact with TYR 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J ASP* 3.4 5.2 - - - -
25J ILE* 2.7 49.8 + - + +
27J ALA* 3.7 13.9 - - + -
29J PHE* 3.8 18.2 - - - -
50J SER* 2.8 44.8 + - - -
51J SER* 4.5 3.8 - - - -
72J ALA* 3.5 18.6 - - + -
89J ILE* 3.3 38.4 - - + +
90J ALA* 1.3 76.1 - - - +
92J PRO* 1.3 67.9 - - + +
95J ALA* 5.6 0.7 - - + -
96J PHE* 3.7 25.8 - + + -
108J ILE* 3.7 25.9 - - + +
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Residues in contact with PRO 92 (chain J).
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* 3.9 13.0 - - - +
23J ARG* 3.8 2.2 - - + +
24J ASP* 3.7 14.1 - - - +
25J ILE* 4.5 0.2 - - - -
69J ASP 3.7 18.6 - - - +
70J LEU* 3.9 23.6 - - - +
71J SER 4.2 12.3 - - - +
72J ALA* 4.9 0.2 - - - -
90J ALA 4.4 1.1 - - - +
91J TYR* 1.3 85.8 - - + +
93J PHE* 1.3 66.5 + - - +
94J HIS* 3.2 24.2 - - + +
95J ALA* 3.0 25.4 + - + +
96J PHE* 3.7 4.2 - - - -
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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