Contacts of the strand formed by residues 88 - 94 (chain B) in PDB entry 3IKK
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 PHE 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B LEU* 3.2 32.5 - - + -
18B PHE* 3.6 12.3 - + - -
30B LEU* 5.9 1.6 - - + -
44B VAL* 5.5 7.0 - - + -
45B LYS 3.6 5.4 - - - +
46B THR* 3.6 18.6 - - - -
52B TYR* 3.6 30.7 - + - -
71B VAL* 4.1 10.5 - - + -
86B HIS* 3.9 3.8 - - + -
87B LYS* 1.3 72.1 - - - +
89B MET* 1.3 62.7 + - - +
90B VAL 4.1 0.2 - - - -
117B SER 3.4 6.4 - - - +
118B LYS* 3.4 2.1 - - - -
119B LEU* 2.9 48.4 + - + +
120B ARG 3.3 9.0 - - - -
121B CYS* 3.0 48.2 - - + -
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Residues in contact with MET 89 (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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43B LYS 3.6 1.2 - - - +
44B VAL* 3.3 0.9 - - - -
45B LYS* 2.4 65.1 + - + +
46B THR* 5.5 0.7 - - - -
87B LYS* 4.1 6.9 - - + +
88B PHE* 1.3 71.2 - - - +
90B VAL* 1.3 65.5 + - - +
91B GLN* 4.0 0.9 - - + -
116B ASP* 3.3 28.5 - - + +
117B SER 2.9 39.9 - - - +
118B LYS* 3.0 40.8 - - + -
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Residues in contact with VAL 90 (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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6B GLN* 3.8 8.2 + - - +
8B LEU* 4.5 13.5 - - + -
10B LEU* 4.9 7.0 - - + -
30B LEU* 3.8 23.3 - - + -
32B LEU* 4.3 25.6 - - + -
42B PHE* 4.6 3.4 - - + -
43B LYS 3.5 3.8 - - - +
44B VAL* 3.4 31.6 - - + -
88B PHE 4.1 0.4 - - - -
89B MET* 1.3 73.1 - - - +
91B GLN* 1.3 71.6 + - - +
115B MET 3.2 10.4 - - - +
116B ASP* 3.4 13.7 - - - -
117B SER 3.4 14.5 + - - +
119B LEU* 4.9 5.6 - - + -
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Residues in contact with GLN 91 (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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42B PHE* 2.9 9.2 - - - +
43B LYS* 2.7 35.7 + - + +
45B LYS* 3.1 44.2 - - + +
89B MET* 4.0 2.0 + - + -
90B VAL* 1.3 73.2 - - - +
92B SER* 1.3 62.1 + - - +
106B TRP* 3.9 14.7 - - + -
114B LEU* 3.2 51.2 - - - +
115B MET 3.1 2.6 - - - +
116B ASP* 3.0 23.1 + - - +
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Residues in contact with SER 92 (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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6B GLN* 2.6 31.7 + - - -
8B LEU* 4.0 8.3 - - - -
40B VAL* 3.9 15.0 - - - -
41B CYS 3.0 9.4 - - - -
91B GLN* 1.3 76.5 - - - +
93B MET* 1.3 66.8 + - - +
106B TRP* 4.3 2.2 - - - -
114B LEU* 3.5 2.3 - - - +
115B MET* 2.6 57.8 + - - +
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Residues in contact with MET 93 (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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40B VAL* 4.1 2.8 - - - +
41B CYS* 2.9 31.5 + - + +
92B SER* 1.3 78.7 - - - +
94B PHE* 1.3 72.2 + - - +
102B MET* 3.3 20.2 - - + -
105B VAL* 3.2 32.5 - - + -
106B TRP* 3.4 38.4 - - + +
109B ALA* 3.4 26.7 - - - -
113B ASP* 3.9 19.1 - - + +
114B LEU* 3.9 8.3 - - + -
115B MET* 5.2 2.2 - - - -
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Residues in contact with PHE 94 (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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4B VAL* 6.2 2.5 - - + -
7B VAL* 3.5 28.9 - - + -
36B THR* 3.7 26.9 - - + -
38B ARG* 3.5 51.6 - - + +
39B ASN 3.7 2.5 - - - -
40B VAL* 4.0 19.6 - - + +
41B CYS* 4.8 0.2 - - - -
93B MET* 1.3 82.1 - - - +
95B ALA* 1.3 58.8 + - - +
96B PRO* 3.0 14.5 - - + +
105B VAL* 5.7 0.5 - - - +
113B ASP 5.3 0.4 + - - -
115B MET* 5.1 7.6 - - + -
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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