Contacts of the strand formed by residues 16 - 23 (chain B) in PDB entry 2JJ6
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 LYS 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B GLY 3.4 15.2 + - - +
15B LYS* 1.3 85.0 - - - +
17B VAL* 1.3 65.2 + - - +
18B LEU* 4.2 17.3 + - + +
90B GLU* 4.7 21.4 + - + +
91B ILE 3.6 5.4 - - - +
92B LEU* 3.9 24.1 - - + +
101B PHE* 6.0 2.6 - - - -
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Residues in contact with VAL 17 (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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7B ILE* 4.4 15.5 - - + -
11B MET* 3.7 34.5 - - + -
15B LYS* 4.8 2.5 - - + -
16B LYS* 1.3 78.1 - - - +
18B LEU* 1.3 66.7 + - - +
19B VAL* 4.3 2.2 - - + +
34B LEU* 4.6 10.1 - - + -
89B VAL 3.6 1.7 - - - +
90B GLU* 3.3 5.4 - - - -
91B ILE* 2.9 46.3 + - + +
123B ILE* 3.9 28.0 - - + -
134B LEU* 5.3 3.1 - - + -
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Residues in contact with LEU 18 (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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16B LYS* 4.2 22.1 + - + +
17B VAL* 1.3 75.7 - - - +
19B VAL* 1.3 72.8 + - - +
20B MET* 5.3 0.7 - - + +
88B ARG* 4.1 23.1 - - + +
89B VAL 3.6 2.2 - - - -
90B GLU* 3.9 25.8 - - + +
133B LYS* 4.6 19.7 - - - +
134B LEU* 2.9 40.5 + - - +
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Residues in contact with VAL 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 4.3 4.3 - - + +
18B LEU* 1.3 82.0 - - - +
20B MET* 1.3 61.5 + - - +
32B ILE* 4.2 20.9 - - + -
87B PHE* 3.7 9.4 - - + -
88B ARG* 4.6 0.4 - - - +
89B VAL* 2.9 34.8 + - + +
91B ILE* 6.1 1.6 - - + -
123B ILE* 3.3 33.7 - - + -
125B ILE* 3.3 27.4 - - + -
129B LEU* 6.0 0.7 - - + -
131B ILE* 4.8 4.9 - - + -
133B LYS 4.0 5.8 - - - +
134B LEU* 4.1 10.1 - - + -
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Residues in contact with MET 20 (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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18B LEU* 4.2 0.8 - - + +
19B VAL* 1.3 76.7 - - - +
21B GLY* 1.3 60.8 + - - +
22B ILE* 6.2 1.1 - - + -
86B PRO* 4.5 22.2 - - + -
87B PHE* 3.0 24.7 - - - +
88B ARG* 3.7 21.5 - - + +
131B ILE* 4.0 2.4 - - - +
132B THR* 3.0 30.4 + - + +
133B LYS* 3.2 57.8 + - + +
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Residues in contact with GLY 21 (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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20B MET* 1.3 78.9 - - - +
22B ILE* 1.3 70.7 + - - +
86B PRO* 3.7 0.9 - - - +
87B PHE* 2.9 43.4 + - - +
130B GLN 3.1 14.4 - - - -
131B ILE* 4.3 1.1 - - - -
132B THR* 3.4 10.2 - - - +
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Residues in contact with ILE 22 (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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20B MET* 6.2 1.1 - - + -
21B GLY* 1.3 82.6 - - - +
23B VAL* 1.3 77.2 + - - +
24B ASP* 4.8 1.3 - - - +
84B ASP* 3.7 15.9 - - - +
85B GLN 3.3 17.3 - - - +
86B PRO* 4.6 7.0 - - + -
87B PHE* 3.5 3.7 - - - -
129B LEU* 3.2 3.5 - - - +
130B GLN* 2.7 50.0 + - + +
132B THR* 5.2 10.5 - - + -
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Residues in contact with VAL 23 (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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22B ILE* 1.3 81.8 - - - +
24B ASP* 1.3 71.2 + - - +
27B PRO* 4.1 4.3 - - + -
30B PHE* 4.7 4.9 - - + -
54B PHE* 3.8 24.2 - - + -
81B PHE* 4.4 20.4 - - + -
82B ILE 4.0 19.7 - - - +
83B PRO* 4.4 5.4 - - + -
84B ASP* 2.5 33.5 + - - +
85B GLN 3.5 4.1 + - - +
87B PHE* 3.9 21.8 - - + -
128B ASP 3.4 17.0 - - - +
129B LEU* 4.2 0.7 - - + +
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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