Contacts of the strand formed by residues 79 - 85 (chain K) in PDB entry 1J5E
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 SER 79 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15K ALA 3.1 8.9 + - - +
16K SER* 4.6 10.1 - - - -
17K GLY 2.9 23.5 + - - -
78K GLN* 1.3 78.4 - - - +
80K VAL* 1.3 64.0 + - - +
81K ASP* 5.3 0.6 + - - -
104K GLN* 3.3 13.4 + - - +
106K LYS* 2.8 46.4 - - - +
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Residues in contact with VAL 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K GLY 2.9 15.9 - - - +
18K ARG 3.2 26.0 - - - +
19K ALA* 3.2 17.7 - - + +
32K ILE* 4.6 1.1 - - + -
77K MET* 3.3 19.3 - - + -
79K SER* 1.3 81.5 + - - +
81K ASP* 1.3 66.3 + - - +
82K VAL* 4.1 3.4 + - + -
98K LEU* 5.9 1.3 - - + -
103K LEU* 3.7 34.1 - - + -
104K GLN 3.0 6.6 + - - +
105K VAL* 3.6 7.7 - - + -
106K LYS* 2.7 32.6 + - - -
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Residues in contact with ASP 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K GLY 2.9 17.5 + - - +
18K ARG* 3.4 18.4 - - + +
19K ALA 2.8 25.6 + - - +
79K SER* 5.3 0.3 + - - -
80K VAL* 1.3 75.9 - - - +
82K VAL* 1.3 63.2 + - - +
83K ILE* 3.8 4.4 + - + +
106K LYS* 4.0 14.8 - - - +
107K SER* 3.6 22.3 + - - +
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Residues in contact with VAL 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K ALA* 3.3 6.7 - - + +
21K ILE* 3.4 35.7 - - + -
80K VAL* 4.8 2.7 - - + +
81K ASP* 1.3 76.3 - - - +
83K ILE* 1.3 68.9 + - - +
84K VAL 4.7 0.2 - - - +
95K ILE* 4.5 6.1 - - + -
98K LEU* 3.8 21.3 - - + -
105K VAL* 3.4 30.7 - - + -
107K SER* 2.6 16.0 + - - +
108K ILE* 4.0 20.4 - - + -
109K VAL* 3.0 25.2 + - - +
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Residues in contact with ILE 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ARG* 4.1 17.5 - - + +
19K ALA 2.8 9.0 + - - +
20K TYR* 3.3 54.3 - - + +
21K ILE 2.7 32.2 + - - +
81K ASP* 4.1 7.4 - - + +
82K VAL* 1.3 82.6 - - - +
84K VAL* 1.3 58.1 + - - +
85K ARG* 3.8 9.3 + - - +
109K VAL* 3.3 14.6 - - + +
111K ASP* 3.9 23.6 - - + +
84R LYS* 5.0 12.1 - - - +
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Residues in contact with VAL 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K ILE* 3.4 12.3 - - + +
82K VAL* 5.0 0.2 - - + -
83K ILE* 1.3 73.4 - - - +
85K ARG* 1.3 63.1 + - - +
91K ARG* 3.4 27.6 - - + -
95K ILE* 3.3 26.9 - - + -
108K ILE* 3.9 19.3 - - + -
109K VAL 2.8 21.3 + - - +
110K ASP* 3.6 1.6 - - - -
111K ASP 2.9 26.3 + - - -
112K THR* 3.5 4.1 + - - -
88R LYS* 3.4 29.6 - - + +
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Residues in contact with ARG 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707A C 2.5 40.5 + - - +
708A C 2.8 29.3 + - - -
20K TYR* 3.5 26.2 - - + -
21K ILE 2.8 14.0 + - - +
22K HIS* 3.5 14.3 + - + +
23K ALA* 3.0 27.2 + - - +
83K ILE* 4.3 8.8 - - + +
84K VAL* 1.3 76.6 - - - +
86K GLY* 1.3 62.5 + - - +
111K ASP* 3.1 50.2 + - - +
112K THR* 3.5 2.7 - - - -
113K PRO* 3.9 15.0 - - + -
84R LYS* 5.3 1.8 - - - +
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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